Vojtěch Janoušek Czech Geological Survey

& Charles University, Prague

Jean-François Moyen Université Saint Etienne, France

Vojtěch Erban Czech Geological Survey, Prague

Colin M. Farrow ex-Computing Service, University of Glasgow,

Scotland

The challenge: Interpretation of whole-rock geochemical data

• Lunar program in the late 1960’s came with the requirement of precise and accurate chemical, and then isotopic, analyses of small samples.

• This led to innovations: in 1970’s appeared analytical techniques for trace-element determinations (e.g., XRF; INAA), later ICP-OES, ICP-MS.

• Advancement of radiogenic isotope methods (originally TIMS, then SIMS, ICP-MS).

• Downside: the current flood of precise geochemical data needs to be interpreted by a potent and widely available software tool.

Spreadsheets (+ AddOns)?

Dedicated programs?

The challenge: Interpretation of whole-rock geochemical data

Spreadsheets

• Scarcity of dedicated applications – – DIY (mostly)

• Complex, prone to errors • Low efficiency for repeated tasks • Limited protection of the

primary data • Low quality of graphical output

• Widespread • Easy to use • Zero extra costs • DIY (mostly)

Program Reference

Petro.calc. plot

Sidder (1994)

PetroPlot Su et al.(2003)

GeoPlot Zhou & Li (2006)

GCDPlot Wang (2008)

Disadvantages:

Advantages:

Dedicated software

• DOS/MS Windows:

Program Reference OS Distribution

NewPet Clarke (1993)

DOS Shareware stopped

Norman Janoušek (2000)

DOS Freeware, stopped

MinPet Richard (1995)

Win Commercial [CAN$ 1000],

dead?

IgPet By M. Carr (TerraSofta)

Win Commercial [US$ 199]

Petro-Graph

Petrelli et al. (2004)

Win Freeware

• Lack of documentation (‘black box’)

• Incomplete & difficult to modify (source not available, legal problems, programming required)

• Complicated data input/import

• Poor quality of graphical output

• (User interface)

• (Price)

Dedicated software

Disadvantages:

Solution ?!

Complex statistical &

computing environments (S-Plus, Statistica,

MatLab, Mathematica & Co.)

???@!??

eRrrr!

A revolution? The Language

• Designed by Ihaka & Gentleman (1996), version 1.0 published on 29 Feb 2000

• Based on syntax of the S language (Becker et al. 1988)

• Since 1997 developed by R Core Team (http://www.r-project.org)

• Open-source (GNU) software

• Frequently updated, large and still growing community • High number of additional packages

• Available for all main OS (Mac, M$ Win, Unix...)

• Large collection of statistical and database tools

• Graphical facilities for data exploration and plotting, high-level graphical output

• Effective object-oriented programming language

• Excellent control over individual functions [= power]

http://www.gcdkit.org MAIN FEATURES:

Geochemical Data Toolkit = GCDkit

• A more human (less inhuman) interface to the wealth of functions in R • Windows-like GUI = no programming

necessary!!

• Data ready for further handling under R (dot prompt veterans)

• Standard geochemical calculations involving whole-rock major-, trace- element data and Sr-Nd isotopes

• Effective data management (searching, subsetting, grouping)

• Common plots (binary, ternary, spider, classification, geotectonic…)

• Publication quality graphic output

• 2000 – launched graduate-level courses on interpretation of geochemical data using R (Masaryk University in Brno & Charles University in Prague)

• 2003 – Goldschmidt Conference, Kurashiki, Japan – GCDkit 1.0 released

• 2006 key publication in Journal of Petrology (134 hits on WOS)

• 11 May 2013, last stable version (3.0, French connection) released

• October 2015 – Monograph on Geochemical modelling in R/GCDkit (Springer Verlag)

• GCDkit 4.0 (Indian summer) released for current R (ver. 3.2.1)

Main ‚milestones‘

Invited workshops on GCDkit and/or R modeling

• Czech Geological Survey, Prague, (11 June 2004),

• TU Bergakademie Freiberg, Germany (16 Oct 2005),

• CGS/EOST, Université Louis Pasteur Strasbourg, France (23–24 Oct 2008),

• University of Tromsø, Norway (16–17 June 2010),

• Université Jean Monnet, Saint-Etienne, France (9–11 May 2011),

• University of Helsinki, Finland (7–11 Nov 2011),

• University of Stellenbosch, South Africa (19–23 Mar 2012),

• National Geophysical Research Institute, Hyderabad, India (12–15 Jan 2013),

• University of Arba Minch, Ethiopia (2–6 April 2015)

• Polish Academy of Sciences, Cracow, Poland (23–27 Nov 2015)

Main features of GCDkit: I/O

• Modular architecture (= easily expandable and modifiable)

• Transparent functionality & availability (open source, WWW)

• Input data by copying from clipboard, files in TXT, XLS, MDB, DBF

• Import from geochemical databases (e.g., GEOROC, PETDB), concurrent geochemical packages (IgPet, MinPet, PetroGraph)

• Common recalculations • Norms (Niggli’s values, CIPW, Catanorm,

Granite Mesonorm....) • Custom variables & formulae (+ scripts) • Results can be copied to clipboard,

appended to the data, saved to HTML, TXT, XLS, MDB

Typical session with GCDkit

Statistics Plotting symbols Plotting colours Special diagrams

GROUP = samples that belong together on the basis of:

• identical label the same rock type, intrusion, locality, ...

• value of a numeric variable SiO2 <65 %, SiO2 = 65-70 %, SiO2 >70 %

• position in a classification diagram e.g. TAS diagram: rhyolites, basalts...

• cluster analysis • groups by outline

(defined interactively on a diagram)

Data handling: Grouping

Data handling: Grouping

Data handling: Grouping

Data handling: Searching & subsets

• Range of samples

• Boolean conditions

• Regular expressions in sample names or textual labels

• Subsets by diagram

Suite=“Sázava“.AND.SiO2>55

Data handling: Grouping

• Subsets by diagram

Data handling: Searching & subsets

Descriptive statistics

• Box-and-whiskers plots

• Correlation matrices

• Principal components

• Cluster analysis

• ...many others (including standard R functions)

• Histograms

SiO2,A/CNK,mg#

Plotting

• XYZ plots

• Coplots

• Binary plots

• Ternary plots

• 3D plots

• Anomaly plots

Multiple plots

Spiderplots

• By groups * shaded fields * for each an extra window

• Spider boxplots (+ normalization by a sample)

• Selected samples * Numerous standards (new added easilly) * by sample * by average

• Eight styles of x-axis annotations

• Double normalized spiderplots to eliminate effects of fractional crystallization in order to look solely on the source characteristics (Thompson et al. 1983).

Spiderplots

• A set of graphical utilities for R implemented in GCDkit

• Tools to create figure objects, containing both data and methods to make subsequent changes to plot

• classification algorithm – gives name of the polygon which the given analysis falls into (or a link to a new plot)

• Allows a degree of interactive editing before committing to hardcopy.

Figaro: Plot editing

Figaro: Plot editing

• edit title, subtitle

• edit axis labels

• zoom in graph

• add legend

• export (.pdf, .eps, .wmf) (e.g, CorelDraw)

• interactive identification

AEOL125

AEOL125

AEOL126

Plates: Figaro-like editing of multiple plots

• Right click the plate, select a diagram (slot) to edit/replace

• Figaro-like commands to change its appearance

• Additional commands to affect the whole plate (set it to B & W, output to PostScript, scaling of common x axes, text size of axis labels…)

• Make you own plates combining binary, ternary, spider plots with classification and geotectonic plots

Calculations

Na2O+K2O SiO2,FeOt/TiO2,3*CaO,MgO

Built-in calculation

engine

• Common recalculations – Millications, anhydrous basis – Various indices (Larsen’s, Kuno’s)

• Norms (Niggli’s values, CIPW, Catanorm, Granite Mesonorm etc.)

• Custom variables & formulae (+ scripts) • Ready for standard R functions

Calculations

Results can be: • copied to clipboard • saved in a text file • exported as HTML, Excel, Access... • appended to the data for further use (ploting,

grouping)

Calculations

Appending calculation

results to the data

CIPW normative compositions

Calculations

Well-formatted output to HTML

Plugins

Standard plugins: • Zrn, Mnz & Ap saturation calculations • Sr–Nd isotopic data • Tetrad effect • Advanced plotting • Isocon plots

• R code files stored in directory Plugin

• All executed upon loading new data

• Additional functions, accessible via newly appended menu items

• Perhaps code for special type of data

• A platform for DIY additions written by R literate geochemists

New features of the GCDkit 4.0

• GCDkit has got a NAMESPACE, which is obligatory for R 3.0 and higher

• Transparency

• Assigning colours according to values of a variable

• New diagrams – e.g., Pearce (2008) and Müller et al. (1992)

• Rutile saturation models

New features of the GCDkit 4.0

• Improved help system/manual in HTML and PDF

• Includes images and hyperlinks via DOI

New features of the GCDkit 4.0

• Commands executed directly, i.e. without pestering dialogues

• Enables writing ‚programs‘ and run them at once

• Good for repeated tasks, mutating datasets

• Allows for reproducible research

• Brings power (not all functions or parameters are available via GUI)

Future?

• Connection to online databases (EathChem.org) – O. Laurent

• Switching between multiple datasets

• Localization to more languages (beyond English, French and Czech)

Future?

• Separation of the core functions from the interface, opening a possibility of building new interfaces (Tcl/Tk, Java, WWW)

• Versions for other OS (Mac, Linux...)

• Automated generation of reports (Latex: Sweave, Open Office: OdfWeave, MS Office: SWORD)

• Example – SWORD (T. Baier, Vienna)

Future?

• Development of new plugins, e.g. for modelling of petrogenetic processes in igneous geochemistry (such as crystallization of the magma), GIS or recalculation of mineral data from EMPA

• Trigger user feedback (bug reports, contributed code)

http://blog.gcdkit.org

“The R Book” – philosophy

• Provides basics of R language and its application to geochemical problems,

• Gives the first comprehensive introduction to the GCDkit system,

• Explains fundamentals of numerical modelling of igneous processes,

• Shows not only formulae, but also the successful modelling strategies,

• Includes numerous worked examples how geochemical modelling helps us to understand geological problems.

Springer Geochemistry series, vol. 1 345 pp., 332 illus., 86 illus. in colour D 85,59 € | UK £72.00 | US $99.00

“The R Book” – contents

• Part I: Practical Modelling – Loading and manipulating data

– Linking Whole-Rock Chemistry with Mineral Stoichiometry

– Statistics

– Classification and Grouping

– Classical Plots (binary, Harker, ternary, spider)

– Specialized Plots (log–log, specialized spiderplots, contour plots, anomaly plots…)

– Radiogenic isotopes (initial ratios, epsilon values, model ages, isochrons…)

“The R Book” – contents

• Parts II–IV: Majors, traces, radiogenic isotopes

– Core of the book

– Explains fundamentals of each direct and reverse modelling, including the relevant formulae

– Then introduces the numerical solution and its implementation in the R language

– Includes a number of real numerical problems

– Each is presented as a numerical receipt with solution in R (± GCDkit )

• Part V: Practical Modelling – Choosing an Appropriate Model

(evidence for crystallization, partial melting, magma mixing and assimilation…)

– Semi-Quantitative Approach (assessing the trace-element compatibility, process identification, mixing test…)

– Constraining a Model (using appropriate strategy, obtaining input parameters for the model, partition coefficients, dealing with accessories…)

– Numerical Tips and Tricks (reducing system, colinearity, breaking minerals to end-members, coupling majors and traces…)

– Common Sense in Action (thermodynamic, rheological constraints, scale and speed of processes, how well can we distinguish between models, dangerous projections…)

“The R Book” – contents

• Part VI: Worked Examples – Differentiation of a Calc-Alkaline Series:

Atacazo-Ninahuilca volcanoes, Ecuador – Progressive Melting of a Metasedimentary

Sequence: the Saint-Malo Migmatitic Complex, France

• Appendix A: R Syntax in a Nutshell

• Appendix B: Introduction to GCDkit • Appendix C: Solving Systems of

Linear Algebraic Equations in R

“The R Book” – contents

• YOU for attention (?!)

• R Development Core Team (for R)

• Brave β testers (for bravery)

• Springer Verlag (Annett Buettner, Ulrike Stricker and Chris Bendall)

• Testing, feedback, localized versions: J. Trubač (Prague)

• O. Laurent (Eartchem module…)

• Eartchem.org (K. Lehnert)

• The Czech brewing industry

Acknowledgements • Austrian Science Foundation (15133-GEO),

• Czech Grant Agency (GAČR 205/01/0331, P210/11/1168),

• Czech Geological Survey (3314, 336200)

• French–Czech program Mobility (7AMB13FR026)

http://www.r-project.org, http://www.gcdkit.org, http://blog.gcdkit.org`