atlantis_bachchange: Change bach/shell Atlantis file.

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

Change bach/shell Atlantis file.

Description

It modifies the name of the output files for the future run in the batch/shell file used to run Atlantis. The name is coded with the code of the functional group selected func_grp and the value of F that will be tested f_test (example: For func_grp = "COD" with a f_test = 0.0002739726 (0.1 y-1) the output file prefix will be MSY_COD_F010).

Usage

atlantis_bachchange(
  func_grp,
  path,
  exe_name,
  f_test,
  batch_file = NULL,
  msy = TRUE,
  output = TRUE
)

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).
f_test	The new value of total fishing mortality to be tested in days.
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.
msy	Add msy to the outputs names or not. Default: TRUE.
output	Return f_test values without the one tested or not. Default: TRUE.

Value

f_test The new value of total fishing mortality to be tested in days, and modify batch/shell Atlantis run file.

Warning

Only work if fmax < 10 y-1.

See Also

atlantis_openfile to open a parameters file and select a parameter.

Examples

atlantis_bachchange("COD", "C:/Atlantis/AtlantisEEC/AtlantisMSY/COD",
 "atlantismain", 0.0002739726, "runAtlantis.bat")
atlantis_bachchange("COD", "/home/Atlantis/AtlantisEEC/AtlantisMSY/COD",
 "atlantisNew", 0.0002739726, "runAtlantis.sh")

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