README.md

In rcheshire/FishGraph: Visualizations for fishery stock-assessment.

FishGraph 2.0.3

FishGraph is a set of R functions that generates diagnostics and data visualizations from stock assessment model output. These functions are designed to process model output from the Beaufort Assessment Model (BAM). Further information on the details of the BAM can be found in (Williams and Shertzer 2015)

Installation

Fish Graph is dependent on the package compResiduals and TMB for calculations of the One Step Ahead (OSA) residuals of the composition data. To install this package

TMB:::install.contrib("https://github.com/vtrijoulet/OSA_multivariate_dists/archive/main.zip")
remotes::install_github("fishfollower/compResidual/compResidual", force=TRUE)

more information can be found at: https://github.com/fishfollower/compResidual

The FishGraph package can be installed using the install_github() function from the devtools library.

# To install the devtools package
install.packages("devtools")

# Load library and install directly from the repo.
library(devtools)
devtools::install_github("mtvincen/FishGraph")

Alternatively, the package can be installed locally from the repository source files.

install.packages("C://Location of files//FishGraph_2.0.3.tar.gz, 
                 repos = NULL, type="source")

Application

Once installed the package offers a series of functions for model diagnostics and evaluations. A full list of available functions can be obtained using:

library(FishGraph)
ls(pos = "package:FishGraph")

Update notes

Recent updates to FishGraph 2.0 functions:

• Comp.plots()
  • a new option was added to create boxplots of residuals by length/age and year, the default is b.plot = FALSE
• Comp.plots.yearly()
  • background shading for years where effective sample size negative (turned off)
• StockRec.plots()
  • option added for no spawner-recruit relationship, rec.model=“mean”
• Index.plots()
  • diagnostic plots now default to subset of previous diagnostics, default is resid.tests=“runs”, “multiple” gives all diagnostics

FishGraph 2.0.3 includes several updated functions. Additionally, version 2.0.3 includes four new functions: Cohort.plots, Phase.plots, Parm.plots, and Bound.vec.plots. All functions can be tested using the included data set data(gag) which is distributed with the package.

A comprehensive description of all included functions and examples of their graphical output is available in NOAA Technical Memorandum NMFS-SEFSC-684

Notice of nonendorsement

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.

rcheshire/FishGraph documentation built on Feb. 23, 2024, 11:27 a.m.