| add_probs | Function to predict prababilities for each sampled data set... |
| adjust_probs | Adjust Cluster Probabilities Function to adjust cluster... |
| calc_bycatch | Calculate Bycatch Function to calculate bycatch from sampled... |
| calc_comb_deltas | Calculate Delta values for each vessel combination in each... |
| calc_ctac_rev | Function to calculate catch-quota balancing and revenues... |
| calc_delta_plot | Calculate values for delta plots Delta plots come from Gillis... |
| calc_deltas_spp | Calculate Delta Species Function to Calculate delta plot... |
| calc_probs | Calculate Probabilities Calculate probabilites based on type... |
| calc_skew | Calculate skew of a catch distribution Function to calculate... |
| ch4_format_data | Format the data based on whatever the input is Format the... |
| ch4_perm_test | Permutation Test Function to conduct permutation test on... |
| change_two | Function to change two things at once Function to change two... |
| clust_by_port | Cluster values by port Function to cluster values by port.... |
| clust_scope | Define scope of potential new clusters Function to define... |
| clust_tows | Cluster the data Funtion that returns cluster output. The... |
| compare_aic | Function to compare AIC and LL values |
| cut_for_merge | Cut for merge Cut cluster data for merge with original data... |
| deg2rad | Convert degrees to radians Convert degrees to radians |
| fish_fleet | Function to resample averages for each vessel in a fleet |
| fish_trip | Function to conduct a fishing trip Function to conduct a... |
| fish_trip_simulation | Run Fish Trip Simulation Function to run fish_trip... |
| fit_rum | Fit Random Utility model Fit Random Utility Model to data.... |
| fleet_trip | Function to start some number of vessels in a number of... |
| format_rum_data | Function to format RUM data Function calls mlogit |
| gcd_slc | Calculate distance based on spherical law of cosines |
| get_aic | Function to calculate predictions and AIC values input a port... |
| get_choice_set | Generate Choice Set Generate Choice Set for Predictions |
| get_filenames | Function to get filenames to read in model results |
| list_to_df | Function to convert a list to dataframe ldply but gives... |
| load_coefs | Load coefficients function Function to load coefficients from... |
| load_tow_data | Load Tow Data Load WC Logbook Data |
| one_trip | Function to conduct one trip One Trip Function |
| plot_clusts | Plot Clusters Function to plot clusters |
| plot_pairs | Function to plot pairs of values Function to plot pairs of... |
| plot_paths | Plot fished clusters Function to plot the paths of vessels.... |
| plot_profits | Plot Profits Function to plot profits associated with... |
| port_rums | port_rums function Function to run and save RUM data for 8... |
| pred_metrics | Prediction Metrics Function that calculates metrics based on... |
| process_aic | Function to process AIC and LL values |
| process_coefficients | Function to process coefficients |
| process_dummys | Process dummy variables Function to calculate revenues and... |
| process_dummys2 | Process dummy variables Function to calculate revenues and... |
| pull_catch | Find catch from unique tows Function to count number of tows... |
| read_files_predict | Read files and calculate model predictions Function to read... |
| resample_training_data | Function to resample tows given a training data set Take... |
| rum_data | Format Data for Random Utility Model Function to format data... |
| rum_probs | rum_probs Function Function to format rum data, fit models,... |
| run_six_years | Run Six Years Function Run six years of model with different... |
| sample_catches | Function to run the catch resampling Order of functions is:... |
| sampled_rums | Format RUM data base on resampled tows Function calls mlogit |
| sampled_rums_clust | Format RUM data base on resampled tows Function calls mlogit |
| sample_hauls | Function to Sample Hauls Function to Sample Hauls |
| sample_tows | Sample Tows Function to sample tows from logbook data |
| simple_permute | Function for simple permutations |
| spp_corrs | Calculate Bycatch Function to calculate catch correlations... |
| spp_delts | Function to calculate deltas for species spp_delts |
| summarize_catch | Summarize catch Function to take haul_id, and count the... |
| training_data | Sample dataset for generating predictions Function calls... |
| values_for_probs | Values for probability calculations Function to format values... |
| when_spp_delta | Function to calculate values for delta plots Skew and... |
| year_spp_delta | Function to calculate values for delta plots Skew and... |
