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) ). License: GPL-3 Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) Depends: R (>= 4.4.0) Imports: abind, cli, digest, dplyr (>= 1.1.0), ggplot2, grDevices, lifecycle, lubridate, methods, parallel, patchwork, 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, snowfall, spict, testthat, tibble, tidyr, TMB, usethis LinkingTo: Rcpp, RcppArmadillo Remotes: DTUAqua/spict/spict BugReports: https://github.com/Blue-Matter/MSEtool/issues URL: https://msetool.openmse.com/ Collate: 'MSEtool-package.R' 'RcppExports.R' 'add-fleet.R' 'add-index.R' 'adjust-seasonal-fecundity.R' 'calc-advice.R' 'calc-age-size-key.R' 'calc-asymptotic-distribution.R' 'calc-blow.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-mgt.R' 'calc-mice.R' 'calc-msy-cpp.R' 'calc-msy.R' 'calc-per-recruit.R' 'calc-pm.R' 'calc-ref-points.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-data-catch.R' 'check-effort-allocation.R' 'check-fleet-allocation.R' 'check-misc.R' 'check-mse-run.R' 'check-obs.R' 'check-om.R' 'check-package.R' 'check-seasonal-allocation.R' 'class-unions.R' 'class-discardmortality.R' 'class-retention.R' 'class-selectivity.R' 'class-advice.R' 'class-ages.R' 'class-aggbaglimit.R' 'class-bioeconomic.R' 'class-catchability.R' 'class-refpointsMSY.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.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-stocktransition.R' 'class-stock-targeting.R' 'class-imp-slot.R' 'class-imp.R' 'class-obs.R' 'class-om.R' 'class-hist.R' 'class-mse.R' 'class-perrecruit.R' 'class-pm.R' 'class-tune.R' 'collapse-seasons.R' 'combine-fleet-allocation.R' 'combine-fleet-settings.R' 'combine-fleet.R' 'combine-mse.R' 'combine-om.R' 'compare-assessment.R' 'compare-bam.R' 'compare-iscam.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-aggbaglimit.R' 'constructor-bioeconomic.R' 'constructor-catchability.R' 'generate-data-hist-sizecomp.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.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-stocktransition.R' 'constructor-weight.R' 'convert-data.R' 'convert-fleet.R' 'convert-imp.R' 'convert-legacy-mp.R' 'convert-mom.R' 'convert-mse-to-slick.R' 'convert-obs.R' 'convert-om.R' 'convert-om2fleet.R' 'convert-om2stock.R' 'convert-stock.R' 'zz_MOM_object.r' 'convert.R' 'data-trim.R' 'doc-om-control.R' 'example-MPs.R' 'example-fleet.R' 'example-imp.R' 'example-obs.R' 'example-om-herm.R' 'example-om.R' 'example-stock.R' 'extract-F-timeseries.R' 'extract-advice.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-sp-spict.R' 'fit-sp.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-index-timing.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-iscam-data.R' 'import-iscam.R' 'import-ss3-data.R' 'import-ss3-report.R' 'import-ss3.R' 'import-wham.R' 'index-nominal.R' 'initialize-hist.R' 'interim-advice.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' 'mp-args.R' 'mp-empirical-index.R' 'mp-hockeystickHCR.R' 'mp-reference.R' 'mp-surplus-production.R' 'mp-utils.R' 'mse-update.R' 'opt-effort-choke.R' 'opt-effort-helpers.R' 'opt-effort-single-stock.R' 'opt-final-depletion.R' 'opt-ref-yield.R' 'opt-targeting-helpers.R' 'opt-targeting-multi-stock.R' 'plot-alk.R' 'plot-awk.R' 'plot-catchability.R' 'plot-closure.R' 'plot-comp.R' 'plot-data.R' 'plot-depletion.R' 'plot-fleet.R' 'plot-hist.R' 'plot-index-fit.R' 'plot-recdevs.R' 'plot-schedule.R' 'plot-spatial.R' 'plot-srr.R' 'plot-stock.R' 'pm-years.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-imp.R' 'populate-length.R' 'populate-maturity.R' 'populate-mean-at.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' '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' 'summarize-convergence.R' 'tune-mp.R' 'unit-conversions.R' 'update-baglimit.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-array-create.R' 'util-convert-to-list.R' 'util-dim.R' 'util-get-metadata.R' 'utils-add.R' 'utils-advice-null.R' 'utils-array-operations.R' 'utils-array-to-df.R' 'utils-atage-atsize.R' 'utils-calc-ageclasses.R' 'utils-check-hist-misc.R' 'utils-cli.R' 'utils-compdata.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-herm.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-management-schedule-table.R' 'utils-misc.R' 'utils-msy-accessors.R' 'utils-parallel.R' 'utils-prep-hist-misc.R' 'utils-recycle-fleets.R' 'utils-refpoints-accessors.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-unit-conversion.R' 'utils-valid-units.R' 'utils-wrapped-normal.R' 'validate-shift.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_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_fit-sr.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_project_Hist.R' 'zz_runMSE.R' 'zz_simulate-OM.R' 'zz_spatial_targ_opt.R' 'zz_utils.R' Config/roxygen2/version: 8.1.0 Config/testthat/edition: 3 Config/pak/sysreqs: libicu-dev Repository: https://blue-matter.r-universe.dev Date/Publication: 2026-10-14 19:08:35 UTC RemoteUrl: https://github.com/Blue-Matter/MSEtool RemoteRef: HEAD RemoteSha: 6b7de16184960a13e20a5d7397a0b999029611a7 NeedsCompilation: yes Packaged: 2026-10-14 22:52:14 UTC; root Author: Adrian Hordyk [aut, cre], Quang Huynh [aut], Tom Carruthers [aut], Chris Grandin [ctb] (iSCAM functions) Maintainer: Adrian Hordyk