convert_atlantis_output: Load Atlantis outputfiles (netcdf)

In cddesja/R4Atlantis-legacy: Atlantis Helper Tool for R

Description

This function loads Atlantis outputfiles (netcdf)

Usage

convert_atlantis_output(model_path, filename, select_groups, select_variable,
  biomasspools, aggregate_layers = T)

Arguments

model_path	Path of the ATLANTIS directory
filename	Name of the ouputfile which shall be read in
select_variable	ATLANTIS variables which shall be loaded! Only one variable can be loaded at a time! "Only 'N', 'Nums', 'ResN' and 'StructN'
aggregate_layers	Specifies of layers shall be aggregated or not? Currently only T is available.
select_groups	Vector of groups for which ouput shall be loaded. Should be derived from "functionalGroups.csv" using the column Name.
biomasspools	Vector of biomasspool names as given in functionalGroups.csv!

Details

This functions converts the ATLANTIS output to a dataframe which can be processed in R.

Value

Dataframe in long format with the following informations: Species, timestep, polygon, agecl and value

Examples

load_atlantis_output(model_path = "Z://Atlantis//ATLANTIS NSmodel", filename = "outputNorthSea.nc", select_variable = "ResN", biomasspools = c("large_crabs", "small_epifauna", "sessile_epifauna", "epifaunal_macrobenthos"))

cddesja/R4Atlantis-legacy documentation built on May 13, 2019, 2:21 p.m.