atlantis_fchange: Change F in Atlantis.

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

Change F in Atlantis.

Description

It modifies the harvest parameters file by applying a new value of F for the functional group func_grp. It looks for mFC_XXX parameter and and change the value of the vector using the new F value f_test that need to be simulated and the distribution of the fishing pressure accross fleets f_prop from the calibrated model.

Usage

atlantis_fchange(
  func_grp,
  path,
  harvest_filename,
  f_prop,
  f_test,
  fishing_para
)

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.
harvest_filename	The name of the harvest parameters file with its extension (ex: file.prm).
f_prop	The proportion of the total fishing pressure applied per each fleet. The order of the fleets is the same as the one used in Atlantis.
f_test	The new value of total fishing mortality to be tested in days.
fishing_para	A dataframe containing data from the fishing fleet csv file plus two extra column, one to indicate if the fleet is active (1) or not (0) named active_flt and one named effortmodel containing the effortmodel option used for each fleet (output from the function atlantis_checkf).

Value

Change value of F in the harvest parameters files.

See Also

atlantis_openfile to open a parameters file and select a parameter.

Examples

atlantis_fchange("COD", "C:/Atlantis/AtlantisEEC/AtlantisMSY/COD",
 "AEEC_harvest.prm", c(0.2, 0.45, 0.05, 0.12, 0.08, 0.1), 0.0002739726,
  fishing_para)
atlantis_fchange("COD", "/home/Atlantis/AtlantisEEC/AtlantisMSY/COD",
 "AEEC_harvest.prm", c(0.2, 0.45, 0.05, 0.12, 0.08, 0.1), 0.0002739726,
  fishing_para)

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