R Code for Stock Synthesis
modified from "stackpoly" by Jim Lemon from "plotrix" package
Use 3.30 q options to create the 3.24 q setup
Use 3.30 variance adjustments to create the 3.24 formatting
Create a plot for the TSC report
Function to write formatted table similar to table written by gdata::w...
Add legend to plots
Create a bubble plot.
Check input argument inputlist
Check input argument model
Copy a the Stock Synthesis input files from one directory to another
Make plots from Rebuilder program
Rename Stock Synthesis files by adding integer value
Collect comments lines starting from "#C" in datfile, ctlfile, starter...
Get the name of the data .ss_new file in a directory
Get the highest phase used in the control file
Gather information for the NOAA Species Information System (SIS)
Get the tuning table
Get time varying parameter labels
Read admodel.hes file
Utility function to test if x is "numerically" integer wrt machine eps...
Create multi-figure plots.
Create multi-figure sex ratio plots.
Summarize nuisance MCMC output
Summarize, analyze and plot key MCMC output.
Make shaded polygons with a mountain-like appearance
Perform SS implementation of Laplace Approximation
Make plot of likelihood contributions by fleet
Plot points with confidence intervals.
Populate multiple Stock Synthesis folders with input files
r4ss: R Code for Stock Synthesis
Make a simple logo for r4ss organization on GitHub
Read ADMB .par and .cor files.
Make a vector of colors.
Run multiple Stock Synthesis models
Open png device and return info on the file being created
Launch a shiny app that displays various selectivity curves
Change parameters, bounds, or phases in the control file.
Extract total catch, spawning output, and fraction unfished from forec...
Run retrospective analyses
Estimate bias adjustment for recruitment deviates
Create table of fixed forecast catches
Create HTML files to view figures in browser.
Make html diagnostic tables
A function to create a list object for the output from Stock Synthesis
Get parameter lines from Stock Synthesis control file
plot many quantities related to output from Stock Synthesis
Run a likelihood profile in Stock Synthesis.
Read all Stock Synthesis input files for a model
read ss_summary file
Read control file from SS
read control file from SS version 3.24
read control file from SS version 3.30
read Stock Synthesis data file
read data file from SS version 2.00
read data file from SS version 3.00
read data file from SS version 3.24
read data file from SS version 3.30
read forecast file
read ss.par file from SS version 3.24
read ss.par file from SS version 3.30
read starter file
Read weight-at-age data file
Insert a vector of recruitment deviations into the control file.
Iteratively apply the jitter option in SS
Create relative sensitivity plots as described in Cope and Gertseva (2...
Split apart bootstrap data to make input file.
Calculate new tunings for length and age compositions and (re)run mode...
Modify variance and sample size adjustments in the control file
Write all Stock Synthesis input files for a model
Write Stock Synthesis control file
write control file
write control file for SS version 3.30
write Stock Synthesis data file
write data file for SS version 3.24
write data file for SS version 3.30
write forecast file
write ss.par file from SS version 3.24
write ss.par file from SS version 3.30
write starter file
Write weight-at-age file
A function to create a table of biology for assessment reporting: leng...
Fit models to parametric bootstraps
Convert Time-Steps
A function to create a executive summary tables from an SS Report.sso ...
Read MCMC output.
Get output from multiple Stock Synthesis models.
Convert a matrix of natural mortality values into inputs for Stock Syn...
Apply Francis composition weighting method TA1.8 for conditional age-a...
Apply Francis composition weighting method TA1.8
Calculate Mohn's Rho values for select quantities
Allow Multi-Plots Set the par() to options suitable for ss3diags multi...
Plot matrix of either length or observed age at true age
Plot biology related quantities.
Plot catch related quantities.
Plot cumulative catch by cohort.
plot model comparisons
Plot composition data and fits.
Timeline of presence/absence of data by type, year, and fleet.
Plot fit to discard fraction.
Plot Dynamic B0
Plot indices of abundance and associated quantities.
Plot uncertainty around chosen selectivity ogive from MCMC.
Plot mean weight data and fits.
Show movement rates on a map.
Plot movement rates from model output
Plot numbers-at-age related data and fits.
Plot distributions of priors, posteriors, and estimates.
Plot likelihood profile results
Plot recruitment deviations
Plot of recruitment distribution among areas and seasons
Make squid plot of retrospectives of recruitment deviations.
Plot selectivity
Plot sex-ratio data and fits for two sex models
Plot spawner-recruit curve.
Plot Spawning Potential Ratio (SPR) quantities.
Plot the summary F (or harvest rate).
Plot tagging data and fits
Plot timeseries data
Plot yield and surplus production.
Summarize the output from multiple Stock Synthesis models.
make table comparing quantities across models
Plot unavailable spawning output
A collection of R functions for use with Stock Synthesis, a fisheries stock assessment modeling platform written in ADMB by Dr. Richard D. Methot at the NOAA Northwest Fisheries Science Center. The functions include tools for summarizing and plotting results, manipulating files, visualizing model parameterizations, and various other common stock assessment tasks. This version of '{r4ss}' is compatible with Stock Synthesis versions 3.24 through 3.30 (specifically version 3.30.19.01, from April 2022).