Function reference • r4ss

All functions

DoProjectPlots(): Deprecated function to make plots from Andre Punt's Rebuilder program.

NegLogInt_Fn(): Perform SS implementation of Laplace Approximation

PinerPlot(): Make plot of likelihood contributions by fleet

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

SS_ForeCatch(): Create table of fixed forecast catches

SS_RunJitter(): Deprecated function to run jitters, renamed to jitter()

SS_Sensi_plot(): Create relative sensitivity plots as described in Cope and Gertseva (2020)

SS_changepars(): Change parameters, bounds, or phases in the control file.

SS_decision_table_stuff(): Extract total catch, spawning output, and fraction unfished from forecast years

SS_doRetro(): Deprecated function to run a retrospective analyses, renamed to retro()

SS_fitbiasramp(): Estimate bias adjustment for recruitment deviates

SS_html(): Create HTML files to view figures in browser.

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(): Deprecated function to run a likelihood profile, renamed to profile().

SS_read(): Read all Stock Synthesis input files for a model

SS_read_summary(): read ss_summary file

SS_readctl(): Read control file from SS

SS_readctl_3.24(): Deprecated: 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(): Deprecated: read data file from SS version 2.00

SS_readdat_3.00(): Deprecate: read data file from SS version 3.00

SS_readdat_3.24(): Deprecated: 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_readpar_3.24(): Deprecated: read ss.par file from SS version 3.24

SS_readpar_3.30(): read .par file from SS version 3.30

SS_readstarter(): Read Stock Synthesis starter file as a list

SS_readwtatage(): Read in a weight-at-age data file as a data frame

SS_recdevs(): Insert a vector of recruitment deviations into the control file.

SS_tune_comps(): Deprecated function to tune composition data, renamed to tune_comps()

SS_varadjust(): Modify variance and sample size adjustments in the control file

SS_write(): Write all Stock Synthesis input files for a model

SS_writectl(): Write Stock Synthesis control file

SS_writectl_3.24(): Deprecated: write 3.24 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(): Deprecated: 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_writepar_3.24(): Deprecated: write ss.par file from SS version 3.24

SS_writepar_3.30(): write .par file from SS version 3.30

SS_writestarter(): write starter file

SS_writewtatage(): Write weight-at-age file

SSbiologytables(): A function to create a table of biology for assessment reporting: length, weight, % mature, fecundity, and selectivity

SSdiagsTime2Year(): Convert Time-Steps

SSexecutivesummary(): Create executive summary tables from an SS3 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

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.

SSplotDynamicB0(): Plot Dynamic B0

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.

SSplotSPR(): Plot Spawning Potential Ratio (SPR) quantities.

SSplotSelex(): Plot selectivity

SSplotSexRatio(): Plot sex-ratio data and fits for two sex models

SSplotSpawnrecruit(): Plot spawner-recruit curve.

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

SSunavailableSpawningOutput(): Plot unavailable spawning output

TSCplot(): Create a plot for the TSC report

add_legend(): Add legend to plots

bubble3(): Create a bubble plot.

calc_var_adjust(): Calculate variance adjustments for discard or mean body weight data

check_exe(): Find location of executable within path or specified directory

check_inputlist(): Check input argument inputlist

copy_SS_inputs(): Copy a the Stock Synthesis input files from one directory to another

download_models(): Download SS3 test models

file_increment(): Rename key Stock Synthesis output files by adding integer value

getADMBHessian(): Read admodel.hes file

get_SIS_info(): Gather information for the NOAA Species Information System (SIS)

get_areacols(): Get default vector of colors for each area

get_comments(): Collect comments lines starting from "#C" in datfile, ctlfile, starter.ss, forecast.ss etc

get_dat_new_name(): Get the name of the data .ss_new file in a directory

get_last_phase(): Get the highest phase used in the control file

get_par_name(): Get the name of the .par file in a directory

get_ss3_exe(): Download the Stock Synthesis (SS3) executable

get_tuning_table(): Get the tuning table

get_tv_parlabs(): Get time varying parameter labels

is.wholenumber(): Utility function to test if x is "numerically" integer wrt machine epsilon taken from example section of help of is.integer

iterate_jitter(): Execute a single jittered model run

jitter(): Iteratively run Stock Synthesis with jittered starting values

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

plotCI(): Plot points with confidence intervals.

populate_multiple_folders(): Populate multiple Stock Synthesis folders with input files

profile(): Run a likelihood profile in Stock Synthesis.

read.admbFit(): Read ADMB .par and .cor files.

retro(): Run a retrospective analyses

rich.colors.short(): Make a vector of colors.

run(): Run a Stock Synthesis model

save_png(): Open png device and return info on the file being created

selShapes(): Launch a shiny app that displays various selectivity curves

sspar(): Allow Multi-Plots Set the par() to options suitable for ss3diags multi plots.

stackpoly(): modified from "stackpoly" by Jim Lemon from "plotrix" package

translate_3.30_to_3.24_Q_setup(): Use 3.30 q options to create the 3.24 q setup

translate_3.30_to_3.24_var_adjust(): Use 3.30 variance adjustments to create the 3.24 formatting

tune_comps(): Calculate new tunings for length and age compositions and (re)run models

write_fwf4(): Function to write formatted table similar to table written by gdata::write.fwf from data.frame or matrix This function does not accept columns or logical with factor