Man pages for MortenVinther/FishStomachs
Compilation of stomach contents data
| add_Aphia_ID | Add WoRMS Aphia Id Add WoRMS Aphia Id to predator or prey... |
| add_missing_boots | Add missing prey and prey size combination for bootstrap... |
| add_NODC_ID | Add NODC Id where missing |
| add_strata | Add temporal and spatial strata to STOMobs |
| aggregate_within_sample | Aggregate stomach contents within sample |
| as.data.frame.STOMdiet | Convert STOMdiet into a data.frame |
| as.data.frame.STOMobs | Convert a STOMobs into a data.frame |
| as_STOMdiet | Convert a data.frame into a STOMdiet object |
| as_STOMobs | Convert a data.frame into a STOMobs object |
| bias_correct_energy_etc | Bias correct stomach content due to energy contents, armament... |
| bias_correct_regurgitated | Bias correct due to regurgitated stomachs |
| bootsMean | Statistics from bootstrap replicates. |
| bootstrap_addVar | Add bootstrap stratification variables. |
| bootstrap_data | Make bootstrap replicates. |
| bootstrap_show | Show bootstrap stratification. |
| calc_population_stom | Compilation of observed stomach contents into population diet |
| change_data | Make changes on STOMobs from user options |
| check_before_strata_aggregation | Check if data are ready for aggregation. |
| check_unique_diet_id | Check uniqueness of diet_id (key) |
| check_unique_sample_id | Check uniqueness of sample_id and fish_id |
| cleanup | close open devices |
| combine_years | Combine years of stomach data. |
| convert_year_of_the_stomach | Read ICES year-of-the-stomach data |
| c.STOMdiet | Combine multiple STOMdiet objects |
| c.STOMobs | Combine multiple STOMobs objects |
| diet_prey_to_other | Transform preys into "other" |
| diet_relative | Calculate diet data as relative weight |
| diet_sum | Sum diet data with the same prey |
| do_detailed_output | Show a subset from test criteria |
| do_detailed_output_diet | Show a subset from test criteria |
| edit_control | Edit control attribute |
| from_to_species_diet | Change predator or prey names. |
| get_control | Get control attribute |
| group_prey_species | Group prey species names. |
| length.STOMobs | Length of predator file |
| make_criteria_set | Extract a subset from test criteria |
| make_from_to_species | Read csv-file with allocation keys for partly identified prey... |
| make_length_classess | Put size classes on predator from observed length. |
| make_template_strata_weighting | Make a template for weighting factors for population diet. |
| model_output | Produce input for the SMS model. |
| pipe | Pipe operator |
| plotboots | Plot bootstrapping diet data. |
| plotboots.size | Plot bootstrapping diet data. |
| plotdif | Plot difference between two diet data set. |
| plotSize | Plot diet data with prey size. |
| plot.STOMdiet | Plot diet data. |
| pool_data | Pool stomach contents within sample and size |
| prey_w_from_pooled_weight | Allocate weight to individual prey lengths from prey-pooled... |
| print-STOMcontrol-method | Print control object |
| print.STOMdiet | Print overview of diet data |
| print.STOMobs | Print STOMobs |
| put_size_class_on_predator | Put size classes on predator from observed length. |
| put_size_class_on_prey | Put size classes on preys from observed length. |
| read_exchange_data | Read stomach contents data on exchange format |
| redist_unidentified_prey_lengths | Redistribute unidentified prey lengths |
| redist_unidentified_prey_sp | Redistribute unidentified prey species |
| STOMcontrol-class | An s4 class for Control object for stomach compilation. |
| strata_aggregate | Aggregate stomach contents within strata (time, area and... |
| subset.STOMdiet | Sub-setting a STOMdiet object. |
| subset.STOMobs | Sub-setting a STOMobs object. |
| summary.STOMdiet | Summary of diet |
| summary.STOMobs | Summary of number of stomachs |
| table_strata_prey_preyl | Table stomach contents within by strata (time, area and... |
| update.STOMobs | Update attributes with added variables |
| validSTOMcontrol | Validation of control object used for stomach data... |
| write_exchange_data | Write stomach contents data of class STOMobs on the exchange... |
