atlantisfmsy_modelcopy: Copy the calibrated Atlantis model for Fmsy simulation.

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

Copy the calibrated Atlantis model for Fmsy simulation.

Description

Create the folder AtlantisMSY in the working directory folder_path and a sub-folder named after the functional group code func_grp for the set of simulation. It copies/pastes inside it the files necessary to run Atlantis from the model_path directory.

Usage

atlantisfmsy_modelcopy(
  func_grp,
  folder_path,
  model_path,
  exe_name,
  batch_file = NULL
)

Arguments

func_grp	The code of the Atlantis functional group for which Fmsy will be estimated.
folder_path	The working directory: where the Fmsy simulations will be run and stored.
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

simu_path The simulation directory for the functional group func_grp considered.

See Also

atlantis_paraselect for parameters file selection, atlantis_openfile to open a parameters file and select a parameter, tail to return the last part of an object and str_split_fixed to split a chain of characters.

Examples

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

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