Package: FishSET 1.1.0

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], Min-Yang Lee [aut], Melanie Harsch [aut], Bryce McManus [aut], Alan Haynie [aut]

FishSET_1.1.0.tar.gz
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 |FishSET.html✨
FishSET/json (API)

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

Peer review:

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

Datasets:

On CRAN:

economicslocation-choice-modelnwfsc-fram

6.63 score 4 stars 12 scripts 345 exports 140 dependencies

Last updated 5 days agofrom:8006601232. Checks:ERROR: 1 WARNING: 6. Indexed: no.

TargetResultDate
Doc / VignettesFAILNov 13 2024
R-4.5-winWARNINGNov 13 2024
R-4.5-linuxWARNINGNov 13 2024
R-4.4-winWARNINGNov 13 2024
R-4.4-macWARNINGNov 13 2024
R-4.3-winWARNINGNov 13 2024
R-4.3-macWARNINGNov 13 2024

Exports:aboutUIaccumarrayadd_prompteradd_varsagg_helperalt_choice_listangled_themeassignment_columnbboxbin_varbycatchcatch_lmcategory_colscentroid_to_fsdbchange_classcheck_model_datacheck_projcheck_spatdatchecklistchoose_directoryclose_namescol_desccolDescUIcombine_zoneconfid_cache_existscontactUIcorr_outcorr_plotcpuecreate_alternative_choicecreate_centroidcreate_dist_betweencreate_dist_between_for_guicreate_dist_matrixcreate_durationcreate_expectationscreate_logit_inputcreate_mid_haulcreate_model_inputcreate_proj_settingscreate_seasonal_IDcreate_startingloccreate_trip_centroidcreate_trip_distancecreate_var_numcross_validationcurrent_db_tablecurrent_logcurrent_outdat_to_sfdata_checkdata_pulldata_verificationdate_checkdate_colsdate_factorizedate_parserdate_time_parserdate_titledd2dmsdegreedelete_metadelete_modelsdeleteButtonColumndensity_plotdeparse_namediscretefish_subroutinedms_to_dddms_to_pdmsdummy_matrixdummy_numdummy_varedit_proj_settingsempty_metaempty_meta_listempty_varsempty_vars_filterepm_lognormalepm_normalepm_predictepm_weibullerase_projectexp_catch_namesexpand_dataexpected_catch_listexplore_startparamsexplore_startparams_discretefilter_datfilter_outsamplefilter_summaryfilter_tablefind_catchfind_centroidfind_datetimefind_devfind_durationfind_firstfind_fishing_centroidfind_lastfind_latfind_lonfind_lonlatfind_original_namefind_portfind_projectfind_valuefishset_comparefishset_tablesfishset_themefishset_viridisfleet_assignfleet_tableformat_gridformat_outsample_coefsfreq_tablefunction_summaryget_closure_scenarioget_confid_cacheget_confid_checkget_grid_logget_latest_projectfileget_proj_settingsget_user_locoutputgetis_ord_statsglobalcheck_viewgridcheckgroup_cumsumgroup_diffgroup_perchaul_to_tripID_varinsert_plotinsert_tableis_emptyis_value_emptyjitter_lonlatlist_dirslist_htmllist_logslist_tableslist_to_htmlload_auxload_dataload_gridload_maindataload_outsampleload_portload_spatiallocloc_dataloc_docloc_maploc_metalocdatabaselocloglocoutputlocprojectlog_calllog_func_modellog_rerunlog_rerun_guilog_resetlogit_clogit_correctionlogit_predictlogit_zonallong_expectationslonlat_to_centroidmain_tablesmake_model_designmake_spat_areamap_kernelmap_plotmap_viewermedium_expectationsmerge_datmerge_expected_catchmeta_file_existsmeta_listmeta_log_callmeta_tablesmetaColLayoutServmetaColLayoutUImetaCreateLoadServmetaCreateProjServmetaCreateSaveUImetaCreateServmetadata_guimetaDeleteServmetaDeleteUImetaEditLoadServmetaEditProjServmetaEditSaveUImetaEditServmetaOutmetaRawOutmetaRawServmetaRawUImetaSaveServmixed_logit_predictmodel_design_listmodel_design_outsamplemodel_error_summarymodel_fitmodel_fit_summarymodel_namesmodel_out_summarymodel_out_viewmodel_paramsmodel_predictionmoran_statsmsg_printmvgrndn_breaksna_filternan_filternan_identifynew_zone_idnfreq_tablenum_breaksnumeric_colsorder_factoroutlier_boxplotoutlier_plotoutlier_plot_intoutlier_removeoutlier_tableparse_data_nameparse_metaparse_meta_delimparse_meta_excelparse_meta_jsonparse_meta_xmlparse_notesparseDeleteEventperc_of_totalplot_formatplot_spatpolicy_metricspolyvalpred_prob_outputspredict_mappredict_outsamplepredict_probabilitypretty_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_policysave_closure_scenariosave_datsave_nplotsave_ntablesave_plotsave_raw_metasave_tableseasonalIDselect_modelselect_varsset_confid_checkset_quantsset_user_locoutputshift_sort_xshort_expectationssim_welfaresimpleCapsimplify_listskewnesssparssparsetablesparsplotspat_qaqc_guispatial_histspatial_qaqcspatial_summaryspecies_catchsplit_checksplit_datsubset_datesubset_varsummary_statssummary_tabletable_existstable_fieldstable_formattable_removetable_savetable_viewtables_databasetemp_obs_tabletemp_plottemp_plot_helpertemporal_modtext_filepathto_html_tabletrim_spacetrip_dur_outtrip_duration_plotunique_closureunique_filterunserialize_tableupdate_folderpathuse_promptervessel_countvgsubview_fleet_tableview_grid_datview_lon_latview_model_designview_spatweek_labellerweekly_catchweekly_effortwelfare_outputswelfare_predictwrite_datxy_plotzone_closurezone_summary

Dependencies:askpassbase64encbigDbitbit64bitopsblobbootbsiconsbslibcachemcellrangerclassclassIntclicliprcolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdeldirdigestdplyrDTe1071evaluatefansifarverfastmapfontawesomefsgenericsgeosphereggplot2gluegridExtragtgtablehighrhmshtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonlitejuicyjuicekableExtraKernSmoothknitrlabelinglaterlatticelazyevalleafletleaflet.providerslifecyclelubridatemagrittrmarkdownMASSMatrixmemoisemgcvmimemunsellnlmeopensslopenxlsxpanderpillarpkgconfigplogrplotlypngprettyunitsprogresspromisesprompterproxypurrrR6rappdirsrasterRColorBrewerRcppRCurlreactablereactRreadrreadxlrematchrlangrmarkdownRSQLiterstudioapis2sassscalesservrsfshinyshinycssloadersshinyjsshinyWidgetssourcetoolsspspDataspdepstringistringrsvglitesyssystemfontsterratibbletidyrtidyselecttimechangetinytextzdbunitsutf8V8vctrsviridisLitevroomwithrwkxfunxml2xtableyamlzipzoo

Create your own likelihood function

Paul Carvalho

Rendered fromlikelihood-template.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2024-11-13
Started: 2024-11-13

FishSET GUI Quickstart Guide

Rendered fromFishSET_GUI_Quickstart_Guide.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2024-08-07
Started: 2022-04-25

FishSET R package functions

Rendered fromFishSET_FunctionList.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2024-04-22
Started: 2020-04-22

Making a spatial grid file

Paul Carvalho

Rendered frommaking_a_spatial_grid.Rmdusingknitr::rmarkdownon Nov 13 2024.

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

Scallop Conditional Logit Model Example

Bryce McManus

Rendered fromscallop-mod-example.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2024-04-30
Started: 2023-06-02

Scallop Example

Rendered fromscallop-example.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2024-04-24
Started: 2022-11-28

Readme and manuals

Help Manual

Help pageTopics
Add removed variables back into dataset - non-interactive versionadd_vars
Add removed variables back into datasetadd_vars_gui
Aggregating functionagg_helper
Get Alternative Choice Listalt_choice_list
Set x-axis labels to 45 degreesangled_theme
Assign each observation in the primary dataset to a fishery management or regulatory zone Assign each observation in the primary dataset to a fishery management or regulatory zone. Function is primarily called by other functions that require zone assignment but can also be used on its own.assignment_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
Linear Model for Catchcatch_lm
Save Primary Table's Centroid Columns to FishSET Databasecentroid_to_fsdb
Change variable data classchange_class
Check for common data quality issues affecting modeling functionscheck_model_data
Check and correct spatial data formatcheck_spatdat
Retrieve closure scenario namesclose_names
Combine zone and closure areacombine_zone
Confidentialy cache existsconfid_cache_exists
View correlation coefficients between numeric variablescorr_out
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 starting location variablecreate_startingloc
Create trip centroid variablecreate_trip_centroid
Create haul level trip distance variablecreate_trip_distance
Create numeric variable using arithmetic expressioncreate_var_num
K-fold cross validationcross_validation
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
Delete models from FishSET Databasedelete_models
Create KDE, CDF, or empirical CDF plotsdensity_plot
Run discrete choice modeldiscretefish_subroutine
Create dummy matrix from a coded ID variabledummy_matrix
Create a binary vector from numeric, date, and character or factor vectors.dummy_num
Create dummy variabledummy_var
Check variables are not emptyempty_vars_filter
Expected profit model with log-normal catch functionepm_lognormal
Expected profit model with normal catch functionepm_normal
Expected profit model with Weibull catch functionepm_weibull
Return names of expected catch matricesexp_catch_names
Get Expected Catch Listexpected_catch_list
Explore starting value parameter spaceexplore_startparams
Remove rows based on filter expressions defined in 'filterTable'filter_dat
Filter out-of-sample data for model predictionsfilter_outsample
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
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
Reformat out-of-sample model coefficientsformat_outsample_coefs
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
View error output from discrete choice model for the defined projectglobalcheck_view
Create a within-group running sum variablegroup_cumsum
Create a within-group lagged difference variablegroup_diff
Create a within-group percentage variablegroup_perc
Collapse data frame from haul to triphaul_to_trip
Create ID variableID_var
Insert plot from user folderinsert_plot
Insert table from user folderinsert_table
Jitter longitude and latitude variablesjitter_lonlat
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
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
Conditional logit likelihoodlogit_c
Full information model with Dahl's correction functionlogit_correction
Zonal logit with area-specific constants procedurelogit_zonal
Assign longitude and latitude points to zonal centroidlonlat_to_centroid
View list of MainDataTables in FishSET databasemain_tables
Make model design filemake_model_design
Add an area/polygon to spatial datamake_spat_area
Kernel density (hotspot) plotmap_kernel
Map observed vessel locationsmap_plot
Interactive vessel locations and fishery zones mapmap_viewer
Merge data tables using a left joinmerge_dat
Merge expected catchmerge_expected_catch
Check if meta file exists for a projectmeta_file_exists
Print meta tables by project and/or typemeta_tables
Import, create, and edit metadatametadata_gui
Get Model Design Listmodel_design_list
Design hold-out modelmodel_design_outsample
Load model comparison metrics to console for the defined projectmodel_fit
Return model namesmodel_names
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
Calculate and view 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
Parse metadata from a data fileparse_meta
Selectively display a note sectionparse_notes
Plot spatial datasetplot_spat
Policy change metricspolicy_metrics
Summarize predicted probabilitiespred_prob_outputs
Map of predicted probabilitiespredict_map
Predict out-of-sample datapredict_outsample
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
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
Runs policy scenariosrun_policy
Save modified primary data table to FishSET databasesave_dat
Save a meta data file to project foldersave_raw_meta
Northeast Scallop Datascallop
Ports from the NE scallop fisheryscallop_ports
Create single binary fishery season identifier variableseasonalID
View model metrics and record best model interactivelyselect_model
Interactive application to select variables to include/exclude in primary datasetselect_vars
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
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
Plot variable by month/yeartemp_plot
Transform units of date variablestemporal_mod
Northeast Ten Minute SquarestenMNSQR
Trip duration table and plottrip_dur_out
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
Welfare plots and tableswelfare_outputs
Welfare analysiswelfare_predict
Northeast wind closure areaswindLease
Write a data table to local file directorywrite_dat
Plot relationship of two variablesxy_plot
Define zone closure scenarioszone_closure
Summarize zones, closure areaszone_summary