atlantis_paraselect: Select Atlantis parameters file.

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

Select Atlantis parameters file.

Description

It looks for the names of the parameters file wanted within the batch or shell file used to run Atlantis.

Usage

atlantis_paraselect(path, exe_name, index, batch_file = NULL)

Arguments

path	The directory of the batch or shell file.
exe_name	The name of the atlantis executable you used (ex: atlantismain, atlantisNew).
index	The index used by Atlantis to determine the type of the different parameters files in the batch/shell file (ex: -i initial condition file; -o output files; -r run file; -f forcing file; -p physics file; -b biology file; -s functional groups csv file; -h fishing file; -q fisheries csv file...).
batch_file	The name of the batch/shell file with extension 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

infilename The name of the parameters file selected.

Examples

atlantis_paraselect("C:/Atlantis/AtlantisEEC/AtlantisMSY/COD",
                    "atlantismain", "-h", "runAtlantis.bat")
atlantis_paraselect("/home/Atlantis/AtlantisEEC/AtlantisMSY/COD",
                    "atlantisNew", "-h", "runAtlantis.sh")

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