Author: Hannah Houts, @hehouts, UC Davis.
Use this to get familiar with the RStudio interface and the unix shell.
Start by opening RStudio.
Use your datalab-XX account to log into farm.
Run:
srun -p high2 --time=3:00:00 --nodes=1 --cpus-per-task 1 --mem 5GB --pty /bin/bash
The first time you run this, create a conda environment with the necessary software:
module load mamba
mamba create -y -n cafe r-rmarkdown r-knitr
mamba activate cafe
this will take ~5 minutes.
Every time thereafter, you will need to run the following after srun:
module load mamba
mamba activate cafe
module load rstudio-server
rstudio-launch
and follow the process to connect to RStudio Server from your laptop.
When you first open RStudio, you'll notice it's divided into several panels, each serving a distinct purpose.
-
Console Panel: This is where R code is executed. You can type commands directly here or run code from a script. It's like a direct line of communication with R.
-
Source Panel: Here, you write and edit files (R scripts, R markdowns, shell scripts). This panel supports features like syntax highlighting and tab-completion to make writing R code easier.
-
Environment/History Panel: The Environment tab displays variables created during your R session, along with their values and types. The History tab keeps a log of all commands you've run, allowing you to revisit and reuse them.
-
Files/Plots/Packages/Help/Viewer Panel: This multifunctional panel has tabs for:
- Files: Browse, view, and manage files in your working directory.
- Plots: View graphs and charts you generate with your code.
- Packages: Install, load, and manage R packages.
- Help: Access R documentation and help files.
- Viewer: Display web content or visualizations.
Go to the Console panel on the left, and then click on the Terminal. At the terminal prompt, type:
cd ~/
git clone https://github.com/ctb/hannahs-unix-cafe
In the Files panel, you'll see a new folder, hannahs-unix-cafe. Go to that
folder and open tutorial.Rmd in RStudio by clicking on it.