%>%                     Pipeoperator
agg_data                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.
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 nitrogen in mg to biomass in tonnes.
get_diet_fishbase       Extract reference for diet information from
                        http:://www.fishbase.se
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_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 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_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_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.
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.
sc_init                 Sanity check initial conditions file
scan_prm                Scan character vector for specific flag!
scan_reference_fishbase
                        Scan list of references for character string
                        for fish species
str_split_twice         Extract numeric values from string.
theme_atlantis          Customized theme used in all plots.
