A function to create a list object for the output from Stock Synthesis
Plot mean weight data and fits.
Run retrospective analyses
Get parameter lines from Stock Synthesis control file
Make plot of likelihood contributions by fleet
Make plots from Rebuilder program
Plot cumulative catch by cohort.
write data file
Run a likelihood profile in Stock Synthesis.
visualize parameterization of cubic spline selectivity in SS
Change parameters in the control file.
Plot SPR quantities.
write forecast file
Read ADMB .par and .cor files.
Summarize, analyze and plot key MCMC output.
A function for converting Stock Synthesis output to the format used by
FishGraph
make a list for SS data
Iteratively apply the jitter option in SS
read starter file
Plot fit to discard fraction.
plot many quantities related to output from Stock Synthesis
Plot indices of abundance and associated quantities.
Plot numbers-at-age related data and fits.
Explore movement parameterizations in a GUI
Plot composition data and fits.
Plot recruitment deviations
Show movement rates on a map.
Timeline of presence/absence of data by type, year, and fleet.
plot model comparisons
Split apart bootstrap data to make input file.
A function to visual parameterization of double normal and double logistic
selectivity in Stock Synthesis
Create multi-figure plots.
Get output from multiple Stock Synthesis models.
a function for drawing selecitivity curves
Plot the summary F (or harvest rate).
Add a model to the list of models to compare
Read admodel.hes file
write starter file
Plot uncertainty around chosen selectivity ogive from MCMC.
Updates r4ss files to newest versions on web.
Make a map of movement for a 5-area Indian Ocean model
R tools for Stock Synthesis
Plot yield and surplus production.
Make a simple logo for r4ss organization on GitHub
Plot likelihood profile results
Estimate bias adjustment for recruitment deviates
Plot spawner-recruit curve.
Insert a vector of recruitment deviations into the control file.
Plot selectivity
Plot of recruitment distribution among areas and seasons
function "stackpoly" by Jim Lemon from "plotrix" package
Plot timeseries data
Plot points with confidence intervals.
Fit models to parametric bootstraps
Plot biology related quantities.
write control file
Make squid plot of retrospectives of recruitment deviations.
Read MCMC output.
read control file
make table comparing quantities across models
Summarize nuisance MCMC output
Plot movement rates from model output
Write length.fit file to be used by the MFCL length-comp viewer.
Convert a matrix of natural mortality values into
inputs for Stock Synthesis
Plot catch related quantities.
Make shaded polygons with a mountain-like appearance
Plot distributions of priors, posteriors, and estimates.
Perform SS implementation of Laplace Approximation
Create HTML files to view figures in browser.
read data file
read forecast file
Plot tagging data and fits
Summarize the output from multiple Stock Synthesis models.
Create a bubble plot.
Make a vector of colors.
Create a plot for the TSC report