Page 1 .... BaseR or a version of it is used at Facebook, Twitter, Foursquare,. Microsoft, Google, Ford, Bank .... (Tools â Global Options â General â Change..).
The R Programming Language for Statistical Computing and Graphics
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R is the lingua franca of data science
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R is • a programming environment • for statistical computing and graphics. • An open source platform, • working on most platforms (GNU/Linux, OS X, Windows) and • extendable via packages. • running all procedures in the workspace (RAM).
1 http://blog.revolutionanalytics.com/2013/11/the-rise-of-r-as-the-language-of-analytics.html Introduction 3 / 136
”We could have chosen to be commercial, and we would have sold five copies of the software.”
Ross Ihaka, R Developer New York Times, 9. January 2009
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A short history...
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1976 John Chambers, Ben Bolker and colleagues begin developing The System”at Bell Labs 1984 First version of S 1993 First public”appearance of R to S news”mailing list 1995 First release of R under GNU general license” 1996 The R-Paperby Ihaka & Gentleman (Google Scholar: 8070 citations) 1997 Established R ”core group” R version 0.49, April 1997 2000 R Version 1.0.0 2009 Article in The New York Times 2014 Most likely, R became the top statistics package used during the summer of this year (Muenchen cited in Nature 517, 109-110)
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Bell Labs/AT&T
Researchers working at Bell Labs are credited with the development of radio astronomy, the transistor, the laser, the charge-coupled device (CCD), information theory, the UNIX operating system, the C programming language, S programming language and the C++ programming language. Eight Nobel Prizes have been awarded for work completed at Bell Laboratories.
Source: https://en.wikipedia.org/wiki/Bell_Labs
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Ross Ihaka & Robert Gentleman, New Zealand We wanted a command driven interface and, since we were both very familiar with S, it seemed natural to use an S-like syntax. This decision, more than anything else, has driven the direction that R development has taken. [...] the adoption of the S syntax for our interpreter produced something which feltremarkably close to S. Having taking this first step we found ourselves adopting more and more features from S.
Ross Ihaka, 1998
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The name is partly based on the (first) names of the first two R authors (Robert Gentleman and Ross Ihaka), and partly a play on the name of the Bell Labs language ’S’.
Hornik (2015), The R FAQ” https://CRAN.R-project.org/doc/FAQ/R-FAQ.html
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The R Core Group
Doug Bates, John Chambers, Peter Dalgaard, Seth Falcon, Robert Gentleman, Kurt Hornik, Stefano Iacus, Ross Ihaka, Friedrich Leisch, Uwe Ligges, Thomas Lumley, Martin Maechler, Duncan Murdoch, Paul Murrell, Martyn Plummer, Brian Ripley, Deepayan Sarkar, Duncan Temple Lang, Luke Tierney, and Simon Urbanek.
Hornik (2015), The R FAQ” https://CRAN.R-project.org/doc/FAQ/R-FAQ.html
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The initial work [...] produced what looked like a potentially useful piece of software and we began preparing it for use in our teaching laboratory.
Ross Ihaka, 1998
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Academic success
• Teaching • R is free and works on many platforms • Methods development • Development, implimentation and application go hand-in-hand • Methods access • How easy is it to run a simple IRT model in SPSS? • Reproducible Research • Open Data • Review scripts, not just manuscripts
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Commercial success
Open Source: Can be task-tailored”(cf. PHP for Facebook)
BaseR or a version of it is used at Facebook, Twitter, Foursquare, Microsoft, Google, Ford, Bank of America, NASA, Beyer, Pfizer, Roche, The New York Times and other newspapers...
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Developer success
http://spectrum.ieee.org/computing/software/ the-2015-top-ten-programming-languages Institute of Electrical and Electronics Engineers
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Extendability: Packages
Functions can be combined to packages. Packages structure R code in a systematic manner. A package can be loaded into the workspace and the according funtions are ready for use. • Expand R’s base capabilities. • R gives common environment/framework, specialists implement specific solutiens. • Tailoredfunctions for routine tasks (A package does not need to be
published) • October 2015: 7395 packages on CRAN
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Comprehensive R Archive Network (CRAN):
• ”Master site”: https://cran.r-project.org/ • Host the R software, packages etc. for available platforms, both
pre-compiled and source code.
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Task Views Collections of packages for specific purposes (e.g. Natural Language Processing, Medical Imaging, or Psychometrics) Examples: • https://cran.r-project.org/web/views/
NaturalLanguageProcessing.html • https:
//cran.r-project.org/web/packages/qdap/index.html • https:
//cran.r-project.org/web/packages/RQDA/index.html • https:
//cran.r-project.org/web/views/MedicalImaging.html • https:
//cran.r-project.org/web/views/Psychometrics.html
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Packages
lavaan Structural Equation Models that mimic e.g. MPlus foreign Read SAS/SPSS/... data xlsx Read/write MS Excel dplyr Easier reshaping/aggregation of data ggplot2 Graphics & plots ggvis Interactive, web based graphics car Regression tools - incl. useful ’recode’ function CTT For Classical Test Theory (cf. also irtoys)
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What is a ’good’ package?
In general, R packages are routinely tested under Debian/Linux. Packages must stick to the ”CRAN Repository Policy” • Who are the authors? • Is it under continuing revision? • How old are the last versions? • How good is the documentation? • Are there resources - books, tutorials, etc. - using this software? • Is the package used in scientific articles?
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http://paulbutler.org/archives/visualizing-facebook-friends/
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Graphics
• https://gjabel.wordpress.com/2014/06/05/
world-cup-players-representation-by-league-system/ • http://motioninsocial.com/tufte/ • http://flowingdata.com/2014/10/23/
moving-past-default-charts/ • http://www.htmlwidgets.org/
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The competition...
R vs. Python
R vs. Matlab/STATA/SAS/SPSS/
....Julia?
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Where (for me) the effort of learning R paid of... • Routine reports: For individuals and insitutions • Research: Integration of various data sources (from cleaning to scale
analyses) • R works always and everywhere • You are often expected to speakR as naturally as English
• Everything is a script • Never touch your raw data (again) • Work with batch-scripts and GUIs • Example: OSCE reports (incl. ID-check and Generalizability ’Study’)
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What R does not
• It’s a pain to enter data manually in R
Rather use Excel and save as *.csv • If you WANT point-and-click, other options are better • Open Source means: Validation and reliability checks of software is
done by the community”. (Usually stressed by commercial companies)
• R is not ”indictable” • The PCs working-memory is the bottle-neck (Usually not relevant in ”ourscenarios)
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”We have customers who build engines for aircraft. I am happy they are not using freeware when I get on a jet.”
Anne H. Milley, Director of technology product marketing at SAS New York Times, 9. January 2009
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Pro & Con
Pro R is from statisicians for statisticians
Con R is from statisicians for statisticians
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Further info and help
https://cran.r-project.org/faqs.html https://www.r-project.org/ http://stackoverflow.com/questions/tagged/r https://stat.ethz.ch/mailman/listinfo/r-help https://journal.r-project.org/ http://www.statmethods.net/ https://www.rstudio.com/resources/cheatsheets/
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Getting started...
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CRAN: The Comprehensive R Archive Network • Search for ”cran”in your preferred search engine...
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• Download for Linux/MacOS/Windows
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• Select Install R for the first time
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• Select Download R
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Install R (without admin rights) 1
Crate new folder (e.g. c:/RTest/) & install to this directory
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Do not install to Program Files”
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Customise installation
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Install R (without admin rights)
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A matter of taste: Seperate windoes
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Install R (without admin rights)
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Plain text help is faster
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Install R (without admin rights)
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Start menu?
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Install R (without admin rights)
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Important: No Registry entries!
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Install R (without admin rights)
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Install...
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Install R (without admin rights) 9
Find R as desktop icon or RGui.exe in either 32bit or 64bit folder:
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If this doesn’t work... • If your (IT’s) security policy is too rigid, • you may need admin rights to even start the installer. • If so, you can run the steps described above at your private PC • The folder RTest”can then be copied (e.g. via a USB drive) to any
other PC. • If the security policy is still to rigid. Well...
If you work on Windows and your connection goestrough a proxy server, let R know via: #Important for instaling packages #Type into script/console setInternet2(use=TRUE)
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R as a calculator
R as a calculator 41 / 136
# Addition and subtraction 1 + 1 - 5 + 3 ## [1] 0 # Multiplication 2 * 13 ## [1] 26 # Square root and exponentiation sqrt(3) ## [1] 1.732051 sqrt(3)^2 ## [1] 3 3^(1/2) ## [1] 1.732051
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# Fraction 3/4 ## [1] 0.75 # Brackets... 2/(4 + 4) * 2 ## [1] 0.5 # ...no brackets 2/4 + 4 * 2 ## [1] 8.5
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Integrated Development Environments (IDEs) (For more convenience...)
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Some options...
• Stick to baseR (Mac has syntax highlighting) • Rstudio (All platforms - Very convienient, but slower than baseR) • Notepad ++ & npptoR (Win only but fast) • Eclipse/Vim/Emacs (Win/Mac/Linux) • .....
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RStudio
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Download at: https://www.rstudio.com/products/rstudio/download/ • Use installers, when possible • In institutional context: ZIP file (no installer - no admin)
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You can select the R-Installation that R Studio works with by hand:
(Tools → Global Options → General → Change..)
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Packages! Packages! Packages!
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Packages and Repositories Packages extend R’s capabilities. They add functions or routines for specific tailored tasks.There are packages for almost every purpose such as psychometrics, machine learing, natural language processing, genetics, medical image processing, or sending emails. Some of the packages used in this work are: • foreign for handling data from e.g. SPSS • ggplot2 for plotting data • TAM for IRT purposes • lme4 for estimating variance componets used in Generalizability
Theory Packages can be retrieved from Repositories (i.e ’online archives’).
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Most popular archives: • CRAN (Comprehensive R Archive Network) • RForge (Often ’Beta’ software) • Bioconductor (Bioinformatics)
Installing manually or via code: → Packages → Install Package(s) → Select Mirror → Select Package
# Example: CRAN packeges form RStudio mirror. install.packages("", repos = "https://cran.rstudio.com/") # Example: R-Forge install.packages("", repos = "http://R-Forge.R-project.org")
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Data Representation in R
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Principles
In R, everything is an object - (incl. paths, variable names, statistic procedures, operators...) R is vector-based Every object is stored and manipulated in the workspace You can mess up litterally everything - but only as long as the session lasts.
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Objects are created with a left arrow (
