ss3sim: Fisheries Stock Assessment Simulation Testing with Stock Synthesis
Version 0.9.5

Develops a framework for fisheries stock assessment simulation testing with Stock Synthesis 3 (SS3) as described in Anderson et al. (2014) .

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AuthorSean 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 publication2017-04-19 03:55:46 UTC
MaintainerSean Anderson <sean@seananderson.ca>
LicenseMIT + file LICENSE
Version0.9.5
URL https://github.com/ss3sim/ss3sim
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("ss3sim")

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...

Functions

add_nulls Man page Source code
bias_ss3 Man page Source code
calculate_data_units Man page Source code
calculate_re Man page Source code
calculate_runtime Man page Source code
case_comp Man page Source code
case_deparse Man page Source code
case_fishing Man page Source code
case_index Man page Source code
case_tv Man page Source code
change_agecomp Man page Source code
change_data Man page Source code
change_e Man page Source code
change_em_binning Man page Source code
change_f Man page Source code
change_fltname Man page Source code
change_index Man page Source code
change_lcomp Man page Source code
change_lcomp_constant Man page Source code
change_maturity Man page Source code
change_pop_bin Source code
change_rec_devs Man page Source code
change_retro Man page Source code
change_tail_compression Man page Source code
change_tv Man page Source code
change_year Man page Source code
check_data Man page Source code
clean_data Man page Source code
cleanup_ss3 Man page Source code
copy_ss3models Man page Source code
create_argfiles Man page Source code
expand_scenarios Man page Source code
extract_expected_data Man page Source code
facet_form Man page Source code
fill_across Man page Source code
get_args Man page Source code
get_bin Man page Source code
get_bin_info Man page Source code
get_caseargs Man page Source code
get_caseval Man page Source code
get_fish600_casefolder Man page Source code
get_model_folder Man page Source code
get_nll_components Man page Source code
get_recdevs Man page Source code
get_results_all Man page Source code
get_results_derived Man page Source code
get_results_scalar Man page Source code
get_results_scenario Man page Source code
get_results_timeseries Man page Source code
get_sigmar Man page Source code
id_scenarios Man page Source code
is_divisible Source code
make_dummy_dat_agecomp Source code
make_dummy_dat_calcomp Source code
make_dummy_dat_index Source code
make_dummy_dat_lencomp Source code
make_dummy_dat_mlacomp Source code
pastef Man page Source code
plot_scalar_boxplot Man page Source code
plot_scalar_points Man page Source code
plot_ts_boxplot Man page Source code
plot_ts_lines Man page Source code
plot_ts_points Man page Source code
profile_fmsy Man page Source code
rename_ss3_files Man page Source code
run_bias_ss3 Man page Source code
run_ss3model Man page Source code
run_ss3sim Man page Source code
sample_agecomp Man page Source code
sample_calcomp Man page Source code
sample_fit_vbgf Source code
sample_index Man page Source code
sample_lcomp Man page Source code
sample_mlacomp Man page Source code
sample_wtatage Man page Source code
sanitize_admb_options Man page Source code
scalar_dat Man page
setup_parallel Man page Source code
ss3sim Man page
ss3sim-package Man page
ss3sim_base Man page Source code
standardize_bounds Man page Source code
substr_r Man page Source code
ts_dat Man page
vbgf_func Man page Source code
verify_input Man page Source code
verify_plot_arguments Man page Source code

Files

inst
inst/CITATION
inst/extdata
inst/extdata/time-varying-case-tests
inst/extdata/time-varying-case-tests/X0-cod.txt
inst/extdata/time-varying-case-tests/K0-cod.txt
inst/extdata/time-varying-case-tests/Y0-cod.txt
inst/extdata/time-varying-case-tests/Z0-cod.txt
inst/extdata/Simple
inst/extdata/Simple/forecast.ss
inst/extdata/Simple/simple.dat
inst/extdata/Simple/ss3.par
inst/extdata/Simple/simple.ctl
inst/extdata/Simple/starter.ss
inst/extdata/example-om
inst/extdata/example-om/data.ss_new
inst/extdata/eg-cases
inst/extdata/eg-cases/tail_compression0-cod.txt
inst/extdata/eg-cases/lcomp0-cod.txt
inst/extdata/eg-cases/index0-cod.txt
inst/extdata/eg-cases/E0-cod.txt
inst/extdata/eg-cases/agecomp100-cod.txt
inst/extdata/eg-cases/M0-cod.txt
inst/extdata/eg-cases/index100-cod.txt
inst/extdata/eg-cases/tail_compression1-cod.txt
inst/extdata/eg-cases/retro1-cod.txt
inst/extdata/eg-cases/lcomp1-cod.txt
inst/extdata/eg-cases/retro0-cod.txt
inst/extdata/eg-cases/E1-cod.txt
inst/extdata/eg-cases/E101-cod.txt
inst/extdata/eg-cases/index1-cod.txt
inst/extdata/eg-cases/agecomp0-cod.txt
inst/extdata/eg-cases/F0-cod.txt
inst/extdata/eg-cases/S0-cod.txt
inst/extdata/eg-cases/G0-cod.txt
inst/extdata/eg-cases/E100-cod.txt
inst/extdata/eg-cases/agecomp1-cod.txt
inst/extdata/models
inst/extdata/models/cod-om
inst/extdata/models/cod-om/codOM.dat
inst/extdata/models/cod-om/forecast.ss
inst/extdata/models/cod-om/ss3.par
inst/extdata/models/cod-om/codOM.ctl
inst/extdata/models/cod-om/starter.ss
inst/extdata/models/cod-em
inst/extdata/models/cod-em/forecast.ss
inst/extdata/models/cod-em/codEM.ctl
inst/extdata/models/cod-em/starter.ss
inst/extdata/output
inst/extdata/output/ss3sim_ts.csv
inst/extdata/output/ss3sim_scalar.csv
inst/extdata/cases
inst/extdata/cases/M3-cod.txt
inst/extdata/cases/E0-sar.txt
inst/extdata/cases/E7-fla.txt
inst/extdata/cases/R2-sar.txt
inst/extdata/cases/F1-cod.txt
inst/extdata/cases/lcomp2-cod.txt
inst/extdata/cases/E5-cod.txt
inst/extdata/cases/F1-sar.txt
inst/extdata/cases/E9-sar.txt
inst/extdata/cases/lcomp1-sar.txt
inst/extdata/cases/R2-fla.txt
inst/extdata/cases/E6-fla.txt
inst/extdata/cases/lcomp0-cod.txt
inst/extdata/cases/G1-cod.txt
inst/extdata/cases/E16-cod.txt
inst/extdata/cases/E20-sar.txt
inst/extdata/cases/index0-cod.txt
inst/extdata/cases/R5-fla.txt
inst/extdata/cases/E8-fla.txt
inst/extdata/cases/E3-fla.txt
inst/extdata/cases/E0-cod.txt
inst/extdata/cases/R2-cod.txt
inst/extdata/cases/S0-sar.txt
inst/extdata/cases/E21-sar.txt
inst/extdata/cases/E3-sar.txt
inst/extdata/cases/R1-cod.txt
inst/extdata/cases/E20-fla.txt
inst/extdata/cases/F2-sar.txt
inst/extdata/cases/E6-sar.txt
inst/extdata/cases/E3-cod.txt
inst/extdata/cases/M0-cod.txt
inst/extdata/cases/S1-fla.txt
inst/extdata/cases/E22-fla.txt
inst/extdata/cases/R4-cod.txt
inst/extdata/cases/E1-sar.txt
inst/extdata/cases/R4-sar.txt
inst/extdata/cases/F0-sar.txt
inst/extdata/cases/G1-sar.txt
inst/extdata/cases/R3-sar.txt
inst/extdata/cases/G2-cod.txt
inst/extdata/cases/index2-cod.txt
inst/extdata/cases/M1-cod.txt
inst/extdata/cases/G1-fla.txt
inst/extdata/cases/R4-fla.txt
inst/extdata/cases/E60-fla.txt
inst/extdata/cases/G0-fla.txt
inst/extdata/cases/E7-sar.txt
inst/extdata/cases/R1-fla.txt
inst/extdata/cases/E21-cod.txt
inst/extdata/cases/E20-cod.txt
inst/extdata/cases/E60-sar.txt
inst/extdata/cases/E22-cod.txt
inst/extdata/cases/E21-fla.txt
inst/extdata/cases/M3-sar.txt
inst/extdata/cases/E5-sar.txt
inst/extdata/cases/E2-fla.txt
inst/extdata/cases/M1-sar.txt
inst/extdata/cases/E5-fla.txt
inst/extdata/cases/lcomp1-fla.txt
inst/extdata/cases/S2-fla.txt
inst/extdata/cases/lcomp1-cod.txt
inst/extdata/cases/E6-cod.txt
inst/extdata/cases/R1-sar.txt
inst/extdata/cases/S2-cod.txt
inst/extdata/cases/M3-fla.txt
inst/extdata/cases/R0-fla.txt
inst/extdata/cases/R5-cod.txt
inst/extdata/cases/data0-cod.txt
inst/extdata/cases/R3-cod.txt
inst/extdata/cases/E8-cod.txt
inst/extdata/cases/E9-fla.txt
inst/extdata/cases/E1-cod.txt
inst/extdata/cases/agecomp2-cod.txt
inst/extdata/cases/R3-fla.txt
inst/extdata/cases/E1-fla.txt
inst/extdata/cases/S1-cod.txt
inst/extdata/cases/F2-fla.txt
inst/extdata/cases/E22-sar.txt
inst/extdata/cases/index1-cod.txt
inst/extdata/cases/index1-sar.txt
inst/extdata/cases/agecomp0-cod.txt
inst/extdata/cases/F0-cod.txt
inst/extdata/cases/E7-cod.txt
inst/extdata/cases/R0-cod.txt
inst/extdata/cases/E8-sar.txt
inst/extdata/cases/agecomp1-sar.txt
inst/extdata/cases/agecomp1-fla.txt
inst/extdata/cases/G0-sar.txt
inst/extdata/cases/S0-fla.txt
inst/extdata/cases/E60-cod.txt
inst/extdata/cases/G2-fla.txt
inst/extdata/cases/F0-fla.txt
inst/extdata/cases/M1-fla.txt
inst/extdata/cases/R0-sar.txt
inst/extdata/cases/S0-cod.txt
inst/extdata/cases/E9-cod.txt
inst/extdata/cases/M0-sar.txt
inst/extdata/cases/E2-cod.txt
inst/extdata/cases/E0-fla.txt
inst/extdata/cases/F1-fla.txt
inst/extdata/cases/S1-sar.txt
inst/extdata/cases/S2-sar.txt
inst/extdata/cases/G0-cod.txt
inst/extdata/cases/G2-sar.txt
inst/extdata/cases/F2-cod.txt
inst/extdata/cases/R5-sar.txt
inst/extdata/cases/M0-fla.txt
inst/extdata/cases/E2-sar.txt
inst/extdata/cases/index1-fla.txt
inst/extdata/cases/agecomp1-cod.txt
inst/extdata/change_f
inst/extdata/change_f/ss3.par
inst/doc
inst/doc/modifying-models.html
inst/doc/making-models.Rmd
inst/doc/introduction.R
inst/doc/modifying-models.Rmd
inst/doc/introduction.html
inst/doc/making-functions.Rmd
inst/doc/introduction.Rmd
inst/doc/making-models.html
inst/doc/making-functions.html
NAMESPACE
NEWS.md
data
data/ts_dat.rda
data/scalar_dat.rda
R
R/sample_index.r
R/change_tv.r
R/sample_mlacomp.R
R/run_ss3sim.r
R/change_data.r
R/expand_scenarios.r
R/ts_dat.r
R/get_model_folder.r
R/growth_estimation.R
R/case-write.R
R/change_em_binning.r
R/change_retro.r
R/change_lcomp_constant.R
R/pastef.r
R/sample_agecomp.R
R/change_rec_devs.r
R/ss3sim_base.r
R/verify_input.r
R/get_recdevs.r
R/ss3sim.r
R/cleanup_ss3.r
R/add_nulls.R
R/change_fltname.r
R/change_maturity.R
R/change_e.r
R/fill_across.r
R/change_year.R
R/bias_ss3.r
R/copy_ss3models.r
R/get-results.r
R/change_f.r
R/sample_lcomp.R
R/extract_expected_data.r
R/clean_data.r
R/case-parsing.r
R/standardize_bounds.R
R/scalar_dat.r
R/get_sigma.r
R/get_fish600_casefolder.r
R/sample_calcomp.R
R/change_tail_compression.R
R/get_bin.R
R/sample_wtatage.R
R/setup_parallel.r
R/create_argfiles.r
R/run_bias_ss3.r
R/run_ss3model.r
R/get_bin_info.r
R/make_dummy_data.r
R/plot_functions.R
R/calculate_re.R
R/profile_fmsy.r
vignettes
vignettes/refs.bib
vignettes/cjfas.csl
vignettes/making-models.Rmd
vignettes/modifying-models.Rmd
vignettes/making-functions.Rmd
vignettes/introduction.Rmd
vignettes/filestructure.png
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/id_scenarios.Rd
man/case_index.Rd
man/pastef.Rd
man/cleanup_ss3.Rd
man/facet_form.Rd
man/expand_scenarios.Rd
man/calculate_data_units.Rd
man/change_lcomp_constant.Rd
man/plot_ts_lines.Rd
man/sample_wtatage.Rd
man/get_fish600_casefolder.Rd
man/sample_calcomp.Rd
man/bias_ss3.Rd
man/change_lcomp.Rd
man/plot_ts_boxplot.Rd
man/get_results_all.Rd
man/calculate_runtime.Rd
man/change_em_binning.Rd
man/case_fishing.Rd
man/profile_fmsy.Rd
man/vbgf_func.Rd
man/substr_r.Rd
man/run_bias_ss3.Rd
man/sample_agecomp.Rd
man/clean_data.Rd
man/get_results_scalar.Rd
man/get_nll_components.Rd
man/get_sigmar.Rd
man/plot_scalar_points.Rd
man/change_agecomp.Rd
man/change_tail_compression.Rd
man/get_caseval.Rd
man/get_caseargs.Rd
man/get_results_derived.Rd
man/rename_ss3_files.Rd
man/change_fltname.Rd
man/change_maturity.Rd
man/ss3sim.Rd
man/change_tv.Rd
man/run_ss3sim.Rd
man/verify_plot_arguments.Rd
man/case_tv.Rd
man/plot_scalar_boxplot.Rd
man/ss3sim_base.Rd
man/extract_expected_data.Rd
man/change_f.Rd
man/scalar_dat.Rd
man/copy_ss3models.Rd
man/get_results_scenario.Rd
man/sample_lcomp.Rd
man/calculate_re.Rd
man/change_data.Rd
man/check_data.Rd
man/sanitize_admb_options.Rd
man/case_deparse.Rd
man/case_comp.Rd
man/change_retro.Rd
man/ts_dat.Rd
man/setup_parallel.Rd
man/get_recdevs.Rd
man/create_argfiles.Rd
man/sample_index.Rd
man/sample_mlacomp.Rd
man/get_args.Rd
man/change_e.Rd
man/get_bin_info.Rd
man/change_rec_devs.Rd
man/fill_across.Rd
man/get_model_folder.Rd
man/run_ss3model.Rd
man/add_nulls.Rd
man/verify_input.Rd
man/get_bin.Rd
man/plot_ts_points.Rd
man/change_index.Rd
man/standardize_bounds.Rd
man/change_year.Rd
man/get_results_timeseries.Rd
.Rinstignore
LICENSE
ss3sim documentation built on May 20, 2017, 4:28 a.m.