Function reference • atlantistools

Loading Functions Functions that load in and process atlantis output
`load_box()`	Load the box specification file for an Atlantis scenario
`load_bps()`	Extracts the names of the epibenthic biomasspools from the initial conditions file.
`load_dietcheck()`	Read in the atlantis dietcheck.txt file and perform some basic data transformations.
`load_dietmatrix()` `write_diet()`	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 conditions file.
`load_init_age()` `load_init_nonage()` `load_init_stanza()` `load_init_physics()` `load_init_weight()`	This function loads weight at age data (in mgN) from the initial conditions file.
`load_mort()`	Load mortality information from outputMort.txt
`load_spec_mort()`	Load mortality information from specificMort.txt
`load_spec_pred_mort()`	Load mortality information from outputSpecificPredMort.txt
`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 run.
`load_txt()`	Function to load various txt files from Atlantis simulations
`preprocess_txt()`	Preprocess dataframes loaded in with `load_txt()`
`preprocess`	preprocess
`calculate_biomass_spatial()`	Calculate spatially explicit biomass (in [t]) for each group and ageclass per timestep.
`calculate_consumed_biomass()`	Calculate the consumed biomass in [t] of prey j by predator i.
`calculate_spatial_overlap()`	Calculate 3d overlap of predator groups with their prey over time using Schoener Index.
Get/manipulate parameter values Functions that pull parameter values from parameter files
`extract_prm()` `extract_prm_cohort()`	Extract values for Atlantis parameters from the biological parameter file.
`scan_prm()`	Scan character vector for specific flag!
`prm_to_df()` `prm_to_df_ages()`	Extract parameters from the biological parameter file and transform them to a dataframe.
`change_prm()`	Change biological parameterfile to simplify automated ATLANTIS calibrations.
`change_avail()`	Change the availability matrix to simplify automated ATLANTIS calibrations.
Get functions Functions that pull other atlantis information
`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 nitrogen in mg to biomass in tonnes.
Get functional group info Functions that pull information from the functionaGroups.csv file
`get_groups()` `get_age_groups()` `get_acronyms()` `get_age_acronyms()` `get_nonage_acronyms()` `get_fish_acronyms()` `get_cohorts_acronyms()` `get_fished_acronyms()` `get_turnedon_acronyms()`	Collection of similar functions which get specific columns from the Atlantis `functionalGroups.csv`
Fishbase/online data Functions that pull information from fishbase and other online sources
`fishbase_data`	fishbase_data
`get_diet_fishbase()`	Extract reference for diet information from http:://www.fishbase.se
`get_ids_fishbase()`	Extract fishbase IDs using the package "rfishbase" to generate species specific fishbase URLs
`get_growth_fishbase()`	Extract growth parameters from http:://www.fishbase.se.
`get_maturity_fishbase()`	Extract maturity parameters from http:://www.fishbase.se.
`get_ref_biotic()`	Extract bibliographic info from www.marlin.ac.uk/biotic.
`get_ref_fishbase()`	Extract the bibliographic info from www.fishbase.org.
`scan_reference_fishbase()`	Scan list of references for character string for fish species
Plotting Plotting functions to output
`theme_atlantis()`	Customized theme used in all plots.
`flip_layers()`	Flip layers for visualization.
`custom_grid()`	Utility functions used for various plotting routines within atlantistools.
`plot_add_box()`	Low level plotting function to add sudo confidence range to calibration plots.
`plot_add_polygon_overview()`	Add spatial representation of polygon layout to a ggplot2 object.
`plot_add_range()`	Low level plotting function to add range of observed values to time series plots.
`plot_bar()`	Function to plot relative contribution of biomass and numbers per cohort.
`plot_boxes()`	Plot layout of boxes!
`plot_consumed_biomass()`	Circle diagram to visualize the consumed biomass for the whole system.
`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 combination.
`plot_spatial_overlap()`	Plot spatial overlap.
`plot_spatial_ts()`	Visualize the spatial distribution per species and stanza combination.
`plot_species()`	Create species specific overview plot.
`sc_init()` `plot_sc_init()`	Sanity check initial conditions file
Miscellaneous Other functions
`str_split_twice()`	Extract numeric values from string.
`convert_time()`	Convert timestep to actual time!
`convert_relative_initial()`	Calculate relative timeseries using the initial value as benchmark.
`convert_factor()`	Function to convert any column with information about functional groups to a factor whose levels use the LongName of the functional groups file.
`convert_bgm()`	Transform data from bgm-file to map dataframe.
`combine_runs()`	This function is used to combine model output from different simulations!
`combine_groups()`	Combine values from different groups if specific groups only have a low contribution to the overall value.
`combine_ages()`	Combine ageclasses to juvenile and adult stanza according to age at maturity.
`check_growth()`	This function is used to check the individual growth per group over time.
`check_df_names()`	Function to check the names of a dataframe.
`change_prm_cohort()`	Change biological parameterfile for parameters which expect multiple values.
`agg_data()` `agg_perc()` `group_data()`	Aggregate data using dplyr functionality.
`%>%`	Pipeoperator
Ref functions ???
`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_lit`	Reference dataframe
`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.

Reference

Loading Functions

Get/manipulate parameter values

Get functions

Get functional group info

Fishbase/online data

Plotting

Miscellaneous

Ref functions