Package: MSEtool
Title: Management Strategy Evaluation Toolkit
Version: 4.0.0
Authors@R: c(
  person("Adrian", "Hordyk", email = "adrian@bluematterscience.com", role = c("aut", "cre")),
  person("Quang", "Huynh", email = "quang@bluematterscience.com", role = "aut"), 
  person("Tom", "Carruthers", email = "tom@bluematterscience.com", role = c("aut")),
  person("Chris", "Grandin", role = "ctb", comment = "iSCAM functions"))
Description: Development, simulation testing, and implementation of
        management procedures for fisheries (see Carruthers & Hordyk
        (2018) <doi:10.1111/2041-210X.13081>).
License: GPL-3
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
Depends: R (>= 4.2.0), snowfall
Imports: abind, cli, digest, dplyr, ggplot2, grDevices, lubridate,
        methods, parallel, purrr, Rcpp, rlang, stats, tidyr, utils
Suggests: boot, broom, covr, crayon, DT, furrr, future, fmsb,
        kableExtra, knitr, ggrepel, gridExtra, Matrix, MASS, mvtnorm,
        openxlsx, pak, pbapply, r4ss, readxl, reshape2, rfishbase,
        rmarkdown, shiny, Slick, testthat, tibble, tidyr, TMB,
        tmvtnorm, usethis
LinkingTo: Rcpp, RcppArmadillo
BugReports: https://github.com/Blue-Matter/MSEtool/issues
URL: https://msetool.openmse.com/
Collate: 'MSEtool-package.R' 'RcppExports.R' 'add-fleet.R'
        'adjust-seasonal-fecundity.R' 'calc-advice.R'
        'calc-age-size-key.R' 'calc-asymptotic-distribution.R'
        'calc-catch-at-size.R' 'calc-conditioned-key.R'
        'calc-equilibrium.R' 'calc-fishery-dynamics.R'
        'calc-initial-timestep.R' 'calc-innovation-cov.R'
        'calc-max-effort.R' 'calc-mgt.R' 'calc-mice.R' 'calc-msy.R'
        'calc-per-recruit.R' 'calc-ref-yield.R'
        'calc-spatial-movement.R' 'calc-spr0.R'
        'calc-survival-unfished.R' 'calc-survival.R'
        'calc-unfished-distribution.R' 'calc-unfished-dynamic.R'
        'calc-unfished-equilibrium.R' 'calc-unfished-number.R'
        'calc-years.R' 'check-advice.R' 'check-allocation.R'
        'check-catchfrac.R' 'check-class.R' 'check-data-catch.R'
        'check-mse-run.R' 'check-obs.R' 'check-om.R' 'check-package.R'
        'check-required-object.R' 'check-selectivity-maximum.R'
        'check-spatial-structure.R' 'check-value.R' 'class-unions.R'
        'class-discardmortality.R' 'class-retention.R'
        'class-selectivity.R' 'class-advice.R' 'class-ages.R'
        'class-bioeconomic.R' 'class-catchability.R'
        'class-data-advice.R' 'class-data-catch.R' 'class-data-comp.R'
        'class-data-effort.R' 'class-data-exploitation.R'
        'class-data-indices.R' 'class-depletion.R' 'class-spatial.R'
        'class-srr.R' 'class-fecundity.R' 'class-maturity.R'
        'class-naturalmortality.R' 'class-weight.R' 'class-length.R'
        'class-stock.R' 'class-data-lifehistory.R'
        'class-refpointsMSY.R' 'class-data-reference.R' 'class-data.R'
        'class-effort.R' 'class-equilibrium.R' 'class-fleet.R'
        'class-popdynamics.R' 'class-reference.R' 'class-timeseries.R'
        'class-unfished.R' 'zz_Class_definitions.R'
        'class-stock-targeting.R' 'class-imp-slot.R' 'class-imp.R'
        'class-obs-comp.R' 'class-obs-indices.R' 'class-obs-catch.R'
        'class-obs-effort.R' 'class-obs-exploitation.R'
        'class-obs-lifehistory.R' 'class-obs.R' 'class-om.R'
        'class-hist.R' 'class-mse.R' 'class-perrecruit.R'
        'combine-fleet.R' 'combine-om.R' 'compare-bam.R'
        'compare-ss3.R' 'condition-obs-catch.R' 'condition-obs-comp.R'
        'condition-obs-effort.R' 'condition-obs-index.R'
        'condition-obs.R' 'constructor-advice.R' 'constructor-ages.R'
        'constructor-bioeconomic.R' 'constructor-catchability.R'
        'constructor-data-catch.R' 'generate-data-hist-sizecomp.R'
        'constructor-data-comp.R' 'constructor-data-effort.R'
        'constructor-data.R' 'constructor-depletion.R'
        'constructor-discardmortality.R' 'constructor-effort.R'
        'constructor-fecundity.R' 'constructor-fleet.R'
        'constructor-hist.R' 'constructor-imp-slot.R'
        'constructor-imp.R' 'constructor-length.R'
        'constructor-maturity.R' 'constructor-naturalmortality.R'
        'constructor-obs-catch.R' 'constructor-obs-comp.R'
        'constructor-obs-effort.R' 'constructor-obs-exploitation.R'
        'constructor-obs-indices.R' 'constructor-obs-lifehistory.R'
        'constructor-obs.R' 'constructor-om.R' 'constructor-ref-MSY.R'
        'constructor-retention.R' 'constructor-selectivity.R'
        'constructor-simcontrol.R' 'constructor-spatial.R'
        'constructor-srr.R' 'constructor-stock-targeting.R'
        'constructor-stock.R' 'constructor-weight.R' 'convert-data.R'
        'convert-fleet.R' 'convert-imp.R' 'convert-mom.R'
        'convert-mse-to-slick.R' 'convert-obs.R' 'convert-om.R'
        'convert-om2fleet.R' 'convert-om2imp.R' 'convert-om2obs.R'
        'convert-om2stock.R' 'convert-stock.R' 'zz_MOM_object.r'
        'convert.R' 'data-trim.R' 'example-fleet-asymp.R'
        'example-fleet-dome.R' 'example-obs-age-structured.R'
        'example-obs-catch-survey.R' 'example-obs-comm-fleet.R'
        'example-obs-data-rich.R' 'example-obs-length-structured.R'
        'example-om-complex.R' 'example-om-multistock.R'
        'example-om-seasonalspatial.R' 'example-om-singlestock.R'
        'example-om-two-fleet.R' 'example-stock-albacore.R'
        'example-stock-butterfish.R' 'example-stock-seasonalspatial.R'
        'examples-MPs.R' 'extract-F-timeseries.R'
        'extract-bio-timeseries.R' 'extract-catch-timeseries.R'
        'extract-effort.R' 'extract-number.R' 'extract-relative.R'
        'extract-unfished.R' 'find-model.R' 'fit-stock-targeting.R'
        'generate-data-hist-agecomp.R' 'generate-data-hist-catch.R'
        'generate-data-hist-effort.R' 'generate-data-hist-indices.R'
        'generate-data-hist.R' 'generate-data-proj-agecomp.R'
        'generate-data-proj-catch.R' 'generate-data-proj-effort.R'
        'generate-data-proj-helpers.R' 'generate-data-proj-indices.R'
        'generate-data-proj-sizecomp.R' 'generate-data-proj.R'
        'generate-hist-effort.R' 'generate-mean-at.R'
        'generate-multistock-recdevs.R' 'generate-rec-devs.R'
        'generate-residuals.R' 'generate-stock-targeting.R'
        'get-catch.R' 'helpers-data.R' 'helpers-mp.R' 'hist-to-mse.R'
        'import-bam-data.R' 'import-bam.R' 'import-ss3-data.R'
        'import-ss3-report.R' 'import-ss3.R' 'initialize-hist.R'
        'models-fecundity.R' 'models-length.R' 'models-maturity.R'
        'models-natural-mortality.R' 'models-retention.R'
        'models-selectivity.R' 'models-srr.R' 'models-weight.R'
        'models.R' 'mse-update.R' 'opt-effort-helpers.R'
        'opt-effort-multi-stock.R' 'opt-effort-single-stock.R'
        'opt-final-depletion.R' 'opt-ref-yield.R' 'populate-ASK.R'
        'populate-catchability.R' 'populate-classes.R'
        'populate-closure.R' 'populate-depletion.R'
        'populate-discard-mortality.R' 'populate-effort.R'
        'populate-fecundity.R' 'populate-fleet.R' 'populate-length.R'
        'populate-maturity.R' 'populate-mean-at-age.R'
        'populate-mean-at-length.R' 'populate-mean-at-weight.R'
        'populate-natural-mortality.R' 'populate-obs-catch.R'
        'populate-obs-comp.R' 'populate-obs-effort.R'
        'populate-obs-helpers.R' 'populate-obs-index.R'
        'populate-obs.R' 'populate-om.R' 'populate-random.R'
        'populate-retention.R' 'populate-selectivity.R'
        'populate-spatial.R' 'populate-srr.R' 'populate-stock.R'
        'populate-weight.R' 'populate.R' 'ppd-access.R' 'print.R'
        'process-eff-factor.R' 'project-hist.R' 'project-mp.R'
        'project.R' 'reduce-nSim.R' 'reduce.R' 'rename.R' 'reorder.R'
        'runMSE.R' 'set-seasonal-R0.R' 'show.R' 'simulate-om.R'
        'simulate.R' 'standardize-effort.R' 'subset.R'
        'todo-SProduction.R' 'todo-get-TACs.R' 'todo-mp-examples.R'
        'todo-plot-schedule.R' 'todo-plot.R'
        'todo-utils-access-timeseries.R' 'unit-conversions.R'
        'update-closure.R' 'update-discardmortality.R'
        'update-effort.R' 'update-object.R' 'update-selectivity.R'
        'update-tac-helpers.R' 'update-tac.R' 'util-accessors.R'
        'util-add-dimension.R' 'util-add-sim-number.R'
        'util-array-create.R' 'util-convert-to-list.R' 'util-dim.R'
        'util-get-metadata.R' 'utils-add-autocorrelation.R'
        'utils-add-dimnames.R' 'utils-add-year-dimnames.R'
        'utils-advice-null.R' 'utils-array-operations.R'
        'utils-array-to-df.R' 'utils-atage-to-atsize.R'
        'utils-atsize-to-atage.R' 'utils-calc-ageclasses.R'
        'utils-check-hist-misc.R' 'utils-cr2h.R'
        'utils-dirichlet-multinomial.R' 'utils-empty-object.R'
        'utils-extend-hist.R' 'utils-extend-om.R' 'utils-extend.R'
        'utils-fill-from-misc.R' 'utils-get_nSim.R' 'utils-helpers.R'
        'utils-identical-age.R' 'utils-identical-sim.R'
        'utils-join-year.R' 'utils-list-to-array.R' 'utils-load-args.R'
        'utils-log-mp-error.R' 'utils-log.R' 'utils-logs-delete.R'
        'utils-make-named-list.R' 'utils-misc.R'
        'utils-msy-accessors.R' 'utils-parallel.R'
        'utils-prep-hist-misc.R' 'utils-recycle-fleets.R'
        'utils-reverse-list.R' 'utils-save.R'
        'utils-set-age-dimnames.R' 'utils-slot-sizes.R'
        'utils-startup.R' 'utils-stocknames.R' 'utils-structure.R'
        'utils-transformation.R' 'utils-unique-years.R'
        'utils-valid-units.R' 'utils-wrapped-normal.R' 'vbiomass.R'
        'zz-project-Hist.R' 'zz_ASAP2OM.R' 'zz_Awatea2OM.R'
        'zz_BAM2OM.R' 'zz_B_Low_functions.R' 'zz_DFO.R' 'zz_Data2csv.R'
        'zz_Data_Functions.R' 'zz_Data_Plotting.R'
        'zz_Data_fit_index.R' 'zz_Data_make_update.R' 'zz_DocData.R'
        'zz_Empirical_MP.R' 'zz_Fease_Functions.R' 'zz_MICE_Rel.R'
        'zz_MMSE_Object.r' 'zz_MMSE_functions.R' 'zz_MMSE_plots.R'
        'zz_MOM_import.R' 'zz_MOM_plots.R' 'zz_MP_tuning.R'
        'zz_MPs_Reference.R' 'zz_MSC.R' 'zz_MSE_Plotting.R'
        'zz_MSE_Plotting_PMs.R' 'zz_MSE_functions.R'
        'zz_Misc_Exported.R' 'zz_Misc_Internal.R' 'zz_Movement_calcs.R'
        'zz_OM_Plotting.R' 'zz_OM_functions.R' 'zz_OM_import.R'
        'zz_OM_init_doc.R' 'zz_OM_plots.R' 'zz_PMobjects.R'
        'zz_PMtable.R' 'zz_Parallel.R' 'zz_SAM2OM.R' 'zz_SS2Data.R'
        'zz_SS2MOM.R' 'zz_SS2MOM_plots.R' 'zz_SS2OM.R'
        'zz_SSinternal.R' 'zz_SampleOM.R' 'zz_Sketch_Functions.R'
        'zz_Splot.R' 'zz_Turing.R' 'zz_VPA2OM.R' 'zz_WHAM2OM.R'
        'zz_aaImportFrom.R' 'zz_applyMMP.R' 'zz_data_documentation.R'
        'zz_iSCAM2OM.R' 'zz_multiMSE.R' 'zz_multiMSE_internal.R'
        'zz_multi_q_estimation.R' 'zz_popdyn.R' 'zz_popdynOneMICEDEV.R'
        'zz_popdyn_MICE.R' 'zz_runMSE.R' 'zz_simulate-OM.R'
        'zz_spatial_targ_opt.R' 'zz_utils.R'
Config/roxygen2/version: 8.0.0
RoxygenNote: 7.3.3
Config/pak/sysreqs: libicu-dev
Repository: https://blue-matter.r-universe.dev
Date/Publication: 2026-07-03 00:17:06 UTC
RemoteUrl: https://github.com/Blue-Matter/MSEtool
RemoteRef: HEAD
RemoteSha: 96820a97f20f6ada368fff1310cdee4d62c609ef
NeedsCompilation: yes
Packaged: 2026-07-03 01:23:11 UTC; root
Author: Adrian Hordyk [aut, cre],
  Quang Huynh [aut],
  Tom Carruthers [aut],
  Chris Grandin [ctb] (iSCAM functions)
Maintainer: Adrian Hordyk <adrian@bluematterscience.com>