README.md

In wStockhausen/rTCSAM02: A set of tools to set up input for, and interact with output from, TCSAM02 model runs

rTCSAM02: A R package for the TCSAM02 stock assessment model

William T. Stockhausen

rTCSAM02

R package with functions for making and extracting results from TCSAM02 (formerly TCSAM2015) model runs for the Bering Sea and Aleutian Islands Tanner crab stock assessment.

TCSAM02 is a modeling framework based on the AD Model Builder c++ automatic differentiation library for stage/size-specific fishery stock assessment models for the Tanner crab (Chionoecetes bairdi) stock in the eastern Bering Sea. This package provides a library of functions to run models and extract results. The R package rCompTCMs provides a related library of functions to compare results (convergence information, model fits to data, predicted and projected quantities, management quantities) from multiple models using standardized plots, tables, and reports.

Installation

The following software is required to install the package:

• R version 4.0.0 or newer
• the following R packages
• cowplot
• dplyr
• ggplot2
• graphics
• grDevices
• grid
• magrittr
• reshape2
• sqldf
• stats
• stringr
• tcltk
• tibble
• tidyr
• utils
• wtsPlots
• wtsUtilities

All packages except the last two are available on CRAN. The last two are available on GitHub.

Configuring as an R project using RStudio

To create a local version of this R project using RStudio:

1. copy the url of the repository from GitHub
2. start RStudio and:
   1. go to “New Project” b select “Version Control/Git”
   2. paste in the repository url, which will also fill in the default project name
   3. click “Create Project”

You can install the current version of rTCSAM02 from GitHub with:

# install.packages("devtools")
devtools::install_github("wStockhausen/rTCSAM02")

Using the package

The principal functions for running a TCSAM02 model are runTCSAM02 and runJitter. The former runs a single model (but can be used in a loop to run multiple models) and the latter makes multiple runs of a single model with randomized (“jittered”) initial parameter values in order to determine convergence properties and provide support for the maximum likelihood solution.

getResLst is used to convert the output text (input/output parameter csv, report, and/or sdrep) files from a TCSAM02 model run to a more compact R object (of class “tcsam02.resLst”), which provides the principal object for functions that extract a dataframe in standardized format of a subset of the model results (the “getMDFR” functions). This function encapsulates the getPrs(), getRep(), and getStd() functions that read the input/output parameter csv, report, and sdreport files (respectively) created during a TCSAM02 model run. The function getResLsts allows the user to convert multiple model runs to tcsam02.resLst objects. Other functions that extract model output include readCorFile() (the .cor file) and readParFile() (the .par file).

NOAA Disclaimer

This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce 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 Department of Commerce. The Department of Commerce 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 DOC or the United States Government.

Software code created by U.S. Government employees is not subject to copyright in the United States (17 U.S.C. §105). The United States/Department of Commerce reserve all rights to seek and obtain copyright protection in countries other than the United States for Software authored in its entirety by the Department of Commerce. To this end, the Department of Commerce hereby grants to Recipient a royalty-free, nonexclusive license to use, copy, and create derivative works of the Software outside of the United States.

U.S. Department of Commerce \| National Oceanographic and Atmospheric Administration \| NOAA Fisheries

wStockhausen/rTCSAM02 documentation built on April 16, 2024, 6:25 a.m.