Man pages for pbs-assess/gfsynopsis
Data Synopsis Reports for PBS Groundfish
| add_upr | Add column containing upper limit for censored poisson |
| central_diff | Calculate the Central Difference Approximation of the First... |
| choose_survey_grid | Choose the survey grid matching the survey type. For the MSSM... |
| clean_name | Clean species names for file names |
| fit_cpue_indices | Fit commercial catch per unit effort standardization models |
| fit_sdmTMB_westcoast | Fit a geostatistical index standardization model to survey... |
| fit_survey_maps | Fit geostatistical survey models and make maps |
| format_final_year_for_map_iphc | Format the final year of IPHC data to use in the spatial map |
| fourth_root_power_trans | Fourth root power transformation |
| get_data | Get all data (includes some IPHC data that will get... |
| get_data_iphc | Get the IPHC data for all years, should get merged into... |
| get_data_iphc_hook_with_bait | Get the IPHC data for all years for hooks with bait (for hook... |
| get_fderiv | Calculate First Derivative and Confidence Intervals for GAM... |
| get_inclusion_table | Get proportion of positive sets in each SYN or HBLL region |
| get_iphc_hook_data | Get IPHC hook counts for all survey years |
| get_iphc_pos_sets | Get table of positive sets for IPHC FISS data |
| get_iphc_stitched_index | Get index using 'sdmTMB' for IPHC surveys |
| get_ll_bait_counts | Download longline baited hook counts |
| get_pstar | Get pstar - Estimate Breakdown Point of Catch Counts |
| get_spp_names | Get spp. names |
| get_stitched_index | Get stitched index across survey regions in synoptic trawl... |
| get_stitch_lu | Get table of positive sets for each region and survey type |
| gfsynopsis | gfsynopsis package |
| gg_color_hue | ggplot2-like colour scale in HCL space |
| make_pages | Make synopsis pages |
| pipe | Pipe operator |
| plot_catches | Plot catches |
| plot_cpue_indices | Plot CPUE indices |
| plot_cpue_spaghetti | Plot locality specific estimates from a CPUE standardization... |
| plot_pstar | Plot pstar - Visualization of pstar Estimation |
| plot_survey_maps | Plot survey maps |
| prep_iphc_stitch_dat | Prepare IPHC FISS data for index stitching |
| prep_mssm_dat | Prepare Multispecies Small Mesh (MSSM) survey set data for... |
| prep_stitch_dat | Prepare survey set data for index stitching |
| prep_stitch_grids | Write grids used for stitching index |
| rougheye_split | Split rougheye species name |
