Man pages for r4ss
R Code for Stock Synthesis

add_legendAdd legend to plots
bubble3Create a bubble plot.
check_inputlistCheck input argument 'inputlist'
check_modelCheck input argument 'model'
copy_SS_inputsCopy a the Stock Synthesis input files from one directory to...
DoProjectPlotsMake plots from Rebuilder program
file_incrementRename Stock Synthesis files by adding integer value
getADMBHessianRead admodel.hes file
get_commentsCollect comments lines starting from "#C" in datfile,...
get_dat_new_nameGet the name of the data .ss_new file in a directory
get_last_phaseGet the highest phase used in the control file
get_SIS_infoGather information for the NOAA Species Information System...
get_tuning_tableGet the tuning table
get_tv_parlabsGet time varying parameter labels
is.wholenumberUtility function to test if x is "numerically" integer wrt...
make_multifigCreate multi-figure plots.
make_multifig_sexratioCreate multi-figure sex ratio plots.
mcmc.nuisanceSummarize nuisance MCMC output
mcmc.outSummarize, analyze and plot key MCMC output.
mountainsMake shaded polygons with a mountain-like appearance
NegLogInt_FnPerform SS implementation of Laplace Approximation
PinerPlotMake plot of likelihood contributions by fleet
plotCIPlot points with confidence intervals.
populate_multiple_foldersPopulate multiple Stock Synthesis folders with input files
r4ss_logoMake a simple logo for r4ss organization on GitHub
r4ss-packager4ss: R Code for Stock Synthesis
read.admbFitRead ADMB .par and .cor files.
rich.colors.shortMake a vector of colors.
run_SS_modelsRun multiple Stock Synthesis models
save_pngOpen png device and return info on the file being created
selShapesLaunch a shiny app that displays various selectivity curves
SSbiologytablesA function to create a table of biology for assessment...
SSbootstrapFit models to parametric bootstraps
SS_changeparsChange parameters, bounds, or phases in the control file.
SS_decision_table_stuffExtract total catch, spawning output, and fraction unfished...
SSdiagsTime2YearConvert Time-Steps
SS_doRetroRun retrospective analyses
SSexecutivesummaryA function to create a executive summary tables from an SS...
SS_fitbiasrampEstimate bias adjustment for recruitment deviates
SS_ForeCatchCreate table of fixed forecast catches
SSgetMCMCRead MCMC output.
SSgetoutputGet output from multiple Stock Synthesis models.
SS_htmlCreate HTML files to view figures in browser.
SS_makeHTMLdiagnostictableMake html diagnostic tables
SSmakeMmatrixConvert a matrix of natural mortality values into inputs for...
SSMethod.Cond.TA1.8Apply Francis composition weighting method TA1.8 for...
SSMethod.TA1.8Apply Francis composition weighting method TA1.8
SSmohnsrhoCalculate Mohn's Rho values for select quantities
SS_outputA function to create a list object for the output from Stock...
ssparAllow Multi-Plots Set the par() to options suitable for...
SS_parlinesGet parameter lines from Stock Synthesis control file
SSplotAgeMatrixPlot matrix of either length or observed age at true age
SSplotBiologyPlot biology related quantities.
SSplotCatchPlot catch related quantities.
SSplotCohortCatchPlot cumulative catch by cohort.
SSplotComparisonsplot model comparisons
SSplotCompsPlot composition data and fits.
SSplotDataTimeline of presence/absence of data by type, year, and...
SSplotDiscardPlot fit to discard fraction.
SSplotDynamicB0Plot Dynamic B0
SSplotIndicesPlot indices of abundance and associated quantities.
SSplotMCMC_ExtraSelexPlot uncertainty around chosen selectivity ogive from MCMC.
SSplotMnwtPlot mean weight data and fits.
SSplotMovementMapShow movement rates on a map.
SSplotMovementRatesPlot movement rates from model output
SSplotNumbersPlot numbers-at-age related data and fits.
SSplotParsPlot distributions of priors, posteriors, and estimates.
SSplotProfilePlot likelihood profile results
SSplotRecdevsPlot recruitment deviations
SSplotRecdistPlot of recruitment distribution among areas and seasons
SSplotRetroRecruitsMake squid plot of retrospectives of recruitment deviations.
SS_plotsplot many quantities related to output from Stock Synthesis
SSplotSelexPlot selectivity
SSplotSexRatioPlot sex-ratio data and fits for two sex models
SSplotSpawnrecruitPlot spawner-recruit curve.
SSplotSPRPlot Spawning Potential Ratio (SPR) quantities.
SSplotSummaryFPlot the summary F (or harvest rate).
SSplotTagsPlot tagging data and fits
SSplotTimeseriesPlot timeseries data
SSplotYieldPlot yield and surplus production.
SS_profileRun a likelihood profile in Stock Synthesis.
SS_readRead all Stock Synthesis input files for a model
SS_readctlRead control file from SS
SS_readctl_3.24read control file from SS version 3.24
SS_readctl_3.30read control file from SS version 3.30
SS_readdatread Stock Synthesis data file
SS_readdat_2.00read data file from SS version 2.00
SS_readdat_3.00read data file from SS version 3.00
SS_readdat_3.24read data file from SS version 3.24
SS_readdat_3.30read data file from SS version 3.30
SS_readforecastread forecast file
SS_readpar_3.24read ss.par file from SS version 3.24
SS_readpar_3.30read ss.par file from SS version 3.30
SS_readstarterread starter file
SS_read_summaryread ss_summary file
SS_readwtatageRead weight-at-age data file
SS_recdevsInsert a vector of recruitment deviations into the control...
SS_RunJitterIteratively apply the jitter option in SS
SS_Sensi_plotCreate relative sensitivity plots as described in Cope and...
SS_splitdatSplit apart bootstrap data to make input file.
SSsummarizeSummarize the output from multiple Stock Synthesis models.
SStableComparisonsmake table comparing quantities across models
SS_tune_compsCalculate new tunings for length and age compositions and...
SSunavailableSpawningOutputPlot unavailable spawning output
SS_varadjustModify variance and sample size adjustments in the control...
SS_writeWrite all Stock Synthesis input files for a model
SS_writectlWrite Stock Synthesis control file
SS_writectl_3.24write control file
SS_writectl_3.30write control file for SS version 3.30
SS_writedatwrite Stock Synthesis data file
SS_writedat_3.24write data file for SS version 3.24
SS_writedat_3.30write data file for SS version 3.30
SS_writeforecastwrite forecast file
SS_writepar_3.24write ss.par file from SS version 3.24
SS_writepar_3.30write ss.par file from SS version 3.30
SS_writestarterwrite starter file
SS_writewtatageWrite weight-at-age file
stackpolymodified from "stackpoly" by Jim Lemon from "plotrix" package
translate_3.30_to_3.24_Q_setupUse 3.30 q options to create the 3.24 q setup
translate_3.30_to_3.24_var_adjustUse 3.30 variance adjustments to create the 3.24 formatting
TSCplotCreate a plot for the TSC report
write_fwf4Function to write formatted table similar to table written by...
r4ss documentation built on May 28, 2022, 1:11 a.m.