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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 |