Function reference • FishSET

All functions

add_vars(): Add removed variables back into dataset - non-interactive version

add_vars_gui(): Add removed variables back into dataset

agg_helper(): Aggregating function

alt_choice_list(): Get Alternative Choice List

angled_theme(): Set x-axis labels to 45 degrees

assignment_column(): 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.

bin_var(): Creates numeric variables divided into equal sized groups

bycatch(): Compare bycatch CPUE and total catch/percent of total catch for one or more species

catch_lm(): Linear Model for Catch

centroid_to_fsdb(): Save Primary Table's Centroid Columns to FishSET Database

change_class(): Change variable data class

check_model_data(): Check for common data quality issues affecting modeling functions

check_spatdat(): Check and correct spatial data format

close_names(): Retrieve closure scenario names

combine_zone(): Combine zone and closure area

confid_cache_exists(): Confidentialy cache exists

corr_out(): View correlation coefficients between numeric variables

cpue(): Create catch or revenue per unit effort variable

create_alternative_choice(): Define alternative fishing choice

create_centroid(): Create Centroid Table

create_dist_between(): Interactive application to create distance between points variable

create_dist_between_for_gui(): Create distance between points variable - non-interactive version

create_duration(): Create duration of time variable

create_expectations(): Create expected catch/expected revenue matrix

create_mid_haul(): Creates haul midpoint latitude and longitude variables

create_seasonal_ID(): Create fishery season identifier variable

create_startingloc(): Create starting location variable

create_trip_centroid(): Create trip centroid variable

create_trip_distance(): Create haul level trip distance variable

create_var_num(): Create numeric variable using arithmetic expression

cross_validation(): K-fold cross validation

data_check(): Check for common data quality issues

data_upload_helper(): Upload data from file, FishSET DB, or working environment

dat_to_sf(): Convert dataframe to sf

degree(): Check and convert lat/lon to decimal degrees

delete_meta(): Delete table meta data or project meta file

delete_models(): Delete models from FishSET Database

density_plot(): Create KDE, CDF, or empirical CDF plots

discretefish_subroutine(): Run discrete choice model

dummy_matrix(): Create dummy matrix from a coded ID variable

dummy_num(): Create a binary vector from numeric, date, and character or factor vectors.

dummy_var(): Create dummy variable

empty_vars_filter(): Check variables are not empty

epm_lognormal(): Expected profit model with log-normal catch function

epm_normal(): Expected profit model with normal catch function

epm_weibull(): Expected profit model with Weibull catch function

expected_catch_list(): Get Expected Catch List

explore_startparams(): Explore starting value parameter space

exp_catch_names(): Return names of expected catch matrices

filter_dat(): Remove rows based on filter expressions defined in 'filterTable'

filter_outsample(): Filter out-of-sample data for model predictions

filter_table(): Define and store filter expressions

find_centroid(): Identify geographic centroid of fishery management or regulatory zone

find_fishing_centroid(): Create fishing or weighted fishing centroid

fishset_compare(): Compare imported data table to the previously saved version of the data table

fishset_tables(): Show all SQL Tables in FishSET Folder

fleet_assign(): Create fleet variable using fleet definition table

fleet_table(): Define and store fleet expressions

format_grid(): Format Gridded Data

format_outsample_coefs(): Reformat out-of-sample model coefficients

function_summary(): Display summary of function calls

getis_ord_stats(): Calculate and view Getis-Ord statistic

get_closure_scenario(): Retrieve closure scenario by project

get_confid_cache(): Return cached confidentiality tables

get_confid_check(): Return the confidentiality settings

get_grid_log(): Retrieve grid log file

get_latest_projectfile(): Pull data from latest project file

get_proj_settings(): Retrieve project settings

globalcheck_view(): View error output from discrete choice model for the defined project

group_cumsum(): Create a within-group running sum variable

group_diff(): Create a within-group lagged difference variable

group_perc(): Create a within-group percentage variable

haul_to_trip(): Collapse data frame from haul to trip

ID_var(): Create ID variable

insert_plot(): Insert plot from user folder

insert_table(): Insert table from user folder

jitter_lonlat(): Jitter longitude and latitude variables

list_logs(): View list of all log files

list_tables(): Display FishSET database tables by type

load_aux(): Import, parse, and save auxiliary data to FishSET database

load_data(): Load data from FishSET database into the R environment

load_grid(): Import, parse, and save gridded data to FishSET database

load_maindata(): Import, parse, and save data to the FishSET Database

load_outsample(): Import, parse, and save out-of-sample data to FishSET database

load_port(): Import, parse, and save port data to FishSET database

load_spatial(): Import, parse, and save spatial data

logit_c(): Conditional logit likelihood

logit_correction(): Full information model with Dahl's correction function

logit_zonal(): Zonal logit with area-specific constants procedure

log_func_model(): Log user-created functions or models

log_rerun(): Console function for rerunning project log

log_rerun_gui(): Interactive function for rerunning project log

log_reset(): Reset log file

lonlat_to_centroid(): Assign longitude and latitude points to zonal centroid

main_tables(): View list of MainDataTables in FishSET database

make_model_design(): Make model design file

make_spat_area(): Add an area/polygon to spatial data

map_kernel(): Kernel density (hotspot) plot

map_plot(): Map observed vessel locations

map_viewer(): Interactive vessel locations and fishery zones map

merge_dat(): Merge data tables using a left join

merge_expected_catch(): Merge expected catch

metadata_gui(): Import, create, and edit metadata

meta_file_exists(): Check if meta file exists for a project

meta_tables(): Print meta tables by project and/or type

model_design_list(): Get Model Design List

model_design_outsample(): Design hold-out model

model_fit(): Load model comparison metrics to console for the defined project

model_names(): Return model names

model_out_view(): Load discrete choice model output to console for the defined project

model_params(): Load model parameter estimates, standard errors, and t-statistic to console for the defined project

moran_stats(): Calculate and view Moran's I statistic

name_check(): Check for unique and syntatcic column names

nan_filter(): Identify, remove, or replace NaNs

nan_identify(): Identify NaNs and NAs

na_filter(): Identify, remove, or replace NAs and NaNs

nfreq_table(): Create one or more binned frequency tables

nmfs_manage_simple.json: Shape file for NMFS fishing zones

outlier_boxplot(): Boxplot to assess outliers

outlier_plot(): Evaluate outliers in plot format

outlier_remove(): Remove outliers from data table

outlier_table(): Evaluate outliers in Data

parse_meta(): Parse metadata from a data file

parse_notes(): Selectively display a note section

plot_spat(): Plot spatial dataset

policy_metrics(): Policy change metrics

predict_map(): Map of predicted probabilities

predict_outsample(): Predict out-of-sample data

pred_prob_outputs(): Summarize predicted probabilities

pretty_lab(): Format numbers in table

pretty_tab(): Format table for R Markdown

pretty_tab_sb(): Scroll box for R Markdown table

previous_loc(): Create Previous Location/Area Variable

projects(): Display projects names

project_files(): List output files by project name

project_logs(): List logs by project

project_tables(): Display database table names by project

proj_settings_exists(): Check if option file exists for a project

pull_meta(): Retrieve/display meta data by project

pull_notes(): Pull notes from output folder

pull_output(): Retrieve output file name by project, function, and type

pull_plot(): Import and format plots to notebook file

pull_table(): Import and format table to notebook file

randomize_lonlat_zone(): Randomize latitude and longitude points by zone

randomize_value_range(): Randomize variable value by percentage range

randomize_value_row(): Randomize value between rows

read_dat(): Import data from local file directory or webpage into the R environment

remove_model_design(): Remove a model design from list in ModelInputData table

replace_sup_code(): Replace suppression code

reset_confid_cache(): Reset confidentiality cache tables

roll_catch(): Apply moving average function to catch

run_fishset_gui(): Guided user interface for FishSET functions

run_policy(): Runs policy scenarios

save_dat(): Save modified primary data table to FishSET database

save_raw_meta(): Save a meta data file to project folder

scallop: Northeast Scallop Data

scallop_ports: Ports from the NE scallop fishery

seasonalID(): Create single binary fishery season identifier variable

select_model(): View model metrics and record best model interactively

select_vars(): Interactive application to select variables to include/exclude in primary dataset

set_confid_check(): Set confidentiality parameters

set_quants(): Create factor variable from quantiles

set_user_locoutput(): Set user folder directory

sparsetable(): Evaluate sparsity in data over time in table format

sparsplot(): Evaluate sparsity in data over time in plot format

spatial_hist(): Histogram of latitude and longitude by grouping variable

spatial_qaqc(): Spatial data quality checks

spatial_summary(): Summarize variable over data and time

spat_qaqc_gui(): GUI for spatial data checks

species_catch(): Summarize species catch

split_dat(): Separate secondary data table from MainDataTable

summary_stats(): View summary statistics

tables_database(): View names of project tables

table_exists(): Check if table exists in the FishSET database for the defined project

table_fields(): Lists fields for FishSET database table

table_remove(): Remove table from FishSET database

table_save(): Save an existing FishSET DB table

table_view(): View FishSET Database table

temporal_mod(): Transform units of date variables

temp_obs_table(): Number of observations by temporal unit

temp_plot(): Plot variable by month/year

tenMNSQR: Northeast Ten Minute Squares

trip_dur_out(): Trip duration table and plot

unique_filter(): Check rows are unique

vessel_count(): Summarize active vessels

view_fleet_table(): View the most recent fleet table by project

view_grid_dat(): Visualize gridded data on a map

view_lon_lat(): View

view_model_design(): View model design file in database

view_spat(): View interactive map of spatial data

weekly_catch(): Summarize weekly catch

weekly_effort(): Summarize average CPUE by week

welfare_outputs(): Welfare plots and tables

welfare_predict(): Welfare analysis

windLease: Northeast wind closure areas

write_dat(): Write a data table to local file directory

xy_plot(): Plot relationship of two variables

zone_closure(): Define zone closure scenarios

zone_summary(): Summarize zones, closure areas