r4ss is a package of tools related to the Stock Synthesis fisheries stock assessment modeling framework. This first Vignette covers installing the package and some basic uses.

Installing the r4ss R package

Basic installation

The package can be run on OS X, Windows, or Linux. The CRAN version of r4ss is not regularly updated and therefore likely out of date. Instead it is recommended to install the from GitHub with the following code which depends on the devtools package (which in turn depends on a variety of additional packages):

# install.packages("devtools") # if needed

# If you would like the vignettes (so far there's just this one):
devtools::install_github("r4ss/r4ss", build_vignettes = TRUE)

Loading the package and reading help pages

You can then load the package with:


You can read the help files and access this vignette (and any others created in the future) with:

help(package = "r4ss")

Although we've made an effort to maintain backward compatibility to at least 3.24S (from July, 2013), there may be cases where it's necessary to install either an older version of r4ss, such as when a recent change to the package causes something to fail, or a development version of the package that isn't in the master repository yet, such as to test upcoming features.

Alternative versions

To install alternative versions of r4ss, provide a reference to the install_github, such as

devtools::install_github("r4ss/r4ss", ref="1.26.0") # install r4ss version 1.26.0

where the ref input can be a release number, the name of a branch on GitHub, or a git SHA-1 code, which are listed with all code changes that are committed to the git repository: https://github.com/r4ss/r4ss/commits/ and can also be found (starting with r4ss version 1.29.0, on the “Home” tab of the HTML view of the plots created by SS_plots as described below).

Reading model output and making default plots

The most important two functions are SS_output and SS_plots, the first for reading the output from a Stock Synthesis model and the second for making a large set of plots illustrating that output.

# it's useful to create a variable for the directory with the model output
mydir <- file.path(path.package("r4ss"), "extdata/simple_3.30")

# read the model output and print some diagnostic messages 
replist <- SS_output(dir = mydir, verbose=TRUE, printstats=TRUE)

# plots the results

By default SS_plots creates a large collection of PNG files in a new plots sub-directory in the same location as your model files, along with a set of HTML files (example excerpt below) to facilitate exploration of the figures in your browser. The home tab should open in your browser automatically after SS_plots completes making all the files.

Illustration of the HTML view of the plots created by the `SS_plots` function.{ width=75% }