A function to create a list object for the output from Stock Synthesis
Get output from multiple Stock Synthesis models.
Make a map of movement for a 5-area Indian Ocean model
Split apart bootstrap data to make input file.
Insert a vector of recruitment deviations into the control
file.
Plot selectivity
write control file
Plot catch related quantities.
read forecast file
read starter file
R tools for Stock Synthesis
Plot timeseries data
Plot uncertainty around chosen selectivity ogive from MCMC.
Plot fit to discard fraction.
Summarize the output from multiple Stock Synthesis models.
Plot points with confidence intervals.
Plot biology related quantities.
Old output reader
make a list for SS data
Make files and set up folders for simulations
Summarize nuisance MCMC output
write forecast file
Plot yield and surplus production.
read control file
Estimate bias adjustment for recruitment deviates
Plot mean weight data and fits.
read data file
Read MCMC output.
Create multi-figure plots.
Make shaded polygons with a mountain-like appearance
Summarize, analyze and plot key MCMC output.
old plot funciton
Plot SPR quantities.
Plot tagging data and fits
Change parameters in the control file.
Make a vector of colors.
function "stackpoly" by Jim Lemon from "plotrix" package
Create a bubble plot.
Add a model to the list of models to compare
Updates r4ss files to newest versions on web.
A function for converting Stock Synthesis output to the format
used by FishGraph
Plot distributions of priors, posteriors, and estimates.
Make plots from Rebuilder program
Timeline of presence/absence of data by type, year, and fleet.
Plot composition data and fits.
write starter file
Show movement rates on a map.
Run a likelihood profile in Stock Synthesis.
Get parameter lines from Stock Synthesis control file
A function to visual parameterization of double normal and
double logistic selectivity in Stock Synthesis
plot model comparisons
Run a collection of simulations for Stock Synthesis.
Plot numbers-at-age related data and fits.
write data file
plot many quantities related to output from Stock Synthesis
Plot recruitment deviations
Plot indices of abundance and associated quantities.
explore movement parameterizations
Plot of recruitment distribution among areas and seasons
a function for drawing selecitivity curves
Show movement rates on a map.
Plot spawner-recruit curve.
make table comparing quantities across models