ss3sim: Fisheries Stock Assessment Simulation Testing with Stock Synthesis

Develops a framework for fisheries stock assessment simulation testing with Stock Synthesis 3 (SS3).

Author
Sean Anderson [aut, cre], Cole Monnahan [aut], Kelli Johnson [aut], Kotaro Ono [aut], Juan Valero [aut], Curry Cunningham [aut], Allan Hicks [aut], Felipe Hurtado-Ferro [aut], Peter Kuriyama [aut], Roberto Licandeo [aut], Carey McGilliard [aut], Melissa Muradian [ctb], Merrill Rudd [aut], Christine Stawitz [aut], Cody Szuwalski [aut], Ian Taylor [aut], Katyana Vert-pre [aut], Athol Whitten [aut]
Date of publication
2016-11-30 13:13:11
Maintainer
Sean Anderson <sean@seananderson.ca>
License
MIT + file LICENSE
Version
0.9.3

View on CRAN

Man pages

add_nulls
Add NULL values to non-existent list elements
bias_ss3
Perform a single bias adjustment run
calculate_data_units
Given sampling arguments, calculate super set of fleets,...
calculate_re
Calculate relative error
calculate_runtime
Calculate run time
case_comp
Write a case file for length- or age-composition data
case_deparse
Turn an argument describing an object into a character.
case_fishing
Write a case file for fishing data to the disk.
case_index
Write a case file for index data to the disk.
case_tv
Write time varying casefiles to the disk
change_agecomp
(Depreciated) Sample age compositions from expected values
change_data
Change the data that is available as output from an SS...
change_e
Methods to alter which parameters are estimated in a SS3...
change_em_binning
Change population and observed length composition bins in an...
change_f
Alter the fishing mortality (_F_) values in an SS3 '.par'...
change_fltname
Standardize column name for FltSvy in event 'r4ss' is not the...
change_index
(Depreciated) Sample the biomass with observation error
change_lcomp
(Depreciated) Sample length compositions from expected values
change_lcomp_constant
Set the robustification constant for length composition data.
change_maturity
Alter a control file to specify the SS3 maturity option
change_rec_devs
Replace recruitment deviations
change_retro
Alter a starter file for a retrospective analysis
change_tail_compression
Replace tail compression value for length composition data.
change_tv
Methods to include time-varying parameters in an SS3...
change_year
Methods to change the years in an ss3sim model
check_data
Check that the SS3 data file looks correct
clean_data
Given sampling arguments remove ("clean") all data in a .dat...
cleanup_ss3
Clean up after an SS3 run
copy_ss3models
Copy the operating and estimation models and create a folder...
create_argfiles
Create template argument input files
expand_scenarios
Create vectors of scenario IDs
extract_expected_data
Extract the expected data values
facet_form
A helper function for building a ggplot facet. Used...
fill_across
Fill in matrix across rows of weight-at-age data by...
get_args
Take a csv file, read it, and turn the first column into the...
get_bin
Get SS3 binary/executable location in package
get_bin_info
Get the parameter values for change_bin
get_caseargs
Take a scenario ID and return argument lists
get_caseval
Take a scenario ID and a case type and return the case number
get_fish600_casefolder
Get the folder location of the FISH600 case files
get_model_folder
Get the folder location of an included SS3 model...
get_nll_components
Get negative log likelihood (NLL) values from a report file...
get_recdevs
Return a set of recruitment deviations
get_results_all
Extract SS3 simulation output
get_results_derived
Extract time series from a model run with the associated...
get_results_scalar
Extract scalar quantities from a model run.
get_results_scenario
Extract SS3 simulation results for one scenario.
get_results_timeseries
Extract time series from a model run.
get_sigmar
Get recruitment deviation sigma
id_scenarios
Identify ss3sim scenarios within a directory
pastef
Paste with "/" as the separator
plot_scalar_boxplot
Print scalar values as boxplots.
plot_scalar_points
Plot scalar values as points.
plot_ts_boxplot
Plot timeseries values as boxplots.
plot_ts_lines
Plot timeseries values as lines.
plot_ts_points
Plot timeseries values as points.
profile_fmsy
Determine Fmsy for a given operating model
rename_ss3_files
Rename SS3-version-specific files
run_bias_ss3
Determine level of bias adjustment for SS3 runs
run_ss3model
Run an operating or estimation model for a specified set of...
run_ss3sim
Master function to run SS3 simulations
sample_agecomp
Sample age compositions from expected values
sample_calcomp
Sample conditional age-at-length (CAL) data and write to file...
sample_index
Sample the biomass with observation error
sample_lcomp
Sample length compositions from expected values
sample_mlacomp
[BETA VERSION] Sample mean length (size-)-at-age data and...
sample_wtatage
Sample empirial weight-at-age data and write to file for use...
sanitize_admb_options
Check admb options to make sure there aren't flags there...
scalar_dat
Example scalar data from the ss3sim vignette
setup_parallel
Setup parallel processing
ss3sim
ss3sim: Fisheries stock assessment simulation testing with...
ss3sim_base
Base wrapper function to run an ss3sim simulation
standardize_bounds
Standardize the bounds of the estimation model control file.
substr_r
Substring from right
ts_dat
Example time series data from the ss3sim vignette
vbgf_func
Predict length given VBGF parameters
verify_input
Verify and standardize SS3 input files
verify_plot_arguments
A helper function to check the correct input for the plotting...

Files in this package

ss3sim
ss3sim/inst
ss3sim/inst/CITATION
ss3sim/inst/extdata
ss3sim/inst/extdata/time-varying-case-tests
ss3sim/inst/extdata/time-varying-case-tests/X0-cod.txt
ss3sim/inst/extdata/time-varying-case-tests/K0-cod.txt
ss3sim/inst/extdata/time-varying-case-tests/Y0-cod.txt
ss3sim/inst/extdata/time-varying-case-tests/Z0-cod.txt
ss3sim/inst/extdata/Simple
ss3sim/inst/extdata/Simple/forecast.ss
ss3sim/inst/extdata/Simple/simple.dat
ss3sim/inst/extdata/Simple/ss3.par
ss3sim/inst/extdata/Simple/simple.ctl
ss3sim/inst/extdata/Simple/starter.ss
ss3sim/inst/extdata/example-om
ss3sim/inst/extdata/example-om/data.ss_new
ss3sim/inst/extdata/eg-cases
ss3sim/inst/extdata/eg-cases/tail_compression0-cod.txt
ss3sim/inst/extdata/eg-cases/lcomp0-cod.txt
ss3sim/inst/extdata/eg-cases/index0-cod.txt
ss3sim/inst/extdata/eg-cases/E0-cod.txt
ss3sim/inst/extdata/eg-cases/agecomp100-cod.txt
ss3sim/inst/extdata/eg-cases/M0-cod.txt
ss3sim/inst/extdata/eg-cases/index100-cod.txt
ss3sim/inst/extdata/eg-cases/tail_compression1-cod.txt
ss3sim/inst/extdata/eg-cases/retro1-cod.txt
ss3sim/inst/extdata/eg-cases/lcomp1-cod.txt
ss3sim/inst/extdata/eg-cases/retro0-cod.txt
ss3sim/inst/extdata/eg-cases/E1-cod.txt
ss3sim/inst/extdata/eg-cases/E101-cod.txt
ss3sim/inst/extdata/eg-cases/index1-cod.txt
ss3sim/inst/extdata/eg-cases/agecomp0-cod.txt
ss3sim/inst/extdata/eg-cases/F0-cod.txt
ss3sim/inst/extdata/eg-cases/S0-cod.txt
ss3sim/inst/extdata/eg-cases/G0-cod.txt
ss3sim/inst/extdata/eg-cases/E100-cod.txt
ss3sim/inst/extdata/eg-cases/agecomp1-cod.txt
ss3sim/inst/extdata/models
ss3sim/inst/extdata/models/cod-om
ss3sim/inst/extdata/models/cod-om/codOM.dat
ss3sim/inst/extdata/models/cod-om/forecast.ss
ss3sim/inst/extdata/models/cod-om/ss3.par
ss3sim/inst/extdata/models/cod-om/codOM.ctl
ss3sim/inst/extdata/models/cod-om/starter.ss
ss3sim/inst/extdata/models/cod-em
ss3sim/inst/extdata/models/cod-em/forecast.ss
ss3sim/inst/extdata/models/cod-em/codEM.ctl
ss3sim/inst/extdata/models/cod-em/starter.ss
ss3sim/inst/extdata/output
ss3sim/inst/extdata/output/ss3sim_ts.csv
ss3sim/inst/extdata/output/ss3sim_scalar.csv
ss3sim/inst/extdata/cases
ss3sim/inst/extdata/cases/M3-cod.txt
ss3sim/inst/extdata/cases/E0-sar.txt
ss3sim/inst/extdata/cases/E7-fla.txt
ss3sim/inst/extdata/cases/R2-sar.txt
ss3sim/inst/extdata/cases/F1-cod.txt
ss3sim/inst/extdata/cases/lcomp2-cod.txt
ss3sim/inst/extdata/cases/E5-cod.txt
ss3sim/inst/extdata/cases/F1-sar.txt
ss3sim/inst/extdata/cases/E9-sar.txt
ss3sim/inst/extdata/cases/lcomp1-sar.txt
ss3sim/inst/extdata/cases/R2-fla.txt
ss3sim/inst/extdata/cases/E6-fla.txt
ss3sim/inst/extdata/cases/lcomp0-cod.txt
ss3sim/inst/extdata/cases/G1-cod.txt
ss3sim/inst/extdata/cases/E16-cod.txt
ss3sim/inst/extdata/cases/E20-sar.txt
ss3sim/inst/extdata/cases/index0-cod.txt
ss3sim/inst/extdata/cases/R5-fla.txt
ss3sim/inst/extdata/cases/E8-fla.txt
ss3sim/inst/extdata/cases/E3-fla.txt
ss3sim/inst/extdata/cases/E0-cod.txt
ss3sim/inst/extdata/cases/R2-cod.txt
ss3sim/inst/extdata/cases/S0-sar.txt
ss3sim/inst/extdata/cases/E21-sar.txt
ss3sim/inst/extdata/cases/E3-sar.txt
ss3sim/inst/extdata/cases/R1-cod.txt
ss3sim/inst/extdata/cases/E20-fla.txt
ss3sim/inst/extdata/cases/F2-sar.txt
ss3sim/inst/extdata/cases/E6-sar.txt
ss3sim/inst/extdata/cases/E3-cod.txt
ss3sim/inst/extdata/cases/M0-cod.txt
ss3sim/inst/extdata/cases/S1-fla.txt
ss3sim/inst/extdata/cases/E22-fla.txt
ss3sim/inst/extdata/cases/R4-cod.txt
ss3sim/inst/extdata/cases/E1-sar.txt
ss3sim/inst/extdata/cases/R4-sar.txt
ss3sim/inst/extdata/cases/F0-sar.txt
ss3sim/inst/extdata/cases/G1-sar.txt
ss3sim/inst/extdata/cases/R3-sar.txt
ss3sim/inst/extdata/cases/G2-cod.txt
ss3sim/inst/extdata/cases/index2-cod.txt
ss3sim/inst/extdata/cases/M1-cod.txt
ss3sim/inst/extdata/cases/G1-fla.txt
ss3sim/inst/extdata/cases/R4-fla.txt
ss3sim/inst/extdata/cases/E60-fla.txt
ss3sim/inst/extdata/cases/G0-fla.txt
ss3sim/inst/extdata/cases/E7-sar.txt
ss3sim/inst/extdata/cases/R1-fla.txt
ss3sim/inst/extdata/cases/E21-cod.txt
ss3sim/inst/extdata/cases/E20-cod.txt
ss3sim/inst/extdata/cases/E60-sar.txt
ss3sim/inst/extdata/cases/E22-cod.txt
ss3sim/inst/extdata/cases/E21-fla.txt
ss3sim/inst/extdata/cases/M3-sar.txt
ss3sim/inst/extdata/cases/E5-sar.txt
ss3sim/inst/extdata/cases/E2-fla.txt
ss3sim/inst/extdata/cases/M1-sar.txt
ss3sim/inst/extdata/cases/E5-fla.txt
ss3sim/inst/extdata/cases/lcomp1-fla.txt
ss3sim/inst/extdata/cases/S2-fla.txt
ss3sim/inst/extdata/cases/lcomp1-cod.txt
ss3sim/inst/extdata/cases/E6-cod.txt
ss3sim/inst/extdata/cases/R1-sar.txt
ss3sim/inst/extdata/cases/S2-cod.txt
ss3sim/inst/extdata/cases/M3-fla.txt
ss3sim/inst/extdata/cases/R0-fla.txt
ss3sim/inst/extdata/cases/R5-cod.txt
ss3sim/inst/extdata/cases/data0-cod.txt
ss3sim/inst/extdata/cases/R3-cod.txt
ss3sim/inst/extdata/cases/E8-cod.txt
ss3sim/inst/extdata/cases/E9-fla.txt
ss3sim/inst/extdata/cases/E1-cod.txt
ss3sim/inst/extdata/cases/agecomp2-cod.txt
ss3sim/inst/extdata/cases/R3-fla.txt
ss3sim/inst/extdata/cases/E1-fla.txt
ss3sim/inst/extdata/cases/S1-cod.txt
ss3sim/inst/extdata/cases/F2-fla.txt
ss3sim/inst/extdata/cases/E22-sar.txt
ss3sim/inst/extdata/cases/index1-cod.txt
ss3sim/inst/extdata/cases/index1-sar.txt
ss3sim/inst/extdata/cases/agecomp0-cod.txt
ss3sim/inst/extdata/cases/F0-cod.txt
ss3sim/inst/extdata/cases/E7-cod.txt
ss3sim/inst/extdata/cases/R0-cod.txt
ss3sim/inst/extdata/cases/E8-sar.txt
ss3sim/inst/extdata/cases/agecomp1-sar.txt
ss3sim/inst/extdata/cases/agecomp1-fla.txt
ss3sim/inst/extdata/cases/G0-sar.txt
ss3sim/inst/extdata/cases/S0-fla.txt
ss3sim/inst/extdata/cases/E60-cod.txt
ss3sim/inst/extdata/cases/G2-fla.txt
ss3sim/inst/extdata/cases/F0-fla.txt
ss3sim/inst/extdata/cases/M1-fla.txt
ss3sim/inst/extdata/cases/R0-sar.txt
ss3sim/inst/extdata/cases/S0-cod.txt
ss3sim/inst/extdata/cases/E9-cod.txt
ss3sim/inst/extdata/cases/M0-sar.txt
ss3sim/inst/extdata/cases/E2-cod.txt
ss3sim/inst/extdata/cases/E0-fla.txt
ss3sim/inst/extdata/cases/F1-fla.txt
ss3sim/inst/extdata/cases/S1-sar.txt
ss3sim/inst/extdata/cases/S2-sar.txt
ss3sim/inst/extdata/cases/G0-cod.txt
ss3sim/inst/extdata/cases/G2-sar.txt
ss3sim/inst/extdata/cases/F2-cod.txt
ss3sim/inst/extdata/cases/R5-sar.txt
ss3sim/inst/extdata/cases/M0-fla.txt
ss3sim/inst/extdata/cases/E2-sar.txt
ss3sim/inst/extdata/cases/index1-fla.txt
ss3sim/inst/extdata/cases/agecomp1-cod.txt
ss3sim/inst/extdata/change_f
ss3sim/inst/extdata/change_f/ss3.par
ss3sim/inst/doc
ss3sim/inst/doc/modifying-models.html
ss3sim/inst/doc/making-models.Rmd
ss3sim/inst/doc/introduction.R
ss3sim/inst/doc/modifying-models.Rmd
ss3sim/inst/doc/introduction.html
ss3sim/inst/doc/making-functions.Rmd
ss3sim/inst/doc/introduction.Rmd
ss3sim/inst/doc/making-models.html
ss3sim/inst/doc/making-functions.html
ss3sim/NAMESPACE
ss3sim/NEWS.md
ss3sim/data
ss3sim/data/ts_dat.rda
ss3sim/data/scalar_dat.rda
ss3sim/R
ss3sim/R/sample_index.r
ss3sim/R/change_tv.r
ss3sim/R/sample_mlacomp.R
ss3sim/R/run_ss3sim.r
ss3sim/R/change_data.r
ss3sim/R/expand_scenarios.r
ss3sim/R/ts_dat.r
ss3sim/R/get_model_folder.r
ss3sim/R/growth_estimation.R
ss3sim/R/case-write.R
ss3sim/R/change_em_binning.r
ss3sim/R/change_retro.r
ss3sim/R/change_lcomp_constant.R
ss3sim/R/pastef.r
ss3sim/R/sample_agecomp.R
ss3sim/R/change_rec_devs.r
ss3sim/R/ss3sim_base.r
ss3sim/R/verify_input.r
ss3sim/R/get_recdevs.r
ss3sim/R/ss3sim.r
ss3sim/R/cleanup_ss3.r
ss3sim/R/add_nulls.R
ss3sim/R/change_fltname.r
ss3sim/R/change_maturity.R
ss3sim/R/change_e.r
ss3sim/R/fill_across.r
ss3sim/R/change_year.R
ss3sim/R/bias_ss3.r
ss3sim/R/copy_ss3models.r
ss3sim/R/get-results.r
ss3sim/R/change_f.r
ss3sim/R/sample_lcomp.R
ss3sim/R/extract_expected_data.r
ss3sim/R/clean_data.r
ss3sim/R/case-parsing.r
ss3sim/R/standardize_bounds.R
ss3sim/R/scalar_dat.r
ss3sim/R/get_sigma.r
ss3sim/R/get_fish600_casefolder.r
ss3sim/R/sample_calcomp.R
ss3sim/R/change_tail_compression.R
ss3sim/R/get_bin.R
ss3sim/R/sample_wtatage.R
ss3sim/R/setup_parallel.r
ss3sim/R/create_argfiles.r
ss3sim/R/run_bias_ss3.r
ss3sim/R/run_ss3model.r
ss3sim/R/get_bin_info.r
ss3sim/R/make_dummy_data.r
ss3sim/R/plot_functions.R
ss3sim/R/calculate_re.R
ss3sim/R/profile_fmsy.r
ss3sim/vignettes
ss3sim/vignettes/refs.bib
ss3sim/vignettes/cjfas.csl
ss3sim/vignettes/making-models.Rmd
ss3sim/vignettes/modifying-models.Rmd
ss3sim/vignettes/making-functions.Rmd
ss3sim/vignettes/introduction.Rmd
ss3sim/vignettes/filestructure.png
ss3sim/README.md
ss3sim/MD5
ss3sim/build
ss3sim/build/vignette.rds
ss3sim/DESCRIPTION
ss3sim/man
ss3sim/man/id_scenarios.Rd
ss3sim/man/case_index.Rd
ss3sim/man/pastef.Rd
ss3sim/man/cleanup_ss3.Rd
ss3sim/man/facet_form.Rd
ss3sim/man/expand_scenarios.Rd
ss3sim/man/calculate_data_units.Rd
ss3sim/man/change_lcomp_constant.Rd
ss3sim/man/plot_ts_lines.Rd
ss3sim/man/sample_wtatage.Rd
ss3sim/man/get_fish600_casefolder.Rd
ss3sim/man/sample_calcomp.Rd
ss3sim/man/bias_ss3.Rd
ss3sim/man/change_lcomp.Rd
ss3sim/man/plot_ts_boxplot.Rd
ss3sim/man/get_results_all.Rd
ss3sim/man/calculate_runtime.Rd
ss3sim/man/change_em_binning.Rd
ss3sim/man/case_fishing.Rd
ss3sim/man/profile_fmsy.Rd
ss3sim/man/vbgf_func.Rd
ss3sim/man/substr_r.Rd
ss3sim/man/run_bias_ss3.Rd
ss3sim/man/sample_agecomp.Rd
ss3sim/man/clean_data.Rd
ss3sim/man/get_results_scalar.Rd
ss3sim/man/get_nll_components.Rd
ss3sim/man/get_sigmar.Rd
ss3sim/man/plot_scalar_points.Rd
ss3sim/man/change_agecomp.Rd
ss3sim/man/change_tail_compression.Rd
ss3sim/man/get_caseval.Rd
ss3sim/man/get_caseargs.Rd
ss3sim/man/get_results_derived.Rd
ss3sim/man/rename_ss3_files.Rd
ss3sim/man/change_fltname.Rd
ss3sim/man/change_maturity.Rd
ss3sim/man/ss3sim.Rd
ss3sim/man/change_tv.Rd
ss3sim/man/run_ss3sim.Rd
ss3sim/man/verify_plot_arguments.Rd
ss3sim/man/case_tv.Rd
ss3sim/man/plot_scalar_boxplot.Rd
ss3sim/man/ss3sim_base.Rd
ss3sim/man/extract_expected_data.Rd
ss3sim/man/change_f.Rd
ss3sim/man/scalar_dat.Rd
ss3sim/man/copy_ss3models.Rd
ss3sim/man/get_results_scenario.Rd
ss3sim/man/sample_lcomp.Rd
ss3sim/man/calculate_re.Rd
ss3sim/man/change_data.Rd
ss3sim/man/check_data.Rd
ss3sim/man/sanitize_admb_options.Rd
ss3sim/man/case_deparse.Rd
ss3sim/man/case_comp.Rd
ss3sim/man/change_retro.Rd
ss3sim/man/ts_dat.Rd
ss3sim/man/setup_parallel.Rd
ss3sim/man/get_recdevs.Rd
ss3sim/man/create_argfiles.Rd
ss3sim/man/sample_index.Rd
ss3sim/man/sample_mlacomp.Rd
ss3sim/man/get_args.Rd
ss3sim/man/change_e.Rd
ss3sim/man/get_bin_info.Rd
ss3sim/man/change_rec_devs.Rd
ss3sim/man/fill_across.Rd
ss3sim/man/get_model_folder.Rd
ss3sim/man/run_ss3model.Rd
ss3sim/man/add_nulls.Rd
ss3sim/man/verify_input.Rd
ss3sim/man/get_bin.Rd
ss3sim/man/plot_ts_points.Rd
ss3sim/man/change_index.Rd
ss3sim/man/standardize_bounds.Rd
ss3sim/man/change_year.Rd
ss3sim/man/get_results_timeseries.Rd
ss3sim/.Rinstignore
ss3sim/LICENSE