atlantis_checkmodule: Test if Atlantis modules are on.

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

Test if Atlantis modules are on.

Description

Test if at least physics, biology and fishery modules are on in the calibrated model. It looks inside the run parameters file and check if flag_fisheries_on = 1, flag_skip_biol = 0, and flag_skip_phys = 0.

Usage

atlantis_checkmodule(model_path, exe_name, batch_file = NULL)

Arguments

model_path	The directory of the calibrated model (containing all the parameters files and one bach file. Forcing files can be stored in a direct parent directory of model_path). WARNING: Only working if the forcing folder is in the main model directory model_path or if it is in the direct parent directory. If not please either modify this package or modify the path structure of your Atlantis input forcing parameters file.
exe_name	The name of the atlantis executable you used (ex: atlantismain, atlantisNew).
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

test A binary variable (1) all the modules are on (0) at least one module is off.

See Also

atlantis_paraselect for parameters file selection, and atlantis_openfile to open a parameters file and select a parameter.

Examples

atlantis_checkmodule("C:/Atlantis/AtlantisEEC/AtlantisEECF_v3",
                     "atlantismain", "runAtlantis.bat")
atlantis_checkmodule("/home/Atlantis/AtlantisEEC/AtlantisEECF_v3",
                     "atlantisNew", "runAtlantis.sh")

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