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Experimental epidemiology analyses with R and R commander

Lars T. FadnesCentre for International Health

University of Bergen

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How to install R commander?

- install.packages("Rcmdr", dependencies=TRUE)-

- Download necessary web files put them in a folder:

http://statistics.fadnes.net/epi

– Fieldtrials12.RData

– Exercises-for-the-exp-epi-2012-03.rtf

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• Install R (if not done already)

– http://www.r-project.org/

• Install package Rcmdr (if not done already)

– Package Install package scroll down to Rcmdr click OK

• Install package Epi

– Package Install package scroll down to Rcmdr click OK

• Download RcmdrPlugin.Cih.Epi from http://statistics.fadnes.net/epi/

• Install package(s) from local zip file (choose the package you just downloaded)

• Open program

– Load package Rcmdr

– Tools -> load Rcmdr plug-in(s) RcmdrPlugin.Cih.Epi

• click ok and Yes

• Now you are ready

Installation of RcmdrPlugin.Cih.Epi

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Aim for this session

• Introduce a brilliant tool

• Analyse a dataset with the tool

• Guide to further knowledge

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What is R?

• R is a free software environment that includes a set of base packages for graphics, math, and statistics.

• You can make use of specialized packages contributed by R users or write your own new functions.

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Why R?

• Very powerful

• Developing extremely quickly

• Working on different platforms (not only Microsoft Windows…)

• Free of all costs

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Why don’t all use R?

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What is R commander?

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Why R commander?

• Powerful

• Free of all costs

• Working on different platforms (not only Microsoft Windows…)

• Easy to learn and to use…

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How to install R?For Windows:• http://cran.r-project.org/bin/windows/base/

– Easy• If here at UiB, the IT department will fix it for you if you just ask them

to add it for you

For Linux (Ubuntu etc):- Very Easy

- Just search for R-base-core in Synaptic Package Manager and add it

- http://socserv.mcmaster.ca/jfox/Misc/Rcmdr/installation-notes.html

(also contains a good description for installation on Mac)

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How to install R commander?

- Is already installed on UiB computers-

- If not:

install.packages("Rcmdr", dependencies=TRUE)

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Some things to note first

• R is case-sensitive – help, Help, HELP and HELF are different…– Recommendation:

• Choose one style and stick to it

• If it’s something you don’t know?– There are lot’s of good information on the web

• Particularly for R

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How to start?

• Open R– Load packages

Rcmdr

or write

• library(Rcmdr)

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Menu• File Menu:

– items for loading and saving script files; – for saving output and the R workspace; – and for exiting

• Edit Menu: – items (Cut, Copy, Paste, etc.) for editing the contents of the script and output

windows.

• Data – Submenus containing menu items for reading and manipulating data.

• Statistics – Submenus containing menu items for a variety of basic statistical analyses.

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Menu• Graphs

– Menu items for creating simple statistical graphs.

• Models – Menu items and submenus for obtaining numerical summaries, confidence intervals,

hypothesis tests, diagnostics, and graphs for a statistical model, and for adding diagnostic quantities, such as residuals, to the data set.

• Distributions – Probabilities, quantiles, and graphs of standard statistical distributions (to be used, for

example, as a substitute for statistical tables) and samples from these distributions.

• Tools – Menu items for loading R packages unrelated to the Rcmdr package (e.g., to access data

saved in another package), and for setting some options.

• Help Menu – items to obtain information about the R Commander (including this manual). As well, each R

Commander dialog box has a Help button (see below).

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• Script Window

– R commands generated by the R Commander

– You can also type R commands directly into the script window or the R Console

– The main purpose of the R Commander, however, is to avoid having to type commands.

• Output Window – Printed output

• Messages Window– Displays error messages, warnings, and

notes

• Graphics Device window – When you create graphs, these will

appear in a separate window outside of the main R Commander window.

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Available functions:

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Click to add title

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Save dataset under your documents folder

Files and documents are available at

http://statistics.fadnes.net/epi

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Let’s get started…

• Change directory (under File)– Find the folder where

you placed your data file

• Import data– Give it the name: fieldtrials

• Save workspace as– Give a name to your file– The file contains the dataset and

any models you might have generated

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Data Types

• Vectors – Quantitative difference (one vs. two apples)– including continuous (numerical) variables

– Number variables coded as vectors as default

• Factors – Qualitative difference (apples vs. pears)– Categorical

– Text variables coded as factors as default

• Matrices, lists, arrays and data frames

http://www.statmethods.net/input/datatypes.html

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Variables in dataset - define the datatypes

id id number

gender male/female - (factor)

treatmentarm Treatment (1=zinc, 0=placebo) - (factor)

childage Age of the child in months - vector

breastfed Is the child breast fed - (factor)

lentils Does the child eat lentils? (0=no, 1= yes) - (factor)

meat Does the child eat meat? (0=no, 1= yes) - (factor)

duration Duration of diarrhea in days - vector

diarsev Severe diarrhoea ≥10 stools per day - (factor)

fever Did the child have fever at enrollment? - (factor)

clusterzn2/4/8/16 cluster variables identifying living areas

- coded as vector, but needs to be transformed into a factor

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How to save?

• Save R workspace as…– This will save your data (in the R format)

• Save output as…– This will save your output– Another strategy is to cut and paste what you want to save

• Always save the commands (syntax)– essential if you want to re-run the analyses later– WordPad is a better option than Word etc (does not autocorrect -

change to upper case etc)

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How to write and a command?

• Simply write the command in the script window, mark it and click ’Submit’ or press Ctrl+R

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Nice to know:

• When writing comments in the syntax, start with the following sign #– R will then not consider the line as a

command

• If you are uncertain about a function, use google or help(name-of-function)

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– Cluster has numbers and is as default coded as vector, but needs to be recoded into a factor (categorical variables for grouping etc)

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Now we’re ready to answer some scientific questions…

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Compute new variable

• Child age in years• Child age now given in months• of vaccination is often calculated by measuring

antibodies before and after vaccination

•childageyear = childage/ 12

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Does the new variable look reasonable?

• View data set

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Summarize variable

• Calculate mean, median and standard deviation for– childageyear

• for each intervention arm (treatmentarm)

• Numerical summaries

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Doing calculations for subsetsby generating new datasets

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• Placebo: treatmentarm == "placebo"

• Zinc: treatmentarm == "zinc"

Make the other subset by changing the syntax and run ('Submit') the syntax

zinc <- subset(fieldtrials3, subset=treatmentarm=="zinc")

placebo <- subset(fieldtrials3, subset=treatmentarm=="placebo")

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– You can now easily change between the datasets

•

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Make a histogram of childageyear

• First for the 'zinc' dataset

• Then for the 'placebo' dataset

• Are they look similar?

Note:– The histograms will be printed in the R window (not

inside R commander)– Right click on the graph and you can copy it as

metafile to paste it into a document, print it or save it

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• Does it look normally distributed?

placebo$childageyear

frequ

ency

0.5 1.0 1.5 2.0 2.5

010

2030

40

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Box plot

• Box plot for childageyear– By treatmentarm– (first remember to select the complete

fieldtrials dataset)

placebo zinc

0.5

1.0

1.5

2.0

2.5

treatmentarm

ch

ild

ag

eye

ar

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Is the baseline child age different in the zinc and placebo arms?

• This can be checked with a robust test not assuming normal distribution?

• Check with a – non-paramethric

» two-sample wilcoxon test (log rank test)» Use the ’Exact’ test

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Recoding variables

Diarrhoea duration can be recoded into an additional categorised variable (diarlong)

– Data manage variables

• value = ”factor”– Factor can be either number or word

• value, value, value = ”factor”– Listed with comma

• value:value = ”factor”– From lowest to highest values

• else all other values• NA missing

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Click to add title

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Are there differenses in syntax between R and R commander?

• Some few:– Commands that extend over more than one line should have the second and

subsequent lines indented by one or more spaces or tabs; all lines of a multiline command must be submitted simultaneously for execution.

– Commands that include an assignment arrow (<-) will not generate printed output, even if such output would normally appear had the command been entered in the R Console [the command print(x <- 10), for example]. On the other hand, assignments made with the equals sign (=) produce printed output even when they normally would not (e.g., x = 10).

– Commands that produce normally invisible output will occasionally cause output to be printed in the output window. This behaviour can be modified by editing the entries of the log-exceptions.txt file in the R Commander’s etc directory.

– Blocks of commands enclosed by braces, i.e., {}, are not handled properly unless each command is terminated with a semicolon (;). This is poor R style, and implies that the script window is of limited use as a programming editor. For serious R programming, it would be preferable to use the script editor provided by the Windows version of R itself, or – even better – a programming editor.

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True or false quiz

• R commander only works for Ms Windows?

• R is case sensitive (difference with small and large letters)

• R is built by a few people with a secret source-code?

• R was the program that gave their shareholders most profit last year?

• There are a lot of enthusiastic people working with R providing help to their peers in the R forum?

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R help forum:

• http://r.789695.n4.nabble.com/

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Further reading:

• The R Commander A Basic-Statistics Graphical User Interface to R - John Fox 2005.pdf– http://www.jstatsoft.org/v14/i09/paper

• Getting started with the R Commander: a basic-statistics graphical user interface to R– http://socserv.mcmaster.ca/jfox/Getting-Started-with-the-Rcmdr.pdf

• Quick-R: magnificent guide– http://www.statmethods.net/

• http://cran.r-project.org/manuals.html

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• You have learnt some basic skills and can now experiment with the program yourself

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Questions and comments

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