Change parameters in the control file.
Get parameter lines from Stock Synthesis control file
read forecast file
Estimate bias adjustment for recruitment deviates
make a list for SS data
Get output from multiple Stock Synthesis models.
Updates r4ss files to newest versions on web.
read control file
Insert a vector of recruitment deviations into the control
file.
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.
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
Plot spawner-recruit curve.
Read MCMC output.
Plot points with confidence intervals.
a function for drawing selecitivity curves
Show movement rates on a map.
Make files and set up folders for simulations
Make a vector of colors.
read data file
write data file
Run a collection of simulations for Stock Synthesis.
Plot timeseries data
Plot SPR quantities.
Summarize nuisance MCMC output
Plot biology related quantities.
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.
write forecast file
R tools for Stock Synthesis
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
make table comparing quantities across models