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software.qmd
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---
eval: false
code-fold: false
engine: knitr
author: "R Félix"
---
# Software
In this chapter we will guide you through the installation of R, RStudio and the packages you will need for this course.
**R** and **RStudio**[^software-1] are separate downloads.
[^software-1]: We will use RStudio, although if you already use other studio such as VScode, that's also fine.
## R
**R** or **R stats** (how it is also known) is a programming language and free software environment for statistical computing and graphics supported by the R Foundation for Statistical Computing.
The download links live at [The Comprehensive R Archive Network](https://cran.r-project.org/) (aka CRAN).
The most recent version is `4.4.1`, but you can use `>= 4.1.x` if you already have it installed.
:::: {.panel-tabset .nav-pills}
### Windows
[Download R-4.4.2 for Windows](https://cran.r-project.org/bin/windows/base/R-4.4.2-win.exe) and run the executable file.
::: {.callout-important icon="false"}
You will also need to install [Rtools](https://cran.r-project.org/bin/windows/Rtools/rtools44/rtools.html), which is a collection of tools necessary to build R packages in Windows.\
Select the second link if you use an ARM processor (more recent), and the first link otherwise.
:::
### Mac
[Download R-4.4.2 for MacOX](https://cran.r-project.org/bin/macosx/).
You will have to choose between the arm64 or the x86-64 version.
Download the `.pkg` file and install it as usual.
### Ubuntu
> These are instructions for Ubuntu.
> If you use other linux distribution, please follow the instructions on [The Comprehensive R Archive Network - CRAN](https://cran.r-project.org/bin/linux/).
You can look for R in the Ubuntu **Software Center** or install it via the terminal:
```{bash}
# sudo apt update && sudo apt upgrade -y
sudo apt install r-base
```
**Or**, if you prefer, you can install the latest version of R from CRAN:
```{bash}
# update indices
sudo apt update -qq
# install two helper packages we need
sudo apt install --no-install-recommends software-properties-common dirmngr
# add the signing key (by Michael Rutter) for these repos
wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
# add the R 4.0 repo from CRAN -- adjust 'focal' to 'groovy' or 'bionic' as needed
sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
```
Then run:
```{bash}
sudo apt install r-base r-base-core r-recommended r-base-dev
```
\[Optional\] To keep up-to-date r version and packages, you can follow the instructions at [r2u](https://eddelbuettel.github.io/r2u/)
::::
After this installation, you don't need to open R base.
Please proceed to install RStudio.
## RStudio
RStudio Desktop is an integrated development environment (IDE) for R.
It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.
RStudio is available for free download from [Posit RStudio](https://posit.co/download/rstudio-desktop/).
::: {.panel-tabset .nav-pills}
### Windows 10/11
[Download RStudio 2024.09](https://download1.rstudio.org/electron/windows/RStudio-2024.09.1-394.exe) and run the executable file.
### MacOS
[Download RStudio 2024.09](https://download1.rstudio.org/electron/macos/RStudio-2024.09.1-394.dmg) and install it as usual.
### Ubuntu
> These are instructions for Ubuntu **24** / Debian 12.
> If you use other linux distribution, please follow the instructions on [Posit RStudio](https://posit.co/download/rstudio-desktop/).
Install it via the terminal:
```{bash}
sudo apt install libssl-dev libclang-dev
wget https://download1.rstudio.org/electron/jammy/amd64/rstudio-2024.09.1-394-amd64.deb
sudo dpkg -i rstudio*
rm -v rstudio*
```
```{bash}
#| echo: false
sudo apt install libcurl4-openssl-dev libgit2-dev libfontconfig1-dev libxml2-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev
sudo apt install libudunits2-dev libgdal-dev libgeos-dev
```
:::
## R packages
You will need to install some packages to work with the data and scripts in this course.
You can install them in RStudio by searching for them in the **Packages** tab:
**or** by running the following code in the console:
```{r}
install.packages("rmarkdown")
install.packages("bookdown")
install.packages("rticles")
install.packages("tidyverse")
install.packages("readxl")
install.packages(c("remotes", "devtools", "usethis"))
```
## rticles
You can install and use **rticles** from CRAN as follows:
```{r}
install.packages("rticles")
```
See [chapter 3](startup.qmd) to setup an rticle template.
## tinytex
To be able to **export** your Rmakdown document to a pdf file, you will need a LaTeX processor.
`tinytex` is a low weight R package with the most used features of LaTeX that you can use with R.
```{r}
# you need to run both lines
install.packages("tinytex")
tinytex::install_tinytex()
```
To use some LaTeX packages, you also need to install some `tlmgr` packages.
Here is a list of the most common ones.
```{r}
tinytex::tlmgr_install(c("algorithmicx", "algorithms", "amscls", "amsfonts", "amsmath", "apacite", "appendix", "atbegshi", "atveryend", "auxhook", "babel", "bibtex", "bigintcalc", "bitset", "booktabs", "cm", "colortbl", "ctablestack", "dehyph", "dvipdfmx", "dvips", "ec", "epstopdf-pkg", "etex", "etexcmds", "etoolbox", "euenc", "everyshi", "fancyvrb", "filehook", "firstaid", "float", "fontspec", "framed", "geometry", "gettitlestring", "glyphlist", "graphics", "graphics-cfg", "graphics-def", "helvetic", "hycolor", "hyperref", "hyph-utf8", "hyphen-base", "iftex", "inconsolata", "infwarerr", "intcalc", "jknapltx", "knuth-lib", "kpathsea", "kvdefinekeys", "kvoptions", "kvsetkeys", "l3backend", "l3kernel", "l3packages", "latex", "latex-amsmath-dev", "latex-bin", "latex-fonts", "latex-tools-dev", "latexconfig", "latexmk", "letltxmacro", "listings", "lm", "lm-math", "ltxcmds", "lua-alt-getopt", "lua-uni-algos", "luahbtex", "lualatex-math", "lualibs", "luaotfload", "luatex", "luatexbase", "makecell", "mdwtools", "metafont", "mfware", "modes", "multirow", "natbib", "ncctools", "pdfescape", "pdflscape", "pdftex", "pdftexcmds", "plain", "psnfss", "refcount", "rerunfilecheck", "rsfs", "scheme-infraonly", "selnolig", "setspace", "siunitx", "stringenc", "sttools", "symbol", "tex", "tex-ini-files", "texlive-scripts", "texlive.infra", "threeparttable", "threeparttablex", "times", "tipa", "tools", "trimspaces", "ulem", "unicode-data", "unicode-math", "uniquecounter", "url", "varwidth", "vruler", "wrapfig", "xcolor", "xetex", "xetexconfig", "xkeyval", "xunicode", "zapfding"))
tinytex::tlmgr_update() # updates all latex pkgs
```
::: {.callout-note appearance="simple"}
#### Note
This may take a bit longer for the first time.
:::
## Word count addin {#wordcount}
This [R package](https://github.com/benmarwick/wordcountaddin) is an [RStudio addin](https://rstudio.github.io/rstudioaddins/) to count words and characters in text in an [R markdown](http://rmarkdown.rstudio.com/) document.
It also has a function to compute readability statistics so you can get an indication of how easy or difficult your document is to read.
Install with:
```{r}
devtools::install_github("benmarwick/wordcountaddin",
type = "source", dependencies = TRUE)
```
Close and reopen RStudio so the WordCountAddin should be available under Addins.
{width="310"}
## Zotero
Zotero is a free reference and bibliography manager, just like *Mendley* and others.
You can use Zotero to organize your papers, and to create automatic in-line citations and references.
To **download**, please visit <https://www.zotero.org/download/> and select your operating system.
You may need to register for a free account at <https://www.zotero.org/user/register>
### Shared libraries
An interest thing in Zotero is that you can share a bibliography collection with others, for instance your research group or lab, and even those collections can be divided in sub-folders.
And in that case, you can benefit from the readings of your colleagues.
See the [U-Shift Zotero collection](https://www.zotero.org/groups/4625639/u-shift/library), for instance.:
[](https://www.zotero.org/groups/4625639/u-shift/library)
::: {.callout-note appearance="simple"}
Keep in mind that automatic fields of references **may need some adjustments**.
Always double check if the fields seem to be correct.
:::