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.
plot model comparisons
write data file
Plot uncertainty around chosen selectivity ogive from MCMC.
read data file
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.
Make squid plot of retrospectives of recruitment deviations.
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.
write forecast file
Create HTML files to view figures in browser.
Updates r4ss files to newest versions on web.
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
Show movement rates on a map.
Timeline of presence/absence of data by type, year, and fleet.
Create multi-figure plots.
Plot recruitment deviations
Show movement rates on a map.
Get output from multiple Stock Synthesis models.
Summarize the output from multiple Stock Synthesis models.
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
write starter file
Write length.fit file to be used by the MFCL length-comp viewer.
Plot spawner-recruit curve.
Create a bubble plot.
Make shaded polygons with a mountain-like appearance
Make a vector of colors.
Plot catch related quantities.
Make plots from Rebuilder program