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afsc-assessments / spmR

Projection model for evaluating outcomes of catch control rules for Alaska groundfish
http://afsc-assessments.github.io/spmR/
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README

Jim Ianelli 2023-09-15

Standard Projection Model for Alaska Groundfish

This is the standard projection code for federally managed Alaskan groundfish species in Tier 3.

The file src/spm.tpl is the main code for running these projections. Required input files are spm.dat, tacpar.dat, and a species-specific data input file with key outputs from an assessment, such as examples/data/ai_spm.dat.

Note: spm.dat combines information from two files used in previous versions of the projection code (setup.dat and spp_catch.dat)

ADMB version 13.0 or higher is required to compile spm.tpl.

These are the steps to run the projection code:

  1. Compile src/spm.tpl using admb and copy spm.exe to a a folder with spm.dat, tacpar.dat, and a file containing assessment outputs, such as ai_spm.dat
  2. Within spm.dat specify the location of the assessment input file relative to the folder with spm.exe
  3. From the command line pointed to the folder with these inputs, type “spm”

spmR

The R package spmR was developed for doing stock projections for groundfish at the AFSC. The model was coded using the Autodif (AD) Model Builder (ADMB) software.

Cloning the repository (optional)

The R package spmR lives on a public GitHub repository. The repository can be cloned to your computer from the command line or using a user interface. From the command line using Linux the repository can be cloned using:

git clone https://github.com/afsc-assessments/spmR

Installation

There are several options for installing the spmR R package.

Option 1

The spmR package can be installed from within R using:

devtools::install_github(repo = "afsc-assessments/spmR", dependencies = TRUE, 
                         build_vignettes = TRUE, auth_token = "your_PAT")

Option 2

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/spmR
R CMD INSTALL spmR

Option 3

This time from within R using:

devtools::install("spmR")

Help

Help for all spmR 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_sel

Alternatively, to see a list of all available functions and data sets use:

help(package = "spmR")

Examples

The package vignettes are a great place to see what spmR can do. You can view the package vignettes from within R using:

browseVignettes(package = "spmR")
vignette(topic = "spmR", package = "spmR")

Website

All of the vignettes and the help pages for each function are bundled together and published on the website https://afsc-assessments.github.io/spmR/.

Developers

Developers will want to do things slightly differently. See the Model development vignette.

Acronymns

NOAA: National Oceanic and Atmospheric Administration
NMFS: National Marine Fisheries Service
AFSC: Alaska Fisheries Science Center
REFM: Resource and Ecology and Fisheries Management

Legal disclaimer

This repository is a software product and is not official communication of the National Oceanic and Atmospheric Administration (NOAA), or the United States Department of Commerce (DOC). All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the DOC or DOC bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation, or favoring by the DOC. The DOC seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by the DOC or the United States Government.