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. |
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