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r4ss (version 1.18)

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

611

Version

1.18

License

GPL-3

Maintainer

Ian Taylor

Last Published

August 24th, 2012

Functions in r4ss (1.18)

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

Make plots from Rebuilder program

Create HTML files to view figures in browser.

Change parameters in the control file.

SSplotComparisons

plot model comparisons

SS_writeforecast

write forecast file

Estimate bias adjustment for recruitment deviates

make a list for SS data

SS_writestarter

write starter file

Get parameter lines from Stock Synthesis control file

Plot distributions of priors, posteriors, and estimates.

SSplotMCMC_ExtraSelex

Plot uncertainty around chosen selectivity ogive from MCMC.

read control file

Plot of recruitment distribution among areas and seasons

write data file

Plot biology related quantities.

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

Plot catch related quantities.

SSplotSpawnrecruit

Plot spawner-recruit curve.

SSplotMovementRates

Show movement rates on a map.

Summarize the output from multiple Stock Synthesis models.

Read MCMC output.

Add a model to the list of models to compare

Make shaded polygons with a mountain-like appearance

Insert a vector of recruitment deviations into the control file.

Plot indices of abundance and associated quantities.

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

Plot cumulative catch by cohort.

Plot likelihood profile results

Plot selectivity

Summarize, analyze and plot key MCMC output.

Create multi-figure plots.

Plot fit to discard fraction.

rich.colors.short

Make a vector of colors.

Summarize nuisance MCMC output

Get output from multiple Stock Synthesis models.

plot many quantities related to output from Stock Synthesis

SSplotMovementMap

Show movement rates on a map.

visualize parameterization of cubic spline selectivity in SS

Plot yield and surplus production.

R tools for Stock Synthesis

Plot numbers-at-age related data and fits.

Plot composition data and fits.

SSplotTimeseries

Plot timeseries data

a function for drawing selecitivity curves

Plot points with confidence intervals.

update_r4ss_files

Updates r4ss files to newest versions on web.

write control file

SStableComparisons

make table comparing quantities across models

SS_readforecast

read forecast file

Plot tagging data and fits

Plot mean weight data and fits.

Create a plot for the TSC report

Plot SPR quantities.

explore movement parameterizations

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

Create a bubble plot.

read starter file

Compute and Plot a 2-Dimensional Histogram

Plot recruitment deviations

Split apart bootstrap data to make input file.

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

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

Run a likelihood profile in Stock Synthesis.