atlantis_avbiomsp: Test if the functional group biomass collapsed.

In rgirardi/atlantisfmsy: Estimation of a functional group's Fmsy in Atlantis ecosystem model

Test if the functional group biomass collapsed.

Description

It opens the output file BiomIndx.txt and calculates the average biomass of the selected functional group func_grp over the 5 last years of simulation. If the average biomass is smaller than 0.1 metric tons, the stock is considered collapsed and it returns 0.

Usage

atlantis_avbiomsp(func_grp, path, exe_name, run_time, batch_file = NULL)

Arguments

func_grp	The code of the Atlantis functional group for which Fmsy will be estimated.
path	The directory of the batch or shell file.
exe_name	The name of the atlantis executable you used (ex: atlantismain, atlantisNew).
run_time	The total duration of the simulation in days (burnin_time + 10950).
batch_file	The name of the batch/shell file you are using to run your model. If not provided, the function will search for the unique batch file in your folder_path. Default: NULL.

Value

biom_sp The average biomass of the 5 last years of simulation. Return 0 if biom_sp < 0.1.

See Also

atlantis_paraselect for parameters file selection, and read.table to open table stored in text files (.txt, .csv ...).

Examples

atlantis_avbiomsp("COD", "C:/Atlantis/AtlantisEEC/AtlantisMSY/COD",
                  "atlantismain", 18250, "runAtlantis.bat")
atlantis_avbiomsp("COD", "/home/Atlantis/AtlantisEEC/AtlantisMSY/COD",
                  "atlantisNew", 18250, "runAtlantis.sh")

rgirardi/atlantisfmsy documentation built on Aug. 30, 2022, 9:11 a.m.