This repository depends mainly on the R package ebswp was developed
for doing stock assessments of eastern Bering Sea walleye pollock for
the AFSC. The stock assessment model was coded using the Autodif Model
Builder (ADMB) software. The ebswp package is used to run the model,
summarize the results, and plot the results. The package is designed to
be user-friendly and to provide a consistent interface for running the
model and summarizing the results.
git clone https://github.com/afsc-assessments/ebswpPresently, the assessment has both the 2023 version (ebswp.qmd) which executes R/pm23.R and recreates the 2023 assessment. The initial “new” layout for the 2024 version is set up as a quarto book via the _quarto.yml file. We need to ensure that variables declared in R in chunks is available throughout each of the child documents (this is why I went with a single file in 2023).
There are several options for installing the ebswp R package.
The ebswp package can be installed from within R using:
devtools::install_github(repo = "afsc-assessments/ebswp", dependencies = TRUE,
build_vignettes = TRUE, auth_token = "your_PAT")The GitHub repository can be cloned to your computer and the package installed from the command line. From Linux this would involve:
git clone https://github.com/afsc-assessments/ebswp
R CMD INSTALL ebswpThis time from within R using:
devtools::install("ebswp")Help for all ebswp functions and data sets can be found on the R help
pages associated with each function and data set. Help for a specific
function can be viewed using ?function_name, for example:
?run_model
?tab_fit
?plot_selAlternatively, to see a list of all available functions and data sets use:
help(package = "ebswp")The package vignettes are a great place to see what ebswp can do. You
can view the package vignettes from within R using:
browseVignettes(package = "ebswp")
vignette(topic = "ebswp", package = "ebswp")All of the vignettes and the help pages for each function are bundled together and published on the website https://afsc-assessments.github.io/ebswp/.
Developers will want to do things slightly differently. See the
Model development vignette.
NOAA: National Oceanic and Atmospheric Administration
NMFS: National Marine Fisheries Service
AFSC: Alaska Fisheries Science Center
REFM: Resource and Ecology and Fisheries Management
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