rr5r.qmd

---
title: "R, RStudio and r5r"
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, for the macro network models.

**R** and **RStudio**[^1] are separate downloads.

[^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 `4.5.1`, but you can use `>= 4.1.x` if you already have it installed.

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### Windows

[Download R-4.5.1 for Windows](https://cran.r-project.org/bin/windows/base/R-4.5.1-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/rtools45/rtools.html), which is a collection of tools necessary to build R packages in Windows.
:::

### Mac

[Download R-4.5.1 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/).

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### Windows 10/11

[Download RStudio 2025.09](https://download1.rstudio.org/electron/windows/RStudio-2025.09.0-387.exe) and run the executable file.

### MacOS

[Download RStudio 2025.09](https://download1.rstudio.org/electron/macos/RStudio-2025.09.0-387.dmg) and install it as usual.

### Ubuntu

> These are instructions for Ubuntu **24**. 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-2025.09.0-387-amd64.deb
sudo dpkg -i rstudio*
rm -v rstudio*
```
:::

## 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){width="393"}

**or** by running the following code in the console:

```{r}
install.packages("tidyverse")

install.packages("sf")
install.packages("mapview")
install.packages("osmextract")
install.packages("elevatr")
install.packages("stplanr")
install.packages("h3jsr")
install.packages("od")

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

## r5r

The simplest way to install `r5r` is by running the code below on RStudio Console. This might take a few minutes if this is the first time you install these packages.

```{r}
pkgs = c("r5r", "accessibility", "rJavaEnv", "interp", "quantreg")

install.packages(pkgs)

# dev version with latest features - optional
utils::remove.packages('r5r')
devtools::install_github("ipeaGIT/r5r", subdir = "r-package")
```

### 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)

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

**Alternatively**, you can manually download and install JDK 21.

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### 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
```
:::

<!-- Check if `r5r` is successfully installed and running with no errors: -->

<!-- ```{r} -->

<!-- r5r::r5r_sitrep() -->

<!-- ``` -->