Docs for r, rstudio, and renv installation

.github/components/dictionary.txt

@@ -37,7 +37,10 @@ README
 redistribution
 renv
 reproducibility
+RStudio
+Rtools
 ScPCA
+SemVar
 socio
 Stumptown
 synched
@@ -47,4 +50,5 @@ triaged
 WIPO
 WisCon
 WSL
+Xcode
 

docs/contributing.md

@@ -107,6 +107,8 @@ To include an image in a docs file, use the following syntax to center the image
 
 Only these items should be in backticks:
 - Actual code
+- Names of packages, e.g. `renv`
+- SemVar software versions
 - References to a specific repository, e.g. `OpenScPCA-analysis`
 
 For consistency, please use the following:

docs/technical-setup/environment-setup/install-r-rstudio.md

@@ -0,0 +1,89 @@
+# Install R, RStudio, and other dependencies
+
+This page provides instructions on the tools you need to install to be able to contribute to or explore analysis modules with R.
+If you do not plan on using R as part of your OpenScPCA contribution, you do not need these tools.
+
+If you plan to use R, you will need to have the following tools installed:
+
+- R
+- The RStudio IDE
+- The `renv` and `BiocManager` R packages
+
+Please read these instructions carefully even if you already have any of these installed on your system because there are a few additional tools you need to make sure you have.
+
+## Install R
+
+The official OpenScPCA project version of R is `4.3.3`, so we recommend that you have at least this version installed.
+Please be aware that if you install a different R version and run existing modules, you may get different results.
+
+The instructions provided here are suitable for the vast majority of contributors, but please refer to [this section](#advanced-considerations) for advanced considerations about R installation.
+
+
+### Install R on macOS
+
+1. Navigate to the [macOS download page on the CRAN website](https://cran.r-project.org/bin/macosx/).
+
+2. Download the R package that matches your computer's architecture, and follow all installation instructions.
+    - If you're on an Apple silicon (M1-3) Mac, install R from the link `R-X.Y.Z-arm64.pkg`, where `X.Y.Z` is the specific R version.
+    - If you're on an Intel Mac, install R from the link `R-X.Y.Z-x86_64.pkg`, where `X.Y.Z` is the specific R version.
+
+
+Next, you need to install additional tools that will let you build R packages that you are likely to encounter in OpenScPCA.
+These tools are available from the [R for macOS website](https://mac.r-project.org/tools/) and are listed under **Mandatory Tools**.
+
+1. Install "**Xcode** developer tools from Apple" as follows:
+    - Launch a Terminal window by searching for "terminal" in spotlight
+      <figure markdown="span">
+        ![Launch the Terminal application.](../../img/terminal-spotlight.png){width="425"}
+      </figure>
+    - Enter the command `sudo xcode-select --install` into Terminal and hit enter
+    - You will then be prompted to enter your computer's password
+  When you type, no symbols will appear - this is expected!
+  Hit enter after your password, and the developer tools will proceed to install
+        - If you receive a message that begins with `xcode-select: note: Command line tools are already installed.`, then you have previously installed this on your system and are all set.
+
+1. Install the **GNU Fortran compiler**.
+Click the link on the [Tools - R for Mac OS](https://mac.r-project.org/tools/) page to download the installer package and follow all installation instructions.
+
+
+### Install R on Windows
+
+
+1. Navigate to the [Windows download page on the CRAN website](https://cran.r-project.org/bin/windows/base/), and follow instructions to download and install R.
+
+2. Next, you need to install Rtools, which provides additional tools that will let you build R packages that you are likely to encounter in OpenScPCA.
+    - Navigate to the [Rtools download page](https://cran.r-project.org/bin/windows/Rtools/)
+    - Click the Rtools version that matches the R version you just downloaded
+    - On the next page, click the link `RtoolsXY installer` (where `XY` is the specific version you clicked) to download Rtools, and follow all installation instructions
+
+
+
+
+## Install the RStudio IDE
+
+If you do not already have RStudio installed, you need to [install the free RStudio Desktop](https://posit.co/download/rstudio-desktop/).
+This website shows Step 1 as installing R itself, which you can skip and proceed straight to Step 2, Install RStudio.
+
+Click the download link and follow all instructions to complete the installation.
+
+## Install R package dependencies
+
+There are two R packages that OpenScPCA frequently uses that we recommend installing before getting started:
+
+- `renv`
+  - OpenScPCA uses [the `renv` package](https://rstudio.github.io/renv/articles/renv.html) to manage R packages in each analysis module.
+- `BiocManager`
+  - You need to use [Bioconductor packages](https://bioconductor.org/) to interact with ScPCA data in R environments.
+  [The `BiocManager` package](https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html) is used to install Bioconductor packages.
+
+
+To install these R packages, open RStudio and enter the following command into the Console:
+
+```
+install.packages(c("renv", "BiocManager"))
+```
+
+
+## Advanced considerations
+
+If you need to have multiple versions of installed on your computer, we recommend using the [`rig`](https://github.com/r-lib/rig) R Installation Manager.

docs/technical-setup/fork-the-repo.md

@@ -37,5 +37,5 @@ Make sure that these conditions are met, and then click the "Create fork" button
     </figure>
 
 
-1. That's it! 🎉
+That's it! 🎉
 In a few moments, GitHub will redirect to your newly forked repository at `https://github.com/YOUR_USERNAME/OpenScPCA-analysis`, and you're ready to proceed to the next step of [cloning your repository](./clone-the-repo.md).

mkdocs.yml

@@ -56,6 +56,7 @@ nav:
     - Environment setup:
       - technical-setup/environment-setup/index.md
       - technical-setup/environment-setup/setup-conda.md
+      - technical-setup/environment-setup/install-r-rstudio.md
   - Tools for communication:   # Slack, issues, discussions
     - communications-tools/tools-for-communication.md
   - Contributing to analyses:  # Setting up an analysis, all the git stuff