[3]{.chapter-number}  [Software]{.chapter-title}

3 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 RStudio¹ are separate downloads.

3.1 R

You will need R installed on your computer. 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 (aka CRAN). The most recent version is 4.4.1, but you can use >= 4.1.x if you already have it installed.

Download R-4.4.1 for Windows and run the executable file.

Important

You will also need to install Rtools, which is a collection of tools necessary to build R packages in Windows.

Download R-4.4.1 for MacOX. You will have to choose between the arm64 or the x86-64 version.

Download the .pkg file and install it as usual.

These are instructions for Ubuntu. If you use other linux distribution, please follow the instructions on The Comprehensive R Archive Network - CRAN.

You can look for R in the Ubuntu Software Center or install it via the terminal:

# 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:

# 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:

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

After this installation, you don’t need to open R base. Please proceed to install RStudio.

3.2 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.

Download RStudio 2024.04 and run the executable file.

Download RStudio 2024.04 and install it as usual.

These are instructions for Ubuntu 22 / Debian 12. If you use other linux distribution, please follow the instructions on Posit RStudio.

Install it via the terminal:

sudo apt install libssl-dev libclang-dev
wget https://download1.rstudio.org/electron/jammy/amd64/rstudio-2024.04.2-764-amd64.deb
sudo dpkg -i rstudio*
rm -v rstudio*

If you already use Ubuntu 24, please check and replace the correct url from RStudio Dailies

3.3 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:

install.packages("tidyverse")
install.packages("readxl")

install.packages("sf")
install.packages("mapview")
install.packages("rmarkdown")
install.packages("centr")
install.packages("od")

install.packages(c("remotes", "devtools", "usethis")) # optional
install.packages("osmextract") # optional
install.packages("stplanr") # optional

3.4 r5r

The workshop “A crash course on urban accessibility with R” uses a few R packages that need to be installed on your machine. The simplest way to do this is running the code below. This might take a few minutes if this is the first time you install these packages.

pkgs = c("r5r", "accessibility", "rJavaEnv", "h3jsr")

install.packages(pkgs)

3.4.1 Java Development Kit

To use the {r5r} package (version v2.0 or higher), you will need to have Java Development Kit (JDK) 21 installed on your computer. There are numerous open-source JDK implementations. The easiest way to install JDK is using the new {rJavaEnv} package in R.

# check version of Java currently installed (if any) 
rJavaEnv::java_check_version_rjava()

## if this is the first time you use {rJavaEnv}, you might need to run this code
## below to consent the installation of Java.
# rJavaEnv::rje_consent(provided = TRUE)

# install Java 21
rJavaEnv::java_quick_install(
  version = 21,
  distribution = 'Corretto')

# check if Java was successfully installed
rJavaEnv::java_check_version_rjava()

Alternatively, you can manually download and install JDK 21.

Windows and MacOS
Ubuntu

Go to Java Development Kit 21, download the latest 21 build corresponding to your operating system and run the executable file.

Install it via the terminal:

sudo apt install -y openjdk-21-jdk openjdk-21-jre
java -version

We will use RStudio, although if you already use other studio such as VScode, that’s also fine.↩︎

--- eval: false code-fold: false engine: knitr --- # 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 You will need **R** installed on your computer. **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-4.4.1 for Windows](https://cran.r-project.org/bin/windows/base/R-4.4.1-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. ::: ### Mac [Download R-4.4.1 for MacOX](https://cran.r-project.org/). 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 2024.04](https://download1.rstudio.org/electron/windows/RStudio-2024.04.2-764.exe) and run the executable file. ### MacOS [Download RStudio 2024.04](https://download1.rstudio.org/electron/macos/RStudio-2024.04.2-764.dmg) and install it as usual. ### Ubuntu > These are instructions for Ubuntu **22** / 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-2024.04.2-764-amd64.deb sudo dpkg -i rstudio* rm -v rstudio* ``` If you already use Ubuntu **24**, please check and replace the correct url from [RStudio Dailies](https://dailies.rstudio.com/) ```{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: ![](images/clipboard-3443685728.png) **or** by running the following code in the console: ```{r} install.packages("tidyverse") install.packages("readxl") install.packages("sf") install.packages("mapview") install.packages("rmarkdown") install.packages("centr") install.packages("od") install.packages(c("remotes", "devtools", "usethis")) # optional install.packages("osmextract") # optional install.packages("stplanr") # optional ``` ## r5r The workshop **“A crash course on urban accessibility with R"** uses a few R packages that need to be installed on your machine. The simplest way to do this is running the code below. This might take a few minutes if this is the first time you install these packages. ```{r} pkgs = c("r5r", "accessibility", "rJavaEnv", "h3jsr") install.packages(pkgs) ``` ### Java Development Kit To use the `{r5r}` package (version v2.0 or higher), you will need to have *Java Development Kit (JDK) 21* installed on your computer. There are numerous open-source JDK implementations. The easiest way to install JDK is using the new [{rJavaEnv}](https://www.ekotov.pro/rJavaEnv/) package in R. ```{r} # check version of Java currently installed (if any) rJavaEnv::java_check_version_rjava() ## if this is the first time you use {rJavaEnv}, you might need to run this code ## below to consent the installation of Java. # rJavaEnv::rje_consent(provided = TRUE) # install Java 21 rJavaEnv::java_quick_install( version = 21, distribution = 'Corretto') # check if Java was successfully installed rJavaEnv::java_check_version_rjava() ``` **Alternatively**, you can manually download and install JDK 21. ::: {.panel-tabset .nav-pills} ### Windows and MacOS Go to [Java Development Kit 21](https://jdk.java.net/archive/), download the latest 21 build corresponding to your operating system and run the executable file. ### Ubuntu Install it via the terminal: ```{bash} sudo apt install -y openjdk-21-jdk openjdk-21-jre java -version ``` :::