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r4ss (version 1.20)

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

1.20

License

GPL-3

Maintainer

Ian Taylor

Last Published

March 15th, 2013

Functions in r4ss (1.20)

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

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

Run retrospective analyses

Insert a vector of recruitment deviations into the control file.

Read MCMC output.

SSplotComparisons

plot model comparisons

write data file

SSplotMCMC_ExtraSelex

Plot uncertainty around chosen selectivity ogive from MCMC.

Split apart bootstrap data to make input file.

Fit models to parametric bootstraps

Get parameter lines from Stock Synthesis control file

Plot tagging data and fits

Plot of recruitment distribution among areas and seasons

Plot selectivity

Estimate bias adjustment for recruitment deviates

Plot cumulative catch by cohort.

Plot numbers-at-age related data and fits.

Plot composition data and fits.

write control file

Summarize nuisance MCMC output

Plot SPR quantities.

Create a plot for the TSC report

a function for drawing selecitivity curves

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

Plot likelihood profile results

explore movement parameterizations

Change parameters in the control file.

Plot biology related quantities.

SSplotRetroDevs

Make squid plot of retrospectives of recruitment deviations.

SStableComparisons

make table comparing quantities across models

Plot the summary F (or harvest rate).

plot many quantities related to output from Stock Synthesis

Plot distributions of priors, posteriors, and estimates.

Plot yield and surplus production.

Summarize, analyze and plot key MCMC output.

SS_writeforecast

write forecast file

Create HTML files to view figures in browser.

update_r4ss_files

Updates r4ss files to newest versions on web.

SSplotTimeseries

Plot timeseries data

Add a model to the list of models to compare

Compute and Plot a 2-Dimensional Histogram

Plot points with confidence intervals.

Plot indices of abundance and associated quantities.

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

read starter file

Run a likelihood profile in Stock Synthesis.

read control file

Plot mean weight data and fits.

R tools for Stock Synthesis

make a list for SS data

SSplotMovementRates

Show movement rates on a map.

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

Create multi-figure plots.

Plot recruitment deviations

SSplotMovementMap

Show movement rates on a map.

Get output from multiple Stock Synthesis models.

Summarize the output from multiple Stock Synthesis models.

SS_readforecast

read forecast file

Plot fit to discard fraction.

visualize parameterization of cubic spline selectivity in SS

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

SS_writestarter

write starter file

SS_write_length.fit

Write length.fit file to be used by the MFCL length-comp viewer.

SSplotSpawnrecruit

Plot spawner-recruit curve.

Create a bubble plot.

Make shaded polygons with a mountain-like appearance

rich.colors.short

Make a vector of colors.

Plot catch related quantities.

Make plots from Rebuilder program