Package index • FishSET

All functions

agg_helper(): Aggregating function
alt_choice_list(): Get Alternative Choice List
angled_theme(): Set x-axis labels to 45 degrees
assignment_column(): Assign observations to fishing zones
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
calc_trip_centroid(): Calculate trip centroid variable
calc_trip_distance(): Calculate Trip Distance
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_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
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_var_num(): Create numeric variable using arithmetic expression
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
density_plot(): Create KDE, CDF, or empirical CDF plots
dummy_matrix(): Create dummy matrix from a coded ID variable
dummy_num(): Create a binary vector from numeric, date, and character or factor vectors.
empty_vars_filter(): Check variables are not empty
expected_catch_list(): Get Expected Catch List
exp_catch_names(): Return names of expected catch matrices
filter_dat(): Remove rows based on filter expressions defined in 'filterTable'
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_cv(): K-Fold Cross Validation for FishSET Models
fishset_design(): Create FishSET Model Design Object
fishset_fit(): Fit FishSET Discrete Choice Model
fishset_iia_test(): Hausman-McFadden Test for IIA
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_model_data(): Format Model Data
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
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 a data frame from haul-level to trip-level
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
lag_zone(): Lag zone variable
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_gui_variables(): load_gui_variables
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_correction(): Full information model with Dahl's correction function
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_spat_area(): Add an area/polygon to spatial data
map_kernel(): Kernel density (hotspot) plot
map_plot(): Map observed vessel locations
merge_dat(): Merge data tables using a left join
merge_expected_catch(): Merge expected catch
meta_tables(): Print meta tables by project and/or type
model_design_list(): Get Model Design List
model_fit(): Load model comparison metrics to console for the defined project
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
model_resid_corr(): Check Spatial Autocorrelation of Model Residuals
moran_stats(): Calculate 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_notes(): Selectively display a note section
plot(<fishset_spatial_resid>): Plot FishSET Spatial Residuals
plot_spat(): Plot spatial dataset
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
print(<fishset_cv>): Print FishSET Cross Validation Results
print(<fishset_fit>): Print FishSET Model Fit Results
print(<fishset_iia>): Print Hausman-McFadden IIA Test Results
print(<fishset_spatial_resid>): Print FishSET Spatial Residuals
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_simulation(): Run Policy and Data Simulations
save_dat(): Save modified primary data table to FishSET database
scallop: Northeast Scallop Data
scallop_ports: Ports from the NE scallop fishery
seasonalID(): Create single binary fishery season identifier variable
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
summarize_policy_effort(): Summarize and Plot Policy Effort Redistribution
summarize_policy_welfare(): Summarize and Plot Policy Welfare Impacts
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
tenMNSQR: Northeast Ten Minute Squares
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
windLease: Northeast wind closure areas
write_dat(): Write a data table to local file directory
zone_closure(): Define zone closure scenarios
zone_summary(): Summarize zones, closure areas