load_bioind: Load Atlantis '[...]BiomIndx.txt' file

In r4atlantis/atlantisom: Generates Data Sets From Atlantis Scenarios

Load Atlantis [...]BiomIndx.txt file

Description

This function loads the Atlantis BiomIndx.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. Also loads ecosystem indicators (PelDemRatio, PiscivPlankRatio, DivCount, InfEpiRatio, BSSslope, HabitCover) available in the BiomInx.txt file.

Usage

load_bioind(dir, file_bioind, fgs, verbose = FALSE)

Arguments

dir	The directory of the atlantis model output, where the default is getwd().
file_bioind	A character value specifying the name of the text file that contains total annual biomass in tonnes output for an Atlantis scenario. An example entry would be "outputSETASBiomIndx.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 BiomIndx.txt file, formatted similarly to the outputs of run_truth.

Author(s)

Sarah Gaichas

See Also

Other load functions: load_agebioind(), 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

d <- system.file("extdata", "SETAS_Example", package = "atlantisom")
file <- "outputsBiomIndx.txt"
fgs <- load_fgs(dir = d, "Functional_groups.csv")
test <- load_bioind(dir = d, file_bioind = file, fgs = fgs)

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