Package: FIMS 0.9.3.9000

Kelli F. Johnson

FIMS: The Fisheries Integrated Modeling System

The Fisheries Integrated Modeling System is a next-generation framework of stock assessment models, assisting fishery managers with the goal of achieving sustainable fisheries. This system, when completed in a few years, offers the NOAA Fisheries and global fisheries science communities an advanced set of stock assessment models. These tools can be used separately or in combination to incorporate ecosystem and socioeconomic data and models, as well as climate effects and other drivers within the marine environment, into stock assessment models.

Authors:Kelli F. Johnson [aut, cre], Grant D. Adams [aut], Jon K. T. Brodziak [aut], Kathryn L. Doering [aut], Daniel R. Goethel [aut], Andrea M. Havron [aut], Ronald Klasky [aut], Peter T. Kuriyama [aut], Emily M. Liljestrand [aut], Christopher M. Legault [aut], Bai Li [aut], Timothy J. Miller [aut], Cole C. Monnahan [aut], Elizabeth F. Perl [aut], Megumi C. Oshima [aut], Kyle W. Shertzer [aut], Christine C. Stawitz [aut], Jane Y. Sullivan [aut], Matthew Supernaw [aut], Ian G. Taylor [aut], Nathan R. Vaughan [aut], Erik H. Williams [aut], Adrianne T. Wilson [aut], Kristan Blackhart [ctb], Edward J. Dick [ctb], James N. Ianelli [ctb], Huihua Lee [ctb]

FIMS_0.9.3.9000.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
FIMS/json (API)
NEWS

# Install 'FIMS' in R:
install.packages('FIMS', repos = c('https://noaa-fisheries-integrated-toolbox.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/noaa-fims/fims/issues

Pkgdown/docs site:https://noaa-fims.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

noaa-nsapstock-assessmentcpp

8.98 score 36 stars 75 scripts 83 exports 32 dependencies

Last updated from:8f4f488515. Checks:11 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
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linux-devel-x86_64WARNING2148
source / vignettesOK639
linux-release-arm64WARNING1267
linux-release-x86_64WARNING2013
macos-release-arm64WARNING1543
macos-release-x86_64WARNING3596
macos-oldrel-arm64WARNING1742
macos-oldrel-x86_64WARNING2850
windows-develWARNING2653
windows-releaseWARNING2692
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wasm-releaseOK554

Exports:AgeCompBevertonHoltRecruitmentCatchAtAgeclearcreate_default_configurationscreate_default_parametersCreateTMBModelDlnormDistributionDmultinomDistributionDnormDistributionDoubleLogisticSelectivityEWAAGrowthFIMSFitFIMSFramefit_fimsFleetget_agesget_dataget_end_yearget_estimatesget_fixedget_fleetsget_inputget_lengthsget_logget_log_errorsget_log_warningsget_max_gradientget_model_outputget_n_agesget_n_fleetsget_n_lengthsget_n_yearsget_number_of_parametersget_objget_optget_parameter_namesget_randomget_random_namesget_reportget_sdreportget_start_yearget_timingget_versionIndexinitialize_data_distributioninitialize_fimsinitialize_process_distributioninitialize_process_structureinv_logitis.FIMSFitLandingsLengthComplog_errorlog_infolog_warningLogDevsRecruitmentProcessLogisticMaturityLogisticSelectivitylogitlognormalLogRRecruitmentProcessMathmodel_age_compmodel_age_to_length_conversionmodel_indexmodel_landingsmodel_length_compmodel_weight_at_agemultinomialOpsParameterParameterVectorplotPopulationRealVectorset_fixedset_log_throw_on_errorset_randomSharedIntSharedRealSharedStringSummary

Dependencies:clicpp11dplyrfarvergenericsggplot2gluegtableisobandjsonlitelabelinglatticelifecyclemagrittrMatrixpillarpkgconfigpurrrR6RColorBrewerRcppRcppEigenrlangS7scalestibbletidyselectTMButf8vctrsviridisLitewithr

Adding a New C++ Module

Rendered fromadding-new-module.Rmdusingknitr::rmarkdownon Jun 19 2026.

Last update: 2026-06-01
Started: 2026-03-18

FIMS Path: Maturity

Rendered fromfims-path-maturity.Rmdusingknitr::rmarkdownon Jun 19 2026.

Last update: 2026-03-16
Started: 2023-07-11

FIMS User Setup Guide

Rendered fromfims-user-setup-guide.Rmdusingknitr::rmarkdownon Jun 19 2026.

Last update: 2026-01-16
Started: 2026-01-16

Intro to C++

Rendered fromtraining-intro-cpp.Rmdusingknitr::rmarkdownon Jun 19 2026.

Last update: 2026-06-19
Started: 2026-01-16

Intro to Rcpp

Rendered fromtraining-intro-rcpp.Rmdusingknitr::rmarkdownon Jun 19 2026.

Last update: 2026-06-19
Started: 2026-01-16

Introducing FIMS input data

Rendered fromfims-input-data.Rmdusingknitr::rmarkdownon Jun 19 2026.

Last update: 2026-06-01
Started: 2026-03-25

Introducing the Fisheries Integrated Modeling System (FIMS)

Rendered fromfims-demo.Rmdusingknitr::rmarkdownon Jun 19 2026.

Last update: 2026-03-29
Started: 2023-07-11

RE Sparsity

Rendered fromRD-re-sparsity.Rmdusingknitr::rmarkdownon Jun 19 2026.

Last update: 2026-05-11
Started: 2026-01-20

Simple projections using FIMS

Rendered fromfims-demo-projections.Rmdusingknitr::rmarkdownon Jun 19 2026.

Last update: 2026-06-18
Started: 2026-01-20

Readme and manuals

Help Manual

Help pageTopics
C++ Classes Exported via RcppAgeComp BevertonHoltRecruitment CatchAtAge Cpp_classes DlnormDistribution DmultinomDistribution DnormDistribution DoubleLogisticSelectivity EWAAGrowth Fleet Index Landings LengthComp LogDevsRecruitmentProcess LogisticMaturity LogisticSelectivity LogRRecruitmentProcess Parameter ParameterVector Population RealVector SharedInt SharedReal SharedString
C++ Functions Exported via Rcppclear Cpp_functions CreateTMBModel get_fixed get_log get_log_errors get_log_warnings get_parameter_names get_random get_random_names inv_logit logit log_error log_info log_warning set_fixed set_log_throw_on_error set_random
Create a default FIMS configuration tibblecreate_default_configurations
Create default parameters for a FIMS modelcreate_default_parameters
FIMS input data framedata_big
Vector of acceptable FIMS input typesfims_input_types
Class constructors for class 'FIMSFit' and associated child classesFIMSFit
Class constructors for 'FIMSFrame' and associated child classesFIMSFrame
Fit a FIMS model (BETA)fit_fims
Get a slot in a FIMSFit objectget_estimates get_estimates,FIMSFit-method get_FIMSFit get_input get_input,FIMSFit-method get_max_gradient get_max_gradient,FIMSFit-method get_model_output get_model_output,FIMSFit-method get_number_of_parameters get_number_of_parameters,FIMSFit-method get_obj get_obj,FIMSFit-method get_opt get_opt,FIMSFit-method get_report get_report,FIMSFit-method get_sdreport get_sdreport,FIMSFit-method get_timing get_timing,FIMSFit-method get_version get_version,FIMSFit-method
Get a slot in a FIMSFrame objectget_ages get_ages,data.frame-method get_ages,FIMSFrame-method get_data get_data,data.frame-method get_data,FIMSFrame-method get_end_year get_end_year,data.frame-method get_end_year,FIMSFrame-method get_FIMSFrame get_fleets get_fleets,data.frame-method get_fleets,FIMSFrame-method get_lengths get_lengths,data.frame-method get_lengths,FIMSFrame-method get_n_ages get_n_ages,data.frame-method get_n_ages,FIMSFrame-method get_n_fleets get_n_fleets,data.frame-method get_n_fleets,FIMSFrame-method get_n_lengths get_n_lengths,data.frame-method get_n_lengths,FIMSFrame-method get_n_years get_n_years,data.frame-method get_n_years,FIMSFrame-method get_start_year get_start_year,data.frame-method get_start_year,FIMSFrame-method
Set up a new distribution for a data type or a processinitialize_data_distribution initialize_process_distribution initialize_process_structure
Initialize C++ modules via Rcpp for a FIMS modelinitialize_fims
Should FIMS be verbose?is_fims_verbose
Check if an object is of class FIMSFitis.FIMSFit
Distributions not available in the stats packagelognormal multinomial
Get a vector of data to be passed to a FIMS module from a FIMSFrame objectmodel_ model_age_comp model_age_comp,data.frame-method model_age_comp,FIMSFrame-method model_age_to_length_conversion model_age_to_length_conversion,data.frame-method model_age_to_length_conversion,FIMSFrame-method model_index model_index,data.frame-method model_index,FIMSFrame-method model_landings model_landings,data.frame-method model_landings,FIMSFrame-method model_length_comp model_length_comp,data.frame-method model_length_comp,FIMSFrame-method model_weight_at_age model_weight_at_age,data.frame-method model_weight_at_age,FIMSFrame-method
Plot a 'FIMSFrame' objectplot,FIMSFrame,missing-method
Remove test dataremove_test_data
Reshape JSON estimatesreshape_json_estimates
Reshape TMB estimatesreshape_tmb_estimates
Run the google test suiterun_gtest
Run R integration testsrun_r_integration_tests
Run R unit testsrun_r_unit_tests
Setup and run the google test suitesetup_and_run_gtest
Set up your local environment to run the google tests locallysetup_gtest
Create tests/google_benchmark/benchmark_*.cpp and register it in CMakeLists.txtuse_google_benchmark_template
Create tests/gtest/test_*.cpp test file and register it in CMakeLists.txtuse_gtest_template
Create tests/testthat/test-*.R test fileuse_testthat_template