Introduction to R

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# Introduction to R
## R Foundations for Life Scientists
### Marcin Kierczak | 06-Nov-2020
### NBIS, SciLifeLab

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## Contents

* [About R](#about)
* [Timeline](#timeline)
* [Ideas behind R](#ideas)
* [Pros and cons of R](#pros_and_cons)
* [Ecosystem of packages](#num_packages)

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## Breifly about R

**R definitely is:**

* a programming language

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* a programming platform (= environment + interpreter)

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* a software project driven by the core team and the community

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* a very powerful tool for statistical computing

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* a very powerful computational tool in general

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* a catalyst between an idea and its realization

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**But NOT!**

* a tool to replace a statistician

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* the very best programming language

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* the most elegant programming solution

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* the most efficient programming language

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**Yet...**

* it is very elegant

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* it becomes more and more efficient

.pull-right-70[.size-20[![](data/slide_intro/Rlogo.png)]]

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## Timeline

* ca. 1992 &mdash; conceived by [Robert Gentleman](https://bit.ly/35kn99L) and [Ross Ihaka](https://en.wikipedia.org/wiki/Ross_Ihaka) (R&R) at the University of Auckland, NZ as a tool for **teaching statistics**

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.size-20[![](data/slide_intro/Ihaka_and_Gentleman.jpg)]

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* 1994 &mdash; initial version
* 2000 &mdash; stable version

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* 2011 &mdash; [RStudio](https://en.wikipedia.org/wiki/RStudio), first release by J.J. Allaire 
.size-20[![](data/slide_intro/jjallaire_siliconangle_com.jpg)]

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* ca. 2017 &mdash; Tidyverse by [Hadley Wickham](https://en.wikipedia.org/wiki/Hadley_Wickham)
.size-20[![](data/slide_intro/hadley-wickham.jpg)]

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## Ideas behind R

* open-source solution &mdash; fast development

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* based on the [S language](https://en.wikipedia.org/wiki/S_%28programming_language%29) created at the Bell Labs by  
[John Mc Kinley Chambers](https://bit.ly/2RhDqUx) to

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> *turn ideas into software, quickly and faithfully*

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* [lexical scope](https://en.wikipedia.org/wiki/Scope_%28computer_science%29%23Lexical_scoping) inspired by [Lisp](https://en.wikipedia.org/wiki/Lisp) syntax

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* since 1997 developed by the R Development Core Team (ca. 20 experts, with Chambers onboard; 6 are active)

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* overviewed by [The R Foundation for Statistical Computing](https://www.r-project.org/foundation/)

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### Packages
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<img src="data/slide_intro/packages.jpg" width="250pt" style="display: block; margin: auto;" />
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* developed by the community

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* cover several very diverse areas of science/life

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* uniformely structured and documented

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* organised in repositiries:
    + [CRAN](https://cran.r-project.org) - The Comprehensive R Archive Network
    + [R-Forge](https://r-forge.r-project.org)
    + [Bioconductor](http://www.bioconductor.org)
    + [GitHub](https://github.com)

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## Pros and cons

steep learning curve

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 uniform, clear and clean system of documentation and help

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 difficulties due to a limited object-oriented programming capabilities, 
e.g. an agent-based simulation is a challenge

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 good interconnectivity with compiled languages like Java or C

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 cannot order a pizza for you (?)

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 a very powerful ecosystem of packages

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 free and open source, GNU GPL and GNU GPL 2.0

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 easy to generate high quality graphics

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## Ecosystem of R packages
 
 
 
<img src="slide_r_intro_files/figure-html/num_pkgs-1.svg" style="display: block; margin: auto;" />

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# Now you know a bit more about R!

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R version 4.0.3 (2020-10-10) Platform: x86_64-pc-linux-gnu (64-bit)OS: Ubuntu 18.04.5 LTS

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Built on : 06-Nov-2020 at 22:20:57

2020 • [SciLifeLab](https://www.scilifelab.se/) • [NBIS](https://nbis.se/)
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