Man pages for r4atlantis/atlantisom
Generates Data Sets From Atlantis Scenarios
| aggregate_comps | Function to aggregate compositions into a shorter range of... |
| aggregateData | Aggregate and select data from Atlantis output |
| aggregateDensityData | Aggregate and select density data from Atlantis output |
| calc_age2length | Calculate length from ages |
| calc_avgwtstage2age | Approximating the average weight at true age from... |
| calc_biomass_age | Calculate biomass in t per age-structured-groups per polygon,... |
| calc_biomass_pool | Calculate biomass in t per non-age-structured groups (biomass... |
| calc_pred_cons | Calculate eaten total biomass in tonnes for each functional... |
| calc_pred_diet | Calculate eaten biomass in tonnes for each functional group. |
| calc_stage2age | Approximating the true numbers at age within each box,... |
| calc_timestep2time | Converts timestep from Atlantis output to real time |
| calc_Z | Calculate total mortality for age structured groups |
| create_fishery_subset | Create fishery subset from Atlantis output |
| create_survey | Create survey observations from Atlantis output |
| create_survey_diet | Create survey diet observations from Atlantis output |
| create_survey_env | Create environmental survey data subset from Atlantis output |
| get_boundary | Get boundary boxes from Atlantis box information. |
| load_agebioind | Load Atlantis '[...]AgeBiomIndx.txt' file |
| load_bioind | Load Atlantis '[...]BiomIndx.txt' file |
| load_biolprm | Load Atlantis '_Biol.prm' file |
| load_box | Load the box specification file for an Atlantis scenario |
| load_boxarea | Extract the box area from the bgm-file |
| load_bps | Extracts the names of the epibenthic biomasspools from the... |
| load_catch | Load Atlantis '[...]catch.txt' file |
| load_detailed_diet_comp | Load Atlantis diet composition by box and layer from... |
| load_diet_comp | Load Atlantis diet composition data from 'diet_check.txt' |
| load_fgs | Load the functional group file |
| load_fisheries | Load the fisheries group file |
| load_meta | Open the necessary files to document the atlantis model used... |
| load_nc | Load Atlantis outputfiles (netcdf) |
| load_nc_annage | Load Atlantis annual age outputfiles (netcdf) |
| load_nc_catchtons | Load Atlantis catch tons by fleet and polygon outputfiles... |
| load_nc_physics | Load Atlantis outputfiles (netcdf) |
| load_runprm | Load Atlantis '_run.prm' file |
| load_yoy | Load Atlantis '[...]YOY.txt' file |
| om_comps | Generate composition data from atlantisom |
| om_consindex | Generate predator total consumption index data from... |
| om_diet | Generate diet composition data from atlantisom |
| om_index | Generate index data from atlantisom |
| om_init | Initializes atlantisom |
| om_species | Species-specific atlantisom outputs |
| read_savedfisheries | Read saved fishery outputs into R object |
| read_savedsurvs | Read saved survey outputs into R object |
| reformat_compositions | Reformat compositional data for input in to Stock Synthesis |
| run_stocksynthesis | Function to execute an SS run |
| run_truth | Load Atlantis scenario output |
| sample_ages | Add observation error to numbers-at-age data |
| sample_diet | Sample total consumption to create diet composition data |
| sample_fish | Sample numbers-at-age to create composition data |
| sample_fishery_totcatch | Sample a fishery catch index from an atlantis scenario |
| sample_survey_biomass | Sample a biomass index of abundance from an atlantis scenario |
| sample_survey_consumption | Sample total consumption by predator from an atlantis... |
| sample_survey_numbers | Sample a numbers index of abundance from an atlantis scenario |
| SS_write_biol | Writes life history parameters |
| SS_write_comps | Function to write age and length composition data from... |
| SS_write_EWAA | Function to write an empirical weight at age SS file... |
| SS_write_ts | Function to write the CPUE from an atlantis OM into a Stock... |
| write_meta | Write metadata to the disk. |
| write_SS_ctl | write SS control |
| write_SS_dat | Read SS dat |
