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r4ss (version 1.14)

R code for Stock Synthesis

Description

Functions for reading output, plotting, exploring and manipulating input files for Richard Methot's Stock Synthesis fisheries stock assessment modeling platform.

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Version

Install

install.packages('r4ss')

Monthly Downloads

373

Version

1.14

License

MIT License

Maintainer

Ian Taylor

Last Published

February 18th, 2011

Functions in r4ss (1.14)

Change parameters in the control file.

Get parameter lines from Stock Synthesis control file

SS_readforecast

read forecast file

Estimate bias adjustment for recruitment deviates

make a list for SS data

Get output from multiple Stock Synthesis models.

update_r4ss_files

Updates r4ss files to newest versions on web.

read control file

Insert a vector of recruitment deviations into the control file.

SSplotComparisons

plot model comparisons

Make plots from Rebuilder program

function "stackpoly" by Jim Lemon from "plotrix" package

A function to create a list object for the output from Stock Synthesis

Summarize the output from multiple Stock Synthesis models.

Make a map of movement for a 5-area Indian Ocean model

Plot mean weight data and fits.

Plot of recruitment distribution among areas and seasons

explore movement parameterizations

plot many quantities related to output from Stock Synthesis

read starter file

Plot indices of abundance and associated quantities.

Run a likelihood profile in Stock Synthesis.

SSplotMovementRates

Show movement rates on a map.

Plot tagging data and fits

old plot funciton

Create multi-figure plots.

A function to visual parameterization of double normal and double logistic selectivity in Stock Synthesis

Plot composition data and fits.

Old output reader

SSplotSpawnrecruit

Plot spawner-recruit curve.

Read MCMC output.

Plot points with confidence intervals.

a function for drawing selecitivity curves

SSplotMovementMap

Show movement rates on a map.

Make files and set up folders for simulations

rich.colors.short

Make a vector of colors.

write data file

Run a collection of simulations for Stock Synthesis.

SSplotTimeseries

Plot timeseries data

Plot SPR quantities.

Summarize nuisance MCMC output

Plot biology related quantities.

SS_writestarter

write starter file

Add a model to the list of models to compare

Plot yield and surplus production.

Split apart bootstrap data to make input file.

SS_writeforecast

write forecast file

R tools for Stock Synthesis

SSplotMCMC_ExtraSelex

Plot uncertainty around chosen selectivity ogive from MCMC.

Plot distributions of priors, posteriors, and estimates.

Summarize, analyze and plot key MCMC output.

Plot selectivity

Create a bubble plot.

Make shaded polygons with a mountain-like appearance

write control file

Plot catch related quantities.

Plot numbers-at-age related data and fits.

Plot fit to discard fraction.

A function for converting Stock Synthesis output to the format used by FishGraph

Timeline of presence/absence of data by type, year, and fleet.

Plot recruitment deviations

SStableComparisons

make table comparing quantities across models