Package: FishSET 2.0.1

Lisa Pfeiffer

FishSET: Spatial Economics Toolbox for Fisheries

The Spatial Economics Toolbox for Fisheries (FishSET) is a set of tools for organizing data; developing, improving and disseminating modeling best practices.

Authors:Lisa Pfeiffer [aut, cre], Paul G Carvalho [aut], Anna Abelman [aut], Alan Haynie [aut]

FishSET_2.0.1.tar.gz
FishSET_2.0.1.zip(r-4.7-x86_64)FishSET_2.0.1.zip(r-4.7-arm64)FishSET_2.0.1.zip(r-4.6-x86_64)FishSET_2.0.1.zip(r-4.6-arm64)FishSET_2.0.1.zip(r-4.5-x86_64)
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FishSET_2.0.1.tar.gz(r-4.7-arm64)FishSET_2.0.1.tar.gz(r-4.7-x86_64)FishSET_2.0.1.tar.gz(r-4.6-arm64)FishSET_2.0.1.tar.gz(r-4.6-x86_64)
FishSET_2.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
FishSET/json (API)

# Install 'FishSET' in R:
install.packages('FishSET', repos = c('https://nmfs-opensci.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/noaa-nwfsc/fishset/issues

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

On CRAN:

Conda:

economicslocation-choice-modelnwfsc-framcpp

6.80 score 9 stars 15 scripts 275 exports 133 dependencies

Last updated from:1bcd81c59c. Checks:10 NOTE, 1 ERROR, 4 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64NOTE280
linux-devel-x86_64NOTE320
source / vignettesERROR423
linux-release-arm64NOTE256
linux-release-x86_64NOTE310
macos-release-arm64NOTE257
macos-release-x86_64NOTE428
macos-oldrel-arm64OK279
macos-oldrel-x86_64OK441
windows-devel-arm64NOTE386
windows-devel-x86_64NOTE360
windows-release-arm64NOTE374
windows-release-x86_64NOTE280
windows-oldrel-x86_64OK300
wasm-releaseOK181

Exports:add_prompteragg_helperalt_choice_listangled_themeassignment_columnbboxbin_varbycatchcalc_trip_centroidcalc_trip_distancecatch_lmcategory_colscentroid_to_fsdbchange_classcheck_projcheck_spatdatchecklistchoose_directoryclose_namescombine_zoneconfid_cache_existscpuecreate_alternative_choicecreate_centroidcreate_dist_betweencreate_dist_between_for_guicreate_dist_matrixcreate_durationcreate_expectationscreate_mid_haulcreate_proj_settingscreate_seasonal_IDcreate_var_numcurrent_db_tablecurrent_logcurrent_outdat_to_sfdata_checkdata_pulldata_verificationdate_checkdate_colsdate_factorizedate_parserdate_time_parserdate_titledd2dmsdegreedelete_metadeleteButtonColumndensity_plotdeparse_namedms_to_dddms_to_pdmsdummy_matrixdummy_numedit_proj_settingsempty_varsempty_vars_filtererase_projectexp_catch_namesexpand_dataexpected_catch_listfilter_datfilter_summaryfilter_tablefind_catchfind_centroidfind_datetimefind_devfind_durationfind_firstfind_fishing_centroidfind_lastfind_latfind_lonfind_lonlatfind_original_namefind_portfind_projectfind_valuefishset_comparefishset_cvfishset_designfishset_fitfishset_iia_testfishset_tablesfishset_themefishset_viridisfit_ar_modelsfleet_assignfleet_tableformat_gridformat_model_datafreq_tablefunction_summaryget_closure_scenarioget_confid_cacheget_confid_checkget_grid_logget_latest_projectfileget_proj_settingsget_user_locoutputgetis_ord_statsgridcheckgroup_cumsumgroup_diffgroup_perchaul_to_tripID_varinsert_plotinsert_tableis_emptyis_value_emptyjitter_lonlatlag_zonelist_dirslist_htmllist_logslist_tableslist_to_htmlload_auxload_dataload_gridload_gui_variablesload_maindataload_outsampleload_portload_spatiallocloc_dataloc_docloc_maploc_metalocdatabaselocloglocoutputlocprojectlog_calllog_func_modellog_rerunlog_rerun_guilog_resetlogit_correctionlonlat_to_centroidmain_tablesmake_spat_areamap_kernelmap_plotmap_predicted_probsmerge_datmerge_expected_catchmeta_tablesmodel_design_listmodel_error_summarymodel_fitmodel_fit_summarymodel_out_summarymodel_out_viewmodel_paramsmodel_resid_corrmoran_statsmsg_printmvgrndn_breaksna_filternan_filternan_identifynew_zone_idnfreq_tablenum_breaksnumeric_colsorder_factoroutlier_boxplotoutlier_plotoutlier_plot_intoutlier_removeoutlier_tableparse_data_nameparse_notesparseDeleteEventperc_of_totalplot_formatplot_spatpolyvalpretty_labpretty_tabpretty_tab_sbprevious_locproj_settings_existsproject_existsproject_filesproject_logsproject_tablesprojectspull_logpull_metapull_notespull_outputpull_plotpull_shiny_outputpull_tableqaqc_helperquietly_testrandomize_lonlat_zonerandomize_value_rangerandomize_value_rowread_datrecast_multipolyremove_model_designreplace_sup_coderepmatreset_confid_cacheroll_catchrun_fishset_guirun_simulationsave_closure_scenariosave_datsave_nplotsave_ntablesave_plotsave_tableseasonalIDset_confid_checkset_quantsset_user_locoutputsimpleCapsimplify_listskewnesssparssparsetablesparsplotspat_qaqc_guispatial_histspatial_qaqcspatial_summaryspecies_catchsplit_checksplit_datsubset_datesubset_varsummarize_policy_effortsummarize_policy_welfaresummary_statssummary_tabletable_existstable_fieldstable_formattable_removetable_savetable_viewtables_databasetemp_obs_tabletemporal_modtext_filepathto_html_tabletrim_spaceunique_closureunique_filterunserialize_tableupdate_folderpathuse_promptervessel_countvgsubview_fleet_tableview_grid_datview_lon_latview_model_designview_spatweek_labellerweekly_catchweekly_effortwrite_datzone_closurezone_summary

Dependencies:askpassbase64encbitbit64bitopsblobbootbsiconsbslibcachemcellrangerclassclassIntclicliprcommonmarkcpp11crayoncrosstalkcurldata.tableDBIdeldirdigestdplyrDTe1071evaluatefarverfastmapfontawesomeFormulafsgenericsgeosphereggplot2gluegridExtragtablehighrhmshtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonlitekableExtraKernSmoothknitrlabelinglaterlatticelazyevalleafletleaflet.providerslifecyclelubridatelwgeommagrittrMASSMatrixmemoisemimeopensslopenxlsxotelpanderpillarpkgconfigplotlypngprettyunitsprogresspromisesprompterproxypurrrR6rappdirsrasterRColorBrewerRcppRcppEigenRCurlreadrreadxlrematchrlangrmarkdownRSQLiterstudioapiRTMBs2S7sassscalessfshinyshinycssloadersshinyjssourcetoolsspspDataspdepstringistringrsvglitesyssystemfontsterratextshapingtibbletidyrtidyselecttimechangetinytexTMBtzdbunitsutf8vctrsviridisLitevroomwithrwkxfunxml2xtableyamlzipzoo

Scallop End-to-End Workflow
Overview | Setup and data loading | Quality assurance and quality control | Prepare and format data | Model design and fit | Model diagnostics and validation | Reproducibility
Rendered fromscallop_trip_vignette.Rmdusingknitr::rmarkdown

Last update: 2026-09-28
Started: 2026-07-22

FishSET GUI Quickstart Guide
Rendered fromFishSET_GUI_Quickstart_Guide.Rmdusingknitr::rmarkdown

Last update: 2026-08-06
Started: 2022-04-25

Create and Integrate Your Custom Model
Introduction | Development guidelines | Step 1: Extract Formatted Data | Step 2: Mock the Design Object | Step 3: Write the RTMB Objective Function | Template: Custom Objective Function | Step 4: Integrate and Submit
Rendered fromlikelihood-template.Rmdusingknitr::rmarkdown

Last update: 2026-08-04
Started: 2024-11-13

Making a spatial grid file
Load packages | Create a spatial grid | Add zone ID variable to the spatial object | Plot | Save spatial grid | Reassign zone ID in primary data
Rendered frommaking_a_spatial_grid.Rmdusingknitr::rmarkdown

Last update: 2026-08-04
Started: 2024-08-07

Readme and manuals

Help Manual

Help pageTopics
Aggregating functionagg_helper
Get Alternative Choice Listalt_choice_list
Set x-axis labels to 45 degreesangled_theme
Assign observations to fishing zonesassignment_column
Creates numeric variables divided into equal sized groupsbin_var
Compare bycatch CPUE and total catch/percent of total catch for one or more speciesbycatch
Calculate trip centroid variablecalc_trip_centroid
Calculate Trip Distancecalc_trip_distance
Linear Model for Catchcatch_lm
Save Primary Table's Centroid Columns to FishSET Databasecentroid_to_fsdb
Change variable data classchange_class
Check and correct spatial data formatcheck_spatdat
Retrieve closure scenario namesclose_names
Combine zone and closure areacombine_zone
Confidentialy cache existsconfid_cache_exists
Create catch or revenue per unit effort variablecpue
Define alternative fishing choicecreate_alternative_choice
Create Centroid Tablecreate_centroid
Interactive application to create distance between points variablecreate_dist_between
Create distance between points variable - non-interactive versioncreate_dist_between_for_gui
Create duration of time variablecreate_duration
Create expected catch/expected revenue matrixcreate_expectations
Creates haul midpoint latitude and longitude variablescreate_mid_haul
Create fishery season identifier variablecreate_seasonal_ID
Create numeric variable using arithmetic expressioncreate_var_num
Convert dataframe to sfdat_to_sf
Check for common data quality issuesdata_check
Upload data from file, FishSET DB, or working environmentdata_upload_helper
Check and convert lat/lon to decimal degreesdegree
Delete table meta data or project meta filedelete_meta
Create KDE, CDF, or empirical CDF plotsdensity_plot
Create dummy matrix from a coded ID variabledummy_matrix
Create a binary vector from numeric, date, and character or factor vectors.dummy_num
Check variables are not emptyempty_vars_filter
Return names of expected catch matricesexp_catch_names
Get Expected Catch Listexpected_catch_list
Remove rows based on filter expressions defined in 'filterTable'filter_dat
Define and store filter expressionsfilter_table
Identify geographic centroid of fishery management or regulatory zonefind_centroid
Create fishing or weighted fishing centroidfind_fishing_centroid
Compare imported data table to the previously saved version of the data tablefishset_compare
K-Fold Cross Validation for FishSET Modelsfishset_cv
Create FishSET Model Design Objectfishset_design
Fit FishSET Discrete Choice Modelfishset_fit
Hausman-McFadden Test for IIAfishset_iia_test
Show all SQL Tables in FishSET Folderfishset_tables
Create fleet variable using fleet definition tablefleet_assign
Define and store fleet expressionsfleet_table
Format Gridded Dataformat_grid
Format Model Dataformat_model_data
Display summary of function callsfunction_summary
Retrieve closure scenario by projectget_closure_scenario
Return cached confidentiality tablesget_confid_cache
Return the confidentiality settingsget_confid_check
Retrieve grid log fileget_grid_log
Pull data from latest project fileget_latest_projectfile
Retrieve project settingsget_proj_settings
Calculate and view Getis-Ord statisticgetis_ord_stats
Create a within-group running sum variablegroup_cumsum
Create a within-group lagged difference variablegroup_diff
Create a within-group percentage variablegroup_perc
Collapse a data frame from haul-level to trip-levelhaul_to_trip
Create ID variableID_var
Insert plot from user folderinsert_plot
Insert table from user folderinsert_table
Jitter longitude and latitude variablesjitter_lonlat
Lag zone variablelag_zone
View list of all log fileslist_logs
Display FishSET database tables by typelist_tables
Import, parse, and save auxiliary data to FishSET databaseload_aux
Load data from FishSET database into the R environmentload_data
Import, parse, and save gridded data to FishSET databaseload_grid
load_gui_variablesload_gui_variables
Import, parse, and save data to the FishSET Databaseload_maindata
Import, parse, and save out-of-sample data to FishSET databaseload_outsample
Import, parse, and save port data to FishSET databaseload_port
Import, parse, and save spatial dataload_spatial
Log user-created functions or modelslog_func_model
Console function for rerunning project loglog_rerun
Interactive function for rerunning project loglog_rerun_gui
Reset log filelog_reset
Full information model with Dahl's correction functionlogit_correction
Assign longitude and latitude points to zonal centroidlonlat_to_centroid
View list of MainDataTables in FishSET databasemain_tables
Add an area/polygon to spatial datamake_spat_area
Kernel density (hotspot) plotmap_kernel
Map observed vessel locationsmap_plot
Map FishSET Predicted Probabilitiesmap_predicted_probs
Merge data tables using a left joinmerge_dat
Merge expected catchmerge_expected_catch
Print meta tables by project and/or typemeta_tables
Get Model Design Listmodel_design_list
Load model comparison metrics to console for the defined projectmodel_fit
Load discrete choice model output to console for the defined projectmodel_out_view
Load model parameter estimates, standard errors, and t-statistic to console for the defined projectmodel_params
Check Spatial Autocorrelation of Model Residualsmodel_resid_corr
Calculate Moran's I statisticmoran_stats
Identify, remove, or replace NAs and NaNsna_filter
Check for unique and syntatcic column namesname_check
Identify, remove, or replace NaNsnan_filter
Identify NaNs and NAsnan_identify
Create one or more binned frequency tablesnfreq_table
Shape file for NMFS fishing zonesnmfs_manage_simple.json
Boxplot to assess outliersoutlier_boxplot
Evaluate outliers in plot formatoutlier_plot
Remove outliers from data tableoutlier_remove
Evaluate outliers in Dataoutlier_table
Selectively display a note sectionparse_notes
Plot spatial datasetplot_spat
Plot FishSET Spatial Residualsplot.fishset_spatial_resid
Format numbers in tablepretty_lab
Format table for R Markdownpretty_tab
Scroll box for R Markdown tablepretty_tab_sb
Create Previous Location/Area Variableprevious_loc
Print FishSET Cross Validation Resultsprint.fishset_cv
Print FishSET Model Fit Resultsprint.fishset_fit
Print Hausman-McFadden IIA Test Resultsprint.fishset_iia
Print FishSET Spatial Residualsprint.fishset_spatial_resid
Check if option file exists for a projectproj_settings_exists
List output files by project nameproject_files
List logs by projectproject_logs
Display database table names by projectproject_tables
Display projects namesprojects
Retrieve/display meta data by projectpull_meta
Pull notes from output folderpull_notes
Retrieve output file name by project, function, and typepull_output
Import and format plots to notebook filepull_plot
Import and format table to notebook filepull_table
Randomize latitude and longitude points by zonerandomize_lonlat_zone
Randomize variable value by percentage rangerandomize_value_range
Randomize value between rowsrandomize_value_row
Import data from local file directory or webpage into the R environmentread_dat
Remove a model design from list in ModelInputData tableremove_model_design
Replace suppression codereplace_sup_code
Reset confidentiality cache tablesreset_confid_cache
Apply moving average function to catchroll_catch
Guided user interface for FishSET functionsrun_fishset_gui
Run Policy and Data Simulationsrun_simulation
Save modified primary data table to FishSET databasesave_dat
Northeast Scallop Datascallop
Ports from the NE scallop fisheryscallop_ports
Create single binary fishery season identifier variableseasonalID
Set confidentiality parametersset_confid_check
Create factor variable from quantilesset_quants
Set user folder directoryset_user_locoutput
Evaluate sparsity in data over time in table formatsparsetable
Evaluate sparsity in data over time in plot formatsparsplot
GUI for spatial data checksspat_qaqc_gui
Histogram of latitude and longitude by grouping variablespatial_hist
Spatial data quality checksspatial_qaqc
Summarize variable over data and timespatial_summary
Summarize species catchspecies_catch
Separate secondary data table from MainDataTablesplit_dat
Summarize and Plot Policy Effort Redistributionsummarize_policy_effort
Summarize and Plot Policy Welfare Impactssummarize_policy_welfare
View summary statisticssummary_stats
Check if table exists in the FishSET database for the defined projecttable_exists
Lists fields for FishSET database tabletable_fields
Remove table from FishSET databasetable_remove
Save an existing FishSET DB tabletable_save
View FishSET Database tabletable_view
View names of project tablestables_database
Number of observations by temporal unittemp_obs_table
Transform units of date variablestemporal_mod
Northeast Ten Minute SquarestenMNSQR
Check rows are uniqueunique_filter
Summarize active vesselsvessel_count
View the most recent fleet table by projectview_fleet_table
Visualize gridded data on a mapview_grid_dat
Viewview_lon_lat
View model design file in databaseview_model_design
View interactive map of spatial dataview_spat
Summarize weekly catchweekly_catch
Summarize average CPUE by weekweekly_effort
Northeast wind closure areaswindLease
Write a data table to local file directorywrite_dat
Define zone closure scenarioszone_closure
Summarize zones, closure areaszone_summary