Process and Visualise Output from Atlantis Models

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Documentation for package ‘atlantistools’ version 0.4.3

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%>% Pipeoperator
agg_data Aggregate data using dplyr functionality.
agg_perc Aggregate data using dplyr functionality.
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.
change_avail Change the availability matrix to simplify automated ATLANTIS calibrations.
change_prm Change biological parameterfile to simplify automated ATLANTIS calibrations.
change_prm_cohort Change biological parameterfile for parameters which expect multiple values.
check_df_names Function to check the names of a dataframe.
check_growth This function is used to check the individual growth per group over time.
combine_ages Combine ageclasses to juvenile and adult stanza according to age at maturity.
combine_groups Combine values from different groups if specific groups only have a low contribution to the overall value.
combine_runs This function is used to combine model output from different simulations!
convert_bgm Transform data from bgm-file to map dataframe.
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_relative_initial Calculate relative timeseries using the initial value as benchmark.
convert_time Convert timestep to actual time!
custom_grid Utility functions used for various plotting routines within atlantistools.
extract_prm Extract values for Atlantis parameters from the biological parameter file.
extract_prm_cohort Extract values for Atlantis parameters from the biological parameter file.
fishbase_data fishbase_data
flip_layers Flip layers for visualization.
get_acronyms Collection of similar functions which get specific columns from the Atlantis 'functionalGroups.csv'
get_age_acronyms Collection of similar functions which get specific columns from the Atlantis 'functionalGroups.csv'
get_age_groups Collection of similar functions which get specific columns from the Atlantis 'functionalGroups.csv'
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_diet_fishbase Extract reference for diet information from http:://www.fishbase.se
get_fish_acronyms Collection of similar functions which get specific columns from the Atlantis 'functionalGroups.csv'
get_groups Collection of similar functions which get specific columns from the Atlantis 'functionalGroups.csv'
get_growth_fishbase Extract growth parameters from http:://www.fishbase.se.
get_ids_fishbase Extract fishbase IDs using the package "rfishbase" to generate species specific fishbase URLs
get_maturity_fishbase Extract maturity parameters from http:://www.fishbase.se.
get_nonage_acronyms Collection of similar functions which get specific columns from the Atlantis 'functionalGroups.csv'
get_ref_fishbase Extract the bibliographic info from www.fishbase.org.
group_data Aggregate data using dplyr functionality.
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 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 This function loads weight at age data (in mgN) from the initial conditions file.
load_init_nonage This function loads weight at age data (in mgN) from the initial conditions file.
load_init_physics This function loads weight at age data (in mgN) from the initial conditions file.
load_init_stanza This function loads weight at age data (in mgN) from the initial conditions file.
load_init_weight This function loads weight at age data (in mgN) from the initial conditions file.
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_spec_mort Load mortality information from outputSpecificPredMort.txt
load_txt Function to load various txt files from Atlantis simulations
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_sc_init Sanity check initial conditions file
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.
preprocess preprocess
preprocess_txt Preprocess dataframes loaded in with 'load_txt()'
prm_to_df Extract parameters from the biological parameter file and transform them to a dataframe.
prm_to_df_ages Extract parameters from the biological parameter file and transform them to a dataframe.
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.
write_diet Extract the dietmatrix from the biological parameterfile