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