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.
plot model comparisons
write forecast file
Estimate bias adjustment for recruitment deviates
make a list for SS data
write starter file
Get parameter lines from Stock Synthesis control file
Plot distributions of priors, posteriors, and estimates.
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.
Plot spawner-recruit curve.
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.
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
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.
Plot timeseries data
a function for drawing selecitivity curves
Plot points with confidence intervals.
Updates r4ss files to newest versions on web.
write control file
make table comparing quantities across models
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
read data file
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.