Man pages for atlantistools
Process and Visualise Output from Atlantis Models
| agg_data | Aggregate data using dplyr functionality. |
| calculate_biomass_spatial | Calculate spatially explicit biomass (in [t]) for each group... |
| calculate_consumed_biomass | Calculate the consumed biomass in [t] of prey j by predator... |
| calculate_spatial_overlap | Calculate 3d overlap of predator groups with their prey over... |
| change_avail | Change the availability matrix to simplify automated ATLANTIS... |
| change_prm | Change biological parameterfile to simplify automated... |
| change_prm_cohort | Change biological parameterfile for parameters which expect... |
| check_df_names | Function to check the names of a dataframe. |
| check_growth | This function is used to check the individual growth per... |
| combine_ages | Combine ageclasses to juvenile and adult stanza according to... |
| combine_groups | Combine values from different groups if specific groups only... |
| combine_runs | This function is used to combine model output from different... |
| convert_bgm | Transform data from bgm-file to map dataframe. |
| convert_factor | Function to convert any column with information about... |
| convert_relative_initial | Calculate relative timeseries using the initial value as... |
| convert_time | Convert timestep to actual time! |
| custom_grid | Utility functions used for various plotting routines within... |
| extract_prm | Extract values for Atlantis parameters from the biological... |
| fishbase_data | fishbase_data |
| flip_layers | Flip layers for visualization. |
| get_boundary | Get boundary boxes from Atlantis box information. |
| get_colpal | Create discrete color palette used in plots. |
| get_conv_mgnbiot | Extract conversion factor used to transform data from... |
| get_diet_fishbase | Extract reference for diet information from... |
| get_groups | Collection of similar functions which get specific columns... |
| get_growth_fishbase | Extract growth parameters from http:://www.fishbase.se. |
| get_ids_fishbase | Extract fishbase IDs using the package "rfishbase" to... |
| get_maturity_fishbase | Extract maturity parameters from http:://www.fishbase.se. |
| get_ref_fishbase | Extract the bibliographic info from www.fishbase.org. |
| load_box | Load the box specification file for an Atlantis scenario |
| load_bps | Extracts the names of the epibenthic biomasspools from the... |
| load_dietcheck | Read in the atlantis dietcheck.txt file and perform some... |
| load_dietmatrix | Extract the dietmatrix from the biological parameterfile |
| load_fgs | Load the functional group file |
| load_init | This function is used to read in data from the initial... |
| load_init_age | This function loads weight at age data (in mgN) from the... |
| load_nc | Load Atlantis outputfiles (netcdf) |
| load_nc_physics | Load Atlantis outputfiles (netcdf) |
| load_rec | Load information for SSB and Recruits from an Atlantis model... |
| load_spec_mort | Load mortality information from outputSpecificPredMort.txt |
| load_txt | Function to load various txt files from Atlantis simulations |
| pipe | Pipeoperator |
| plot_add_box | Low level plotting function to add sudo confidence range to... |
| plot_add_polygon_overview | Add spatial representation of polygon layout to a ggplot2... |
| plot_add_range | Low level plotting function to add range of observed values... |
| plot_bar | Function to plot relative contribution of biomass and numbers... |
| plot_boxes | Plot layout of boxes! |
| plot_consumed_biomass | Circle diagram to visualize the consumed biomass for the... |
| plot_diet | Plot contribution of diet contents for each functional group. |
| plot_diet_bec_dev | Plot contribution of diet contents for each functional group. |
| plot_line | Function to plot time series of atlantis ncdf output. |
| plot_rec | Plot recruitment. |
| plot_spatial_box | Visualize the spatial distribution per species and stanza... |
| plot_spatial_overlap | Plot spatial overlap. |
| plot_spatial_ts | Visualize the spatial distribution per species and stanza... |
| plot_species | Create species specific overview plot. |
| preprocess | preprocess |
| preprocess_txt | Preprocess dataframes loaded in with 'load_txt()' |
| prm_to_df | Extract parameters from the biological parameter file and... |
| ref_agemat | agemat. |
| ref_bio_cons | Consumed biomass. |
| ref_bio_sp | Spatial biomass. |
| ref_dietmatrix | Dietmatrix. |
| ref_dm | Dietcheck. |
| ref_eat | Eat. |
| ref_grazing | Grazing. |
| ref_growth | Growth. |
| ref_n | Nitrogen. |
| ref_nums | Numbers at age data. |
| ref_physics | Physical variables. |
| ref_resn | Reserve nitrogen. |
| ref_structn | Structural nitrogen. |
| ref_to_bibkey | Convert reference to bib-tex-key. |
| ref_vol | Volume. |
| ref_vol_dz | Volume and dz. |
| scan_prm | Scan character vector for specific flag! |
| scan_reference_fishbase | Scan list of references for character string for fish species |
| sc_init | Sanity check initial conditions file |
| str_split_twice | Extract numeric values from string. |
| theme_atlantis | Customized theme used in all plots. |
