Getting set up

In this guide

• Software to install
• R packages to install
• Additional software to install
• Some additional guidance

Software to install

The easiest way to set up your system is to install:

• R: cran.r-project.org/
• Rstudio: www.rstudio.com/products/rstudio/download

It is highly recommended to have a recent version of R (less than a year out of date), ideally at least R 2.4.0. And also to have a recent version of R Studio installed. This is because GitHub, for example, has made changes to how it authenticates with applications and only the newer versions of R studio are set up to deal with this.

R packages to install

Once you have installed R (and RStudio) you can begin to install some R packages. For TAF to work you need only one package: icesTAF. You install this by running the line:

install.packages("icesTAF")

Additional software to install

The stockassessment R package which is used to run SAM stock assessments in ICES is used in this wiki. The easiest way to install this package is by running the following in R:

install.packages("stockassessment", repos = c("https://fishfollower.r-universe.dev", "https://cloud.r-project.org"))

Also, the cat3advice R package is used to run the ICES Category 3 assessment example. The easiest way to install this package is by running the following in R:

# Install cat3advice in R:
install.packages("cat3advice", repos = c("https://ices-tools-prod.r-universe.dev", "https://cloud.r-project.org"))

If you wish to also use GitHub to version control your code, then you also need to install:

• Git: git-scm.com/downloads

And finally if you are using Windows, and you wish to install some special R packages from GitHub you will need to install:

• Rtools: cran.r-project.org/bin/windows/Rtools

Some additional guidance

If you have not updated your R packages in a while, it may be advisable to update them by running:

update.packages(checkBuilt = TRUE, ask = FALSE)

if asked, you can safely say no to installing from source packages which need compilation.

Help pages for setting up Git with RStudio can be found here: - using-git-and-github-with-r-rstudio

It is beneficial to have a GitHub account if you want to version control your work. If you wish to interact with ICES working group GitHub repositories and TAF repositories it is a requirement to have a GitHub account:

• To create a GitHub account see github.com
• for ICES people please connect your GitHub account with your ICES username here: taf.ices.dk/github