load_agebioind: Load Atlantis '[...]AgeBiomIndx.txt' file

In r4atlantis/atlantisom: Generates Data Sets From Atlantis Scenarios

Load Atlantis [...]AgeBiomIndx.txt file

Description

This function loads the Atlantis AgeBiomIndx.txt output file. Biomass (total annual tonnes) is only available for species that are turned on in the functionalGroups.csv file. Function does not load relative biomass for these species.

Usage

load_agebioind(dir, file_agebioind, fgs, verbose = FALSE)

Arguments

dir	The directory of the atlantis model output, where the default is getwd().
file_agebioind	A character value specifying the name of the output text file that contains total annual biomass by age (in tonnes) for an Atlantis scenario. An example entry would be "outputSETASAgeBiomIndx.txt".
fgs	A data frame created by load_fgs that reads in the csv file containing functional group names, usually "functionalGroups.csv".
verbose	A logical value specifying if output should be written to the screen or not. The default value is FALSE.

Value

A data frame of total biomass outputs from the AgeBiomIndx.txt file, formatted similarly to the outputs of run_truth.

Author(s)

Sarah Gaichas

See Also

Other load functions: load_bioind(), load_biolprm(), load_boxarea(), load_box(), load_bps(), load_catch(), load_detailed_diet_comp(), load_diet_comp(), load_fgs(), load_fisheries(), load_meta(), load_nc_annage(), load_nc_catchtons(), load_nc(), load_runprm(), load_yoy()

Examples

## Not run: 
d <- system.file("extdata", "SETAS_Example", package = "atlantisom")
file <- "outputsAgeBiomIndx.txt"
fgs <- load_fgs(dir = d, "Functional_groups.csv")
test <- load_agebioind(dir = d, file_bioind = file, fgs = fgs)

## End(Not run)

r4atlantis/atlantisom documentation built on Nov. 12, 2023, 2:59 a.m.