Package index • 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

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.

Reference data

Exported data

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.