Man pages for ss3sim
Fisheries Stock Assessment Simulation Testing with Stock Synthesis

add_colnamesCreate matching column names across a list of data frames
add_CPUEAdd a q setup line into an SS control file
add_nullsAdd 'NULL' values to non-existent list elements
add_tv_parlinesAdd short time varying parameter lines. At time of writing,...
calculate_data_unitsGiven sampling arguments, calculate super set of fleets,...
calculate_reCalculate relative error
case_compWrite a case file for length- or age-composition data
case_deparseTurn an argument describing an object into a character.
case_fishingWrite a case file for fishing data to the disk.
case_indexWrite a case file for index data to the disk.
case_tvWrite time varying casefiles to the disk
change_dataChange the data that is available as output from an SS...
change_eMethods to alter which parameters are estimated in a SS3...
change_e_fcast_yrsCheck and change forecast file years if necessary
change_em_binningChange population and observed length composition bins in an...
change_fAlter fishing mortality (_F_) using the SS control file
change_f_parAlter the fishing mortality (_F_) values in an SS3 '.par'...
change_lcomp_constantSet the robustification constant for length composition data.
change_oMethods to include parameters in an SS3operating model
change_pop_binSet up population length bin structure
change_rec_devsReplace recruitment deviations
change_rec_devs_parReplace recruitment deviations
change_retroAlter a starter file for a retrospective analysis
change_tail_compressionReplace tail compression value for length composition data.
change_tvMethods to include time-varying parameters in an SS3...
check_dataCheck that the SS data file looks correct
check_data_str_rangeCheck input arguments for data
clean_dataGiven sampling arguments remove ("clean") all data in a .dat...
cleanup_ss3Clean up after an SS3 run
copy_ss3modelsCopy the operating and estimation models and create a folder...
create_argfilesCreate template argument input files
expand_scenariosCreate vectors of scenario IDs
facet_formA helper function for building a ggplot facet. Used...
fill_acrossFill in matrix across rows of weight-at-age data by...
get_argsTake a csv file, read it, and turn the first column into the...
get_binGet SS3 binary/executable location in package
get_bin_infoGet the parameter values for change_bin
get_caseargsTake a scenario ID and return argument lists
get_casevalTake a scenario ID and a case type and return the case number
get_fish600_casefolderGet the folder location of the FISH600 case files
get_model_folderGet the folder location of an included SS3 model...
get_nll_componentsGet negative log likelihood (NLL) values from a report file...
get_recdevsReturn a set of recruitment deviations
get_results_allExtract SS3 simulation output
get_results_derivedExtract time series from a model run with the associated...
get_results_scalarExtract scalar quantities from a model run.
get_results_scenarioExtract SS3 simulation results for one scenario.
get_results_timeseriesExtract time series from a model run.
get_sigmarGet Variability About Recruitment Deviations (sigma_R)
get_ss_ver_dlGet the ss version (either 3.24 or 3.30) from a 'dat_list'...
get_ss_ver_fileGet the ss version (either 3.24 or 3.30) from an ss file
id_scenariosIdentify ss3sim scenarios within a directory
plot_scalar_boxplotPrint scalar values as boxplots.
plot_scalar_pointsPlot scalar values as points.
plot_ts_boxplotPlot timeseries values as boxplots.
plot_ts_linesPlot timeseries values as lines.
plot_ts_pointsPlot timeseries values as points.
profile_fmsyDetermine Fmsy for a given operating model
remove_CPUERemove a q setup line into an SS control file
remove_q_ctlRemove a q setup line into an SS control file only
rename_ss3_filesRename SS3-version-specific files
run_ss3modelRun an operating or estimation model for a specified set of...
run_ss3simMaster function to run SS3 simulations
sample_agecompSample age compositions from a Stock Synthesis data file
sample_calcompSample conditional age-at-length (CAL) data and write to file...
sample_compSample composition data from expected values
sample_indexSample the biomass with observation error
sample_lcompSample length compositions from a Stock Synthesis data file
sample_mlacomp[BETA VERSION] Sample mean length (size-)-at-age data and...
sample_wtatageSample empirical weight-at-age data and write to file for use...
sanitize_admb_optionsCheck admb options to make sure there aren't flags there...
scalar_datExample scalar data from the ss3sim vignette
setup_parallelSetup parallel processing
ss3simss3sim: Fisheries stock assessment simulation testing with...
ss3sim_baseBase wrapper function to run an ss3sim simulation
standardize_boundsStandardize the bounds of the estimation model control file.
substr_rSubstring from right
ts_datExample time series data from the ss3sim vignette
vbgf_funcPredict length given VBGF parameters
verify_inputVerify and standardize SS3 input files
verify_plot_argumentsA helper function to check the correct input for the plotting...
ss3sim documentation built on Nov. 9, 2019, 1:06 a.m.