load_catch: Load Atlantis '[...]catch.txt' file

In r4atlantis/atlantisom: Generates Data Sets From Atlantis Scenarios

Load Atlantis [...]catch.txt file

Description

This function loads the Atlantis catch.txt output file. Where catch (total annual tonnes) is only available for species that are fished in the functionalGroups.csv file.

Usage

load_catch(dir, file_catch, fgs, verbose = FALSE)

Arguments

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

Author(s)

Sarah Gaichas

See Also

Other load functions: load_agebioind(), load_bioind(), load_biolprm(), load_boxarea(), load_box(), load_bps(), 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 <- "outputsCatch.txt"
fgs <- load_fgs(dir = d, "Functional_groups.csv")
test <- load_catch(dir = d, fgs = fgs, file_catch = file)

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