Package: FIMS 0.3.0.1

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], Jon K. T. Brodziak [aut], Kathryn L. Doering [aut], Andrea M. Havron [aut], Ronald Klasky [aut], Peter T. Kuriyama [aut], Christopher M. Legault [aut], Bai Li [aut], Timothy J. Miller [aut], Cole C. Monnahan [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], Kristan Blackhart [ctb], James N. Ianelli [ctb]

FIMS_0.3.0.1.tar.gz

FIMS_0.3.0.1.tgz(r-4.4-x86_64)FIMS_0.3.0.1.tgz(r-4.4-arm64)FIMS_0.3.0.1.tgz(r-4.3-x86_64)FIMS_0.3.0.1.tgz(r-4.3-arm64)
FIMS_0.2.0.0.tar.gz(r-4.5-noble)FIMS_0.3.0.1.tar.gz(r-4.4-noble)
FIMS_0.3.0.1.tgz(r-4.4-emscripten)FIMS_0.3.0.1.tgz(r-4.3-emscripten)
FIMS.pdf |FIMS.html✨
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'))

Peer review:

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

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • data1 - FIMS input data frame

On CRAN:

cpp

5.63 score 19 stars 23 scripts 72 exports 36 dependencies

Last updated 14 hours agofrom:eca8095469. Checks:1 ERROR, 1 FAILURE, 4 WARNING. Indexed: no.

TargetResultLatest binary
Doc / VignettesFAILJan 17 2025
R-4.5-linux-x86_64OUTDATEDOct 24 2024
R-4.4-mac-x86_64WARNINGJan 17 2025
R-4.4-mac-aarch64WARNINGJan 17 2025
R-4.3-mac-x86_64WARNINGJan 17 2025
R-4.3-mac-aarch64WARNINGJan 17 2025

Exports:AgeCompBevertonHoltRecruitmentclearcreate_default_parametersCreateTMBModelDlnormDistributionDmultinomDistributionDnormDistributionDoubleLogisticSelectivityEWAAgrowthFIMSFitFIMSFramefinalizefit_fimsFleetget_agesget_dataget_end_yearget_estimatesget_fixedget_fleetsget_inputget_lengthsget_logget_log_errorsget_log_moduleget_log_warningsget_max_gradientget_n_agesget_n_lengthsget_n_yearsget_number_of_parametersget_objget_optget_outputget_randomget_reportget_sdreportget_start_yearget_timingget_versionIndexinitialize_data_distributioninitialize_fimsinitialize_process_distributionis.FIMSFitis.FIMSFitsLengthComplog_errorlog_infolog_warningLogisticMaturityLogisticSelectivitylognormalm_age_to_length_conversionm_agecompm_indexm_landingsm_lengthcompm_weight_at_ageMathmultinomialOpsParameterParameterVectorPopulationrun_gtestset_log_throw_on_errorsetup_and_run_gtestsetup_gtestSummaryupdate_parameters

Dependencies:clicolorspacedplyrfansifarvergenericsggplot2gluegtableisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpurrrR6RColorBrewerRcppRcppEigenrlangscalestibbletidyselectTMButf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Setter for 'Rcpp_ParameterVector'dim,Rcpp_ParameterVector-method length,Rcpp_ParameterVector-method sum,Rcpp_ParameterVector-method Summary,Rcpp_ParameterVector-method [,Rcpp_ParameterVector,numeric,ANY,ANY-method [<-,Rcpp_ParameterVector,ANY,ANY,ANY-method
Create default parameters for a FIMS modelcreate_default_parameters update_parameters
FIMS input data framedata1
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_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_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 FIMS modulesinitialize_fims
Should FIMS be verbose?is_fims_verbose
Check if an object is of class FIMSFitis.FIMSFit
Check if an object is a list of FIMSFit objectsis.FIMSFits
Distributions not available in the stats packagelognormal multinomial
Get a vector of data to be passed to a FIMS module from a FIMSFrame objectm_ m_agecomp m_agecomp,data.frame-method m_agecomp,FIMSFrame-method m_age_to_length_conversion m_age_to_length_conversion,data.frame-method m_age_to_length_conversion,FIMSFrame-method m_index m_index,data.frame-method m_index,FIMSFrame-method m_landings m_landings,data.frame-method m_landings,FIMSFrame-method m_lengthcomp m_lengthcomp,data.frame-method m_lengthcomp,FIMSFrame-method m_weight_at_age m_weight_at_age,data.frame-method m_weight_at_age,FIMSFrame-method
Sets methods for operators under the S4 Generic Group, OpsMath,Rcpp_ParameterVector-method Ops,numeric,Rcpp_Parameter-method Ops,numeric,Rcpp_ParameterVector-method Ops,Rcpp_Parameter,numeric-method Ops,Rcpp_Parameter,Rcpp_Parameter-method Ops,Rcpp_ParameterVector,numeric-method Ops,Rcpp_ParameterVector,Rcpp_ParameterVector-method
Run the google test suiterun_gtest
Setup and run the google test suitesetup_and_run_gtest
Set up your local environment to run the google tests locallysetup_gtest