r4ss-package |
R tools for Stock Synthesis |
bubble3 |
Create a bubble plot. |
DoProjectPlots |
Make plots from Rebuilder program |
getADMBHessian |
Read admodel.hes file |
make_multifig |
Create multi-figure plots. |
make_multifig_sexratio |
Create multi-figure sex ratio plots. |
mcmc.nuisance |
Summarize nuisance MCMC output |
mcmc.out |
Summarize, analyze and plot key MCMC output. |
mountains |
Make shaded polygons with a mountain-like appearance |
NegLogInt_Fn |
Perform SS implementation of Laplace Approximation |
PinerPlot |
Make plot of likelihood contributions by fleet |
plotCI |
Plot points with confidence intervals. |
r4ss |
R tools for Stock Synthesis |
r4ss_logo |
Make a simple logo for r4ss organization on GitHub |
read.admbFit |
Read ADMB .par and .cor files. |
rich.colors.short |
Make a vector of colors. |
selShapes |
A Shiny app that displays various selectivity curves given parameters that would be input into SS |
SSbiologytables |
A function to create a table of biology for assessment reporting: length, weight, % mature, fecundity, and selectivity |
SSbootstrap |
Fit models to parametric bootstraps |
SSexecutivesummary |
A function to create a executive summary tables from an SS Report.sso file |
SSgetMCMC |
Read MCMC output. |
SSgetoutput |
Get output from multiple Stock Synthesis models. |
SSmakeMmatrix |
Convert a matrix of natural mortality values into inputs for Stock Synthesis |
SSMethod.Cond.TA1.8 |
Apply Francis composition weighting method TA1.8 for conditional age-at-length fits |
SSMethod.TA1.8 |
Apply Francis composition weighting method TA1.8 |
SSmohnsrho |
Calculate Mohn's Rho values for select quantities |
SSplotAgeMatrix |
Plot matrix of either length or observed age at true age |
SSplotBiology |
Plot biology related quantities. |
SSplotCatch |
Plot catch related quantities. |
SSplotCohortCatch |
Plot cumulative catch by cohort. |
SSplotComparisons |
plot model comparisons |
SSplotComps |
Plot composition data and fits. |
SSplotData |
Timeline of presence/absence of data by type, year, and fleet. |
SSplotDiscard |
Plot fit to discard fraction. |
SSplotIndices |
Plot indices of abundance and associated quantities. |
SSplotMCMC_ExtraSelex |
Plot uncertainty around chosen selectivity ogive from MCMC. |
SSplotMnwt |
Plot mean weight data and fits. |
SSplotMovementMap |
Show movement rates on a map. |
SSplotMovementRates |
Plot movement rates from model output |
SSplotNumbers |
Plot numbers-at-age related data and fits. |
SSplotPars |
Plot distributions of priors, posteriors, and estimates. |
SSplotProfile |
Plot likelihood profile results |
SSplotRecdevs |
Plot recruitment deviations |
SSplotRecdist |
Plot of recruitment distribution among areas and seasons |
SSplotRetroRecruits |
Make squid plot of retrospectives of recruitment deviations. |
SSplotSelex |
Plot selectivity |
SSplotSexRatio |
Plot sex-ratio data and fits for two sex models |
SSplotSpawnrecruit |
Plot spawner-recruit curve. |
SSplotSPR |
Plot SPR quantities. |
SSplotSummaryF |
Plot the summary F (or harvest rate). |
SSplotTags |
Plot tagging data and fits |
SSplotTimeseries |
Plot timeseries data |
SSplotYield |
Plot yield and surplus production. |
SSsummarize |
Summarize the output from multiple Stock Synthesis models. |
SStableComparisons |
make table comparing quantities across models |
SStimeseries |
A function to create a time-series table from an SS Report.sso file |
SSunavailableSpawningOutput |
Plot unavailable spawning output |
SS_changepars |
Change parameters, bounds, or phases in the control file. |
SS_doRetro |
Run retrospective analyses |
SS_fitbiasramp |
Estimate bias adjustment for recruitment deviates |
SS_ForeCatch |
Create table of fixed forecast catches |
SS_html |
Create HTML files to view figures in browser. |
SS_makedatlist |
make a list for SS data |
SS_makeHTMLdiagnostictable |
Make html diagnostic tables |
SS_output |
A function to create a list object for the output from Stock Synthesis |
SS_parlines |
Get parameter lines from Stock Synthesis control file |
SS_plots |
plot many quantities related to output from Stock Synthesis |
SS_profile |
Run a likelihood profile in Stock Synthesis. |
SS_readctl |
read control file from SS |
SS_readctl_3.24 |
read control file from SS version 3.24 |
SS_readctl_3.30 |
read control file from SS version 3.30 |
SS_readdat |
read Stock Synthesis data file |
SS_readdat_2.00 |
read data file from SS version 2.00 |
SS_readdat_3.00 |
read data file from SS version 3.00 |
SS_readdat_3.24 |
read data file from SS version 3.24 |
SS_readdat_3.30 |
read data file from SS version 3.30 |
SS_readforecast |
read forecast file |
SS_readstarter |
read starter file |
SS_readwtatage |
Read weight-at-age data file |
SS_read_summary |
read ss_summary file |
SS_recdevs |
Insert a vector of recruitment deviations into the control file. |
SS_RunJitter |
Iteratively apply the jitter option in SS |
SS_splitdat |
Split apart bootstrap data to make input file. |
SS_tune_comps |
Calculate new tunings for length and age compositions |
SS_varadjust |
Modify variance and sample size adjustments in the control file |
SS_writectl |
Srite Stock Synthesis control file |
SS_writectl_3.24 |
write control file |
SS_writectl_3.30 |
write control file for SS version 3.30 |
SS_writedat |
write Stock Synthesis data file |
SS_writedat_3.24 |
write data file for SS version 3.24 |
SS_writedat_3.30 |
write data file for SS version 3.30 |
SS_writeforecast |
write forecast file |
SS_writestarter |
write starter file |
SS_writewtatage |
Write weight-at-age file |
stackpoly |
modified from "stackpoly" by Jim Lemon from "plotrix" package |
TSCplot |
Create a plot for the TSC report |