THE EMACS ORG-MODEReproducible Research and Beyond
Andreas Leha
Department for Medical StatisticsUniversity Medical Center Goumlttingen
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Outline
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 2
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 3
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Reproducible ResearchPossible Definition
a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication
(Hothorn Held and Friede 2009)
+ code + parameters +
Bioinformatics (Vol26)(Hothorn and Leisch 2011)
I Better but similar results
The Emacs Org-mode Andreas Leha 16 August 2011 4
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Reproducible ResearchPossible Definition
a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication
(Hothorn Held and Friede 2009)
A piece of reproducible research is usually notmethods section + published data
+ code + parameters +
Nature Genetics (200506)(Ioannidis et al 2009)
not reproducible
56
Bioinformatics (Vol26)(Hothorn and Leisch 2011)
I Better but similar results
The Emacs Org-mode Andreas Leha 16 August 2011 4
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Reproducible ResearchPossible Definition
a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication
(Hothorn Held and Friede 2009)
A piece of reproducible research should ideally containmethods section + published data + code
+ parameters +
Biometrical Journal (Vol50)(Hothorn Held and Friede 2009)
potentially reproducible
89
Bioinformatics (Vol26)(Hothorn and Leisch 2011)
I Better but similar results
The Emacs Org-mode Andreas Leha 16 August 2011 4
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Reproducible ResearchPossible Definition
a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication
(Hothorn Held and Friede 2009)
A piece of reproducible research should ideally containmethods section + published data + code + parameters +
Biometrical Journal (Vol50)(Hothorn Held and Friede 2009)
potentially reproducible
89
Bioinformatics (Vol26)(Hothorn and Leisch 2011)
I Better but similar results
The Emacs Org-mode Andreas Leha 16 August 2011 4
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Why to use Reproducible Research
I Benefits for the researcher herselfIn the mid-1980s we realized that our laboratoryrsquosresearchers often had difficulty reproducing their owncomputations without considerable agony
(Schwab Karrenbach and Claerbout 2000)
I Benefits for othersI Precise lsquodescriptionrsquo of methodsI Easy re-use of applied methodsI No forensic bioinformatics
(Baggerly and Coombes 2009 Ioannidis et al 2009)
The Emacs Org-mode Andreas Leha 16 August 2011 5
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Barriers for Reproducible Research
(Banks 2011)
I Deliberate non-reproducibilityI Vagueness to cover potential mistakes
I External reasonsI Ownership of the dataI Collaboration partners
I Perception of effortI DisciplineI ResourcesI Change of work flow
The Emacs Org-mode Andreas Leha 16 August 2011 6
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 7
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Existing Tools for Reproducible Research
I ReDoc (Schwab Karrenbach and Claerbout 2000)GNU make rules synchronize code and output
I Sweave (Leisch 2002)interwoven R and LATEX by means of literate programming
I Compendium (Gentleman and Temple Lang 2007 Gentlemanet al 2005)scientific paper as R-package (including data code)based on Sweave
I Org-mode
The Emacs Org-mode Andreas Leha 16 August 2011 8
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 9
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Org-mode
Org-mode is for keeping notes maintaining ToDo lists doingproject planning and authoring with a fast and effectiveplain-text system
httporgmodeorg
I Major mode of emacsI File formatI Created in 2003 by Carsten DominikI Current Version 77 maintainer Bastien GuerryI Very active development
The Emacs Org-mode Andreas Leha 16 August 2011 10
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode and Reproducible Research
I Through Org Babel a literate programming (Knuth 1984)system
I Written by Eric Schulte and Dan Davison
code
ltcodegt
+ org
lttextgt
document
tangle
weave
The Emacs Org-mode Andreas Leha 16 August 2011 11
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Outline
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 2
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 3
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Reproducible ResearchPossible Definition
a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication
(Hothorn Held and Friede 2009)
+ code + parameters +
Bioinformatics (Vol26)(Hothorn and Leisch 2011)
I Better but similar results
The Emacs Org-mode Andreas Leha 16 August 2011 4
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Reproducible ResearchPossible Definition
a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication
(Hothorn Held and Friede 2009)
A piece of reproducible research is usually notmethods section + published data
+ code + parameters +
Nature Genetics (200506)(Ioannidis et al 2009)
not reproducible
56
Bioinformatics (Vol26)(Hothorn and Leisch 2011)
I Better but similar results
The Emacs Org-mode Andreas Leha 16 August 2011 4
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Reproducible ResearchPossible Definition
a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication
(Hothorn Held and Friede 2009)
A piece of reproducible research should ideally containmethods section + published data + code
+ parameters +
Biometrical Journal (Vol50)(Hothorn Held and Friede 2009)
potentially reproducible
89
Bioinformatics (Vol26)(Hothorn and Leisch 2011)
I Better but similar results
The Emacs Org-mode Andreas Leha 16 August 2011 4
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Reproducible ResearchPossible Definition
a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication
(Hothorn Held and Friede 2009)
A piece of reproducible research should ideally containmethods section + published data + code + parameters +
Biometrical Journal (Vol50)(Hothorn Held and Friede 2009)
potentially reproducible
89
Bioinformatics (Vol26)(Hothorn and Leisch 2011)
I Better but similar results
The Emacs Org-mode Andreas Leha 16 August 2011 4
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Why to use Reproducible Research
I Benefits for the researcher herselfIn the mid-1980s we realized that our laboratoryrsquosresearchers often had difficulty reproducing their owncomputations without considerable agony
(Schwab Karrenbach and Claerbout 2000)
I Benefits for othersI Precise lsquodescriptionrsquo of methodsI Easy re-use of applied methodsI No forensic bioinformatics
(Baggerly and Coombes 2009 Ioannidis et al 2009)
The Emacs Org-mode Andreas Leha 16 August 2011 5
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Barriers for Reproducible Research
(Banks 2011)
I Deliberate non-reproducibilityI Vagueness to cover potential mistakes
I External reasonsI Ownership of the dataI Collaboration partners
I Perception of effortI DisciplineI ResourcesI Change of work flow
The Emacs Org-mode Andreas Leha 16 August 2011 6
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 7
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Existing Tools for Reproducible Research
I ReDoc (Schwab Karrenbach and Claerbout 2000)GNU make rules synchronize code and output
I Sweave (Leisch 2002)interwoven R and LATEX by means of literate programming
I Compendium (Gentleman and Temple Lang 2007 Gentlemanet al 2005)scientific paper as R-package (including data code)based on Sweave
I Org-mode
The Emacs Org-mode Andreas Leha 16 August 2011 8
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 9
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Org-mode
Org-mode is for keeping notes maintaining ToDo lists doingproject planning and authoring with a fast and effectiveplain-text system
httporgmodeorg
I Major mode of emacsI File formatI Created in 2003 by Carsten DominikI Current Version 77 maintainer Bastien GuerryI Very active development
The Emacs Org-mode Andreas Leha 16 August 2011 10
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode and Reproducible Research
I Through Org Babel a literate programming (Knuth 1984)system
I Written by Eric Schulte and Dan Davison
code
ltcodegt
+ org
lttextgt
document
tangle
weave
The Emacs Org-mode Andreas Leha 16 August 2011 11
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 3
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Reproducible ResearchPossible Definition
a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication
(Hothorn Held and Friede 2009)
+ code + parameters +
Bioinformatics (Vol26)(Hothorn and Leisch 2011)
I Better but similar results
The Emacs Org-mode Andreas Leha 16 August 2011 4
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Reproducible ResearchPossible Definition
a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication
(Hothorn Held and Friede 2009)
A piece of reproducible research is usually notmethods section + published data
+ code + parameters +
Nature Genetics (200506)(Ioannidis et al 2009)
not reproducible
56
Bioinformatics (Vol26)(Hothorn and Leisch 2011)
I Better but similar results
The Emacs Org-mode Andreas Leha 16 August 2011 4
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Reproducible ResearchPossible Definition
a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication
(Hothorn Held and Friede 2009)
A piece of reproducible research should ideally containmethods section + published data + code
+ parameters +
Biometrical Journal (Vol50)(Hothorn Held and Friede 2009)
potentially reproducible
89
Bioinformatics (Vol26)(Hothorn and Leisch 2011)
I Better but similar results
The Emacs Org-mode Andreas Leha 16 August 2011 4
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Reproducible ResearchPossible Definition
a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication
(Hothorn Held and Friede 2009)
A piece of reproducible research should ideally containmethods section + published data + code + parameters +
Biometrical Journal (Vol50)(Hothorn Held and Friede 2009)
potentially reproducible
89
Bioinformatics (Vol26)(Hothorn and Leisch 2011)
I Better but similar results
The Emacs Org-mode Andreas Leha 16 August 2011 4
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Why to use Reproducible Research
I Benefits for the researcher herselfIn the mid-1980s we realized that our laboratoryrsquosresearchers often had difficulty reproducing their owncomputations without considerable agony
(Schwab Karrenbach and Claerbout 2000)
I Benefits for othersI Precise lsquodescriptionrsquo of methodsI Easy re-use of applied methodsI No forensic bioinformatics
(Baggerly and Coombes 2009 Ioannidis et al 2009)
The Emacs Org-mode Andreas Leha 16 August 2011 5
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Barriers for Reproducible Research
(Banks 2011)
I Deliberate non-reproducibilityI Vagueness to cover potential mistakes
I External reasonsI Ownership of the dataI Collaboration partners
I Perception of effortI DisciplineI ResourcesI Change of work flow
The Emacs Org-mode Andreas Leha 16 August 2011 6
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 7
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Existing Tools for Reproducible Research
I ReDoc (Schwab Karrenbach and Claerbout 2000)GNU make rules synchronize code and output
I Sweave (Leisch 2002)interwoven R and LATEX by means of literate programming
I Compendium (Gentleman and Temple Lang 2007 Gentlemanet al 2005)scientific paper as R-package (including data code)based on Sweave
I Org-mode
The Emacs Org-mode Andreas Leha 16 August 2011 8
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 9
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Org-mode
Org-mode is for keeping notes maintaining ToDo lists doingproject planning and authoring with a fast and effectiveplain-text system
httporgmodeorg
I Major mode of emacsI File formatI Created in 2003 by Carsten DominikI Current Version 77 maintainer Bastien GuerryI Very active development
The Emacs Org-mode Andreas Leha 16 August 2011 10
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode and Reproducible Research
I Through Org Babel a literate programming (Knuth 1984)system
I Written by Eric Schulte and Dan Davison
code
ltcodegt
+ org
lttextgt
document
tangle
weave
The Emacs Org-mode Andreas Leha 16 August 2011 11
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Reproducible ResearchPossible Definition
a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication
(Hothorn Held and Friede 2009)
+ code + parameters +
Bioinformatics (Vol26)(Hothorn and Leisch 2011)
I Better but similar results
The Emacs Org-mode Andreas Leha 16 August 2011 4
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Reproducible ResearchPossible Definition
a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication
(Hothorn Held and Friede 2009)
A piece of reproducible research is usually notmethods section + published data
+ code + parameters +
Nature Genetics (200506)(Ioannidis et al 2009)
not reproducible
56
Bioinformatics (Vol26)(Hothorn and Leisch 2011)
I Better but similar results
The Emacs Org-mode Andreas Leha 16 August 2011 4
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Reproducible ResearchPossible Definition
a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication
(Hothorn Held and Friede 2009)
A piece of reproducible research should ideally containmethods section + published data + code
+ parameters +
Biometrical Journal (Vol50)(Hothorn Held and Friede 2009)
potentially reproducible
89
Bioinformatics (Vol26)(Hothorn and Leisch 2011)
I Better but similar results
The Emacs Org-mode Andreas Leha 16 August 2011 4
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Reproducible ResearchPossible Definition
a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication
(Hothorn Held and Friede 2009)
A piece of reproducible research should ideally containmethods section + published data + code + parameters +
Biometrical Journal (Vol50)(Hothorn Held and Friede 2009)
potentially reproducible
89
Bioinformatics (Vol26)(Hothorn and Leisch 2011)
I Better but similar results
The Emacs Org-mode Andreas Leha 16 August 2011 4
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Why to use Reproducible Research
I Benefits for the researcher herselfIn the mid-1980s we realized that our laboratoryrsquosresearchers often had difficulty reproducing their owncomputations without considerable agony
(Schwab Karrenbach and Claerbout 2000)
I Benefits for othersI Precise lsquodescriptionrsquo of methodsI Easy re-use of applied methodsI No forensic bioinformatics
(Baggerly and Coombes 2009 Ioannidis et al 2009)
The Emacs Org-mode Andreas Leha 16 August 2011 5
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Barriers for Reproducible Research
(Banks 2011)
I Deliberate non-reproducibilityI Vagueness to cover potential mistakes
I External reasonsI Ownership of the dataI Collaboration partners
I Perception of effortI DisciplineI ResourcesI Change of work flow
The Emacs Org-mode Andreas Leha 16 August 2011 6
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 7
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Existing Tools for Reproducible Research
I ReDoc (Schwab Karrenbach and Claerbout 2000)GNU make rules synchronize code and output
I Sweave (Leisch 2002)interwoven R and LATEX by means of literate programming
I Compendium (Gentleman and Temple Lang 2007 Gentlemanet al 2005)scientific paper as R-package (including data code)based on Sweave
I Org-mode
The Emacs Org-mode Andreas Leha 16 August 2011 8
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 9
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Org-mode
Org-mode is for keeping notes maintaining ToDo lists doingproject planning and authoring with a fast and effectiveplain-text system
httporgmodeorg
I Major mode of emacsI File formatI Created in 2003 by Carsten DominikI Current Version 77 maintainer Bastien GuerryI Very active development
The Emacs Org-mode Andreas Leha 16 August 2011 10
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode and Reproducible Research
I Through Org Babel a literate programming (Knuth 1984)system
I Written by Eric Schulte and Dan Davison
code
ltcodegt
+ org
lttextgt
document
tangle
weave
The Emacs Org-mode Andreas Leha 16 August 2011 11
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Reproducible ResearchPossible Definition
a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication
(Hothorn Held and Friede 2009)
A piece of reproducible research is usually notmethods section + published data
+ code + parameters +
Nature Genetics (200506)(Ioannidis et al 2009)
not reproducible
56
Bioinformatics (Vol26)(Hothorn and Leisch 2011)
I Better but similar results
The Emacs Org-mode Andreas Leha 16 August 2011 4
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Reproducible ResearchPossible Definition
a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication
(Hothorn Held and Friede 2009)
A piece of reproducible research should ideally containmethods section + published data + code
+ parameters +
Biometrical Journal (Vol50)(Hothorn Held and Friede 2009)
potentially reproducible
89
Bioinformatics (Vol26)(Hothorn and Leisch 2011)
I Better but similar results
The Emacs Org-mode Andreas Leha 16 August 2011 4
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Reproducible ResearchPossible Definition
a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication
(Hothorn Held and Friede 2009)
A piece of reproducible research should ideally containmethods section + published data + code + parameters +
Biometrical Journal (Vol50)(Hothorn Held and Friede 2009)
potentially reproducible
89
Bioinformatics (Vol26)(Hothorn and Leisch 2011)
I Better but similar results
The Emacs Org-mode Andreas Leha 16 August 2011 4
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Why to use Reproducible Research
I Benefits for the researcher herselfIn the mid-1980s we realized that our laboratoryrsquosresearchers often had difficulty reproducing their owncomputations without considerable agony
(Schwab Karrenbach and Claerbout 2000)
I Benefits for othersI Precise lsquodescriptionrsquo of methodsI Easy re-use of applied methodsI No forensic bioinformatics
(Baggerly and Coombes 2009 Ioannidis et al 2009)
The Emacs Org-mode Andreas Leha 16 August 2011 5
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Barriers for Reproducible Research
(Banks 2011)
I Deliberate non-reproducibilityI Vagueness to cover potential mistakes
I External reasonsI Ownership of the dataI Collaboration partners
I Perception of effortI DisciplineI ResourcesI Change of work flow
The Emacs Org-mode Andreas Leha 16 August 2011 6
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 7
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Existing Tools for Reproducible Research
I ReDoc (Schwab Karrenbach and Claerbout 2000)GNU make rules synchronize code and output
I Sweave (Leisch 2002)interwoven R and LATEX by means of literate programming
I Compendium (Gentleman and Temple Lang 2007 Gentlemanet al 2005)scientific paper as R-package (including data code)based on Sweave
I Org-mode
The Emacs Org-mode Andreas Leha 16 August 2011 8
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 9
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Org-mode
Org-mode is for keeping notes maintaining ToDo lists doingproject planning and authoring with a fast and effectiveplain-text system
httporgmodeorg
I Major mode of emacsI File formatI Created in 2003 by Carsten DominikI Current Version 77 maintainer Bastien GuerryI Very active development
The Emacs Org-mode Andreas Leha 16 August 2011 10
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode and Reproducible Research
I Through Org Babel a literate programming (Knuth 1984)system
I Written by Eric Schulte and Dan Davison
code
ltcodegt
+ org
lttextgt
document
tangle
weave
The Emacs Org-mode Andreas Leha 16 August 2011 11
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Reproducible ResearchPossible Definition
a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication
(Hothorn Held and Friede 2009)
A piece of reproducible research should ideally containmethods section + published data + code
+ parameters +
Biometrical Journal (Vol50)(Hothorn Held and Friede 2009)
potentially reproducible
89
Bioinformatics (Vol26)(Hothorn and Leisch 2011)
I Better but similar results
The Emacs Org-mode Andreas Leha 16 August 2011 4
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Reproducible ResearchPossible Definition
a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication
(Hothorn Held and Friede 2009)
A piece of reproducible research should ideally containmethods section + published data + code + parameters +
Biometrical Journal (Vol50)(Hothorn Held and Friede 2009)
potentially reproducible
89
Bioinformatics (Vol26)(Hothorn and Leisch 2011)
I Better but similar results
The Emacs Org-mode Andreas Leha 16 August 2011 4
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Why to use Reproducible Research
I Benefits for the researcher herselfIn the mid-1980s we realized that our laboratoryrsquosresearchers often had difficulty reproducing their owncomputations without considerable agony
(Schwab Karrenbach and Claerbout 2000)
I Benefits for othersI Precise lsquodescriptionrsquo of methodsI Easy re-use of applied methodsI No forensic bioinformatics
(Baggerly and Coombes 2009 Ioannidis et al 2009)
The Emacs Org-mode Andreas Leha 16 August 2011 5
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Barriers for Reproducible Research
(Banks 2011)
I Deliberate non-reproducibilityI Vagueness to cover potential mistakes
I External reasonsI Ownership of the dataI Collaboration partners
I Perception of effortI DisciplineI ResourcesI Change of work flow
The Emacs Org-mode Andreas Leha 16 August 2011 6
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 7
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Existing Tools for Reproducible Research
I ReDoc (Schwab Karrenbach and Claerbout 2000)GNU make rules synchronize code and output
I Sweave (Leisch 2002)interwoven R and LATEX by means of literate programming
I Compendium (Gentleman and Temple Lang 2007 Gentlemanet al 2005)scientific paper as R-package (including data code)based on Sweave
I Org-mode
The Emacs Org-mode Andreas Leha 16 August 2011 8
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 9
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Org-mode
Org-mode is for keeping notes maintaining ToDo lists doingproject planning and authoring with a fast and effectiveplain-text system
httporgmodeorg
I Major mode of emacsI File formatI Created in 2003 by Carsten DominikI Current Version 77 maintainer Bastien GuerryI Very active development
The Emacs Org-mode Andreas Leha 16 August 2011 10
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode and Reproducible Research
I Through Org Babel a literate programming (Knuth 1984)system
I Written by Eric Schulte and Dan Davison
code
ltcodegt
+ org
lttextgt
document
tangle
weave
The Emacs Org-mode Andreas Leha 16 August 2011 11
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Reproducible ResearchPossible Definition
a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication
(Hothorn Held and Friede 2009)
A piece of reproducible research should ideally containmethods section + published data + code + parameters +
Biometrical Journal (Vol50)(Hothorn Held and Friede 2009)
potentially reproducible
89
Bioinformatics (Vol26)(Hothorn and Leisch 2011)
I Better but similar results
The Emacs Org-mode Andreas Leha 16 August 2011 4
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Why to use Reproducible Research
I Benefits for the researcher herselfIn the mid-1980s we realized that our laboratoryrsquosresearchers often had difficulty reproducing their owncomputations without considerable agony
(Schwab Karrenbach and Claerbout 2000)
I Benefits for othersI Precise lsquodescriptionrsquo of methodsI Easy re-use of applied methodsI No forensic bioinformatics
(Baggerly and Coombes 2009 Ioannidis et al 2009)
The Emacs Org-mode Andreas Leha 16 August 2011 5
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Barriers for Reproducible Research
(Banks 2011)
I Deliberate non-reproducibilityI Vagueness to cover potential mistakes
I External reasonsI Ownership of the dataI Collaboration partners
I Perception of effortI DisciplineI ResourcesI Change of work flow
The Emacs Org-mode Andreas Leha 16 August 2011 6
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 7
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Existing Tools for Reproducible Research
I ReDoc (Schwab Karrenbach and Claerbout 2000)GNU make rules synchronize code and output
I Sweave (Leisch 2002)interwoven R and LATEX by means of literate programming
I Compendium (Gentleman and Temple Lang 2007 Gentlemanet al 2005)scientific paper as R-package (including data code)based on Sweave
I Org-mode
The Emacs Org-mode Andreas Leha 16 August 2011 8
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 9
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Org-mode
Org-mode is for keeping notes maintaining ToDo lists doingproject planning and authoring with a fast and effectiveplain-text system
httporgmodeorg
I Major mode of emacsI File formatI Created in 2003 by Carsten DominikI Current Version 77 maintainer Bastien GuerryI Very active development
The Emacs Org-mode Andreas Leha 16 August 2011 10
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode and Reproducible Research
I Through Org Babel a literate programming (Knuth 1984)system
I Written by Eric Schulte and Dan Davison
code
ltcodegt
+ org
lttextgt
document
tangle
weave
The Emacs Org-mode Andreas Leha 16 August 2011 11
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Why to use Reproducible Research
I Benefits for the researcher herselfIn the mid-1980s we realized that our laboratoryrsquosresearchers often had difficulty reproducing their owncomputations without considerable agony
(Schwab Karrenbach and Claerbout 2000)
I Benefits for othersI Precise lsquodescriptionrsquo of methodsI Easy re-use of applied methodsI No forensic bioinformatics
(Baggerly and Coombes 2009 Ioannidis et al 2009)
The Emacs Org-mode Andreas Leha 16 August 2011 5
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Barriers for Reproducible Research
(Banks 2011)
I Deliberate non-reproducibilityI Vagueness to cover potential mistakes
I External reasonsI Ownership of the dataI Collaboration partners
I Perception of effortI DisciplineI ResourcesI Change of work flow
The Emacs Org-mode Andreas Leha 16 August 2011 6
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 7
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Existing Tools for Reproducible Research
I ReDoc (Schwab Karrenbach and Claerbout 2000)GNU make rules synchronize code and output
I Sweave (Leisch 2002)interwoven R and LATEX by means of literate programming
I Compendium (Gentleman and Temple Lang 2007 Gentlemanet al 2005)scientific paper as R-package (including data code)based on Sweave
I Org-mode
The Emacs Org-mode Andreas Leha 16 August 2011 8
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 9
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Org-mode
Org-mode is for keeping notes maintaining ToDo lists doingproject planning and authoring with a fast and effectiveplain-text system
httporgmodeorg
I Major mode of emacsI File formatI Created in 2003 by Carsten DominikI Current Version 77 maintainer Bastien GuerryI Very active development
The Emacs Org-mode Andreas Leha 16 August 2011 10
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode and Reproducible Research
I Through Org Babel a literate programming (Knuth 1984)system
I Written by Eric Schulte and Dan Davison
code
ltcodegt
+ org
lttextgt
document
tangle
weave
The Emacs Org-mode Andreas Leha 16 August 2011 11
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Barriers for Reproducible Research
(Banks 2011)
I Deliberate non-reproducibilityI Vagueness to cover potential mistakes
I External reasonsI Ownership of the dataI Collaboration partners
I Perception of effortI DisciplineI ResourcesI Change of work flow
The Emacs Org-mode Andreas Leha 16 August 2011 6
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 7
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Existing Tools for Reproducible Research
I ReDoc (Schwab Karrenbach and Claerbout 2000)GNU make rules synchronize code and output
I Sweave (Leisch 2002)interwoven R and LATEX by means of literate programming
I Compendium (Gentleman and Temple Lang 2007 Gentlemanet al 2005)scientific paper as R-package (including data code)based on Sweave
I Org-mode
The Emacs Org-mode Andreas Leha 16 August 2011 8
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 9
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Org-mode
Org-mode is for keeping notes maintaining ToDo lists doingproject planning and authoring with a fast and effectiveplain-text system
httporgmodeorg
I Major mode of emacsI File formatI Created in 2003 by Carsten DominikI Current Version 77 maintainer Bastien GuerryI Very active development
The Emacs Org-mode Andreas Leha 16 August 2011 10
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode and Reproducible Research
I Through Org Babel a literate programming (Knuth 1984)system
I Written by Eric Schulte and Dan Davison
code
ltcodegt
+ org
lttextgt
document
tangle
weave
The Emacs Org-mode Andreas Leha 16 August 2011 11
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 7
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Existing Tools for Reproducible Research
I ReDoc (Schwab Karrenbach and Claerbout 2000)GNU make rules synchronize code and output
I Sweave (Leisch 2002)interwoven R and LATEX by means of literate programming
I Compendium (Gentleman and Temple Lang 2007 Gentlemanet al 2005)scientific paper as R-package (including data code)based on Sweave
I Org-mode
The Emacs Org-mode Andreas Leha 16 August 2011 8
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 9
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Org-mode
Org-mode is for keeping notes maintaining ToDo lists doingproject planning and authoring with a fast and effectiveplain-text system
httporgmodeorg
I Major mode of emacsI File formatI Created in 2003 by Carsten DominikI Current Version 77 maintainer Bastien GuerryI Very active development
The Emacs Org-mode Andreas Leha 16 August 2011 10
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode and Reproducible Research
I Through Org Babel a literate programming (Knuth 1984)system
I Written by Eric Schulte and Dan Davison
code
ltcodegt
+ org
lttextgt
document
tangle
weave
The Emacs Org-mode Andreas Leha 16 August 2011 11
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Existing Tools for Reproducible Research
I ReDoc (Schwab Karrenbach and Claerbout 2000)GNU make rules synchronize code and output
I Sweave (Leisch 2002)interwoven R and LATEX by means of literate programming
I Compendium (Gentleman and Temple Lang 2007 Gentlemanet al 2005)scientific paper as R-package (including data code)based on Sweave
I Org-mode
The Emacs Org-mode Andreas Leha 16 August 2011 8
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 9
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Org-mode
Org-mode is for keeping notes maintaining ToDo lists doingproject planning and authoring with a fast and effectiveplain-text system
httporgmodeorg
I Major mode of emacsI File formatI Created in 2003 by Carsten DominikI Current Version 77 maintainer Bastien GuerryI Very active development
The Emacs Org-mode Andreas Leha 16 August 2011 10
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode and Reproducible Research
I Through Org Babel a literate programming (Knuth 1984)system
I Written by Eric Schulte and Dan Davison
code
ltcodegt
+ org
lttextgt
document
tangle
weave
The Emacs Org-mode Andreas Leha 16 August 2011 11
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 9
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Org-mode
Org-mode is for keeping notes maintaining ToDo lists doingproject planning and authoring with a fast and effectiveplain-text system
httporgmodeorg
I Major mode of emacsI File formatI Created in 2003 by Carsten DominikI Current Version 77 maintainer Bastien GuerryI Very active development
The Emacs Org-mode Andreas Leha 16 August 2011 10
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode and Reproducible Research
I Through Org Babel a literate programming (Knuth 1984)system
I Written by Eric Schulte and Dan Davison
code
ltcodegt
+ org
lttextgt
document
tangle
weave
The Emacs Org-mode Andreas Leha 16 August 2011 11
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
What is Org-mode
Org-mode is for keeping notes maintaining ToDo lists doingproject planning and authoring with a fast and effectiveplain-text system
httporgmodeorg
I Major mode of emacsI File formatI Created in 2003 by Carsten DominikI Current Version 77 maintainer Bastien GuerryI Very active development
The Emacs Org-mode Andreas Leha 16 August 2011 10
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode and Reproducible Research
I Through Org Babel a literate programming (Knuth 1984)system
I Written by Eric Schulte and Dan Davison
code
ltcodegt
+ org
lttextgt
document
tangle
weave
The Emacs Org-mode Andreas Leha 16 August 2011 11
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode and Reproducible Research
I Through Org Babel a literate programming (Knuth 1984)system
I Written by Eric Schulte and Dan Davison
code
ltcodegt
+ org
lttextgt
document
tangle
weave
The Emacs Org-mode Andreas Leha 16 August 2011 11
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
A Simple Example
The Data
We first generate some data
a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)
1radic2πσ2
eminus(xminusmicro)2
2σ2
Descriptive Values
mean sda -021 104b 071 092
Visualization
Analysis
A t-test shows that the means are signifi-cantly different (p-value )
Skip Screenshots
The Emacs Org-mode Andreas Leha 16 August 2011 12
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
code
ltcodegt
+ org
lttextgt
document
tangle
weavetexpdfhtmlodt
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Export
The Emacs Org-mode Andreas Leha 16 August 2011 13
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
code
ltcodegt
+ org
lttextgt
document
tangle
weave
RPythonShellJava
texpdf
html
odt
The Emacs Org-mode Andreas Leha 16 August 2011 14
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Various Languages
Example Commit Sizes in Org-mode v76 and v77
release
lines
100
101
102
103
104
v76 v77
lrr mean sdv76 1392 240196v77 4048 8134
A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)
Skip Screenshot
The Emacs Org-mode Andreas Leha 16 August 2011 15
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
More Examples on Org Babel
I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml
I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo
I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial
I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)
on Org-mode itselfhttpsgithubcomeschulteCiSE
I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization
The Emacs Org-mode Andreas Leha 16 August 2011 16
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Org-mode for lsquobeyondrsquo
Some Highlights
I Note takingI Outlining FoldingI Rearrangement of whole branches
I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps
I Tables Spreadsheet
The Emacs Org-mode Andreas Leha 16 August 2011 17
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Orientation
Reproducible Research
Existing Tools for Reproducible Research
Org-mode
Summary
The Emacs Org-mode Andreas Leha 16 August 2011 18
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Summary
Using Org-mode for Research Can Give You
I Reproducibility
I Plain Text FilesI Visual User Experience
I Various Export Formats
I Various Programming Languages
I Intuitive Organizer
I
ButI Reproducibility is still limited by active development
I Less editing support than Sweave
The Emacs Org-mode Andreas Leha 16 August 2011 19
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Disclaimer
Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures
(Buckheit and Donoho 1995)
CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers
The Emacs Org-mode Andreas Leha 16 August 2011 20
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature I
Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334
Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)
Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81
Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania
Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23
Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc
Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5
The Emacs Org-mode Andreas Leha 16 August 2011 21
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Literature II
Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300
Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55
Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111
Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580
Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73
Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67
The Emacs Org-mode Andreas Leha 16 August 2011 22
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-
Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References
Thank you for your attention
The Emacs Org-mode Andreas Leha 16 August 2011 23
- Reproducible Research
- Existing Tools for Reproducible Research
- Org-mode
- Summary
-