atlantis_fdistri: Atlantis F distribution.

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

Atlantis F distribution.

Description

Extract the fishing mortality distribution accross fleets in Atlantis. It opens the harvest parameters file, select the mFC_XXX vector for the considered functional group func_grp and return the proportion of the total F allocated to each fleet. If the functional group func_grp is unfished in the calibrated model this function will attribute fishing pressure evenly accross active fleets.

Usage

atlantis_fdistri(
  func_grp,
  model_path,
  harvest_filename,
  fishing_para,
  raw.distri = F
)

Arguments

func_grp	The code of the Atlantis functional group for which Fmsy will be estimated.
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.
harvest_filename	The name of the harvest parameters file with its extension (ex: file.prm).
fishing_para	A dataframe containing data from the fishing fleet csv file plus two extra columns, 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).
raw.distri	If TRUE return the raw value of fishing mortality (F) for active fleets (non-active fleets are set to 0), else the distribution of F is returned (vector of values between [0-1] and their sum is 1). Default: FALSE.

Value

f_prop A vector with the proportion of fishing pressure applied per each fleet. The order of the fleets is the same as the one used in Atlantis.

See Also

atlantis_openfile to open a parameters file and select a parameter.

Examples

atlantis_fdistri("COD", "C:/Atlantis/AtlantisEEC/AtlantisEECF_v3",
 "AEEC_harvest.prm", fishing_para)
atlantis_fdistri("COD", "/home/Atlantis/AtlantisEEC/AtlantisEECF_v3",
 "AEEC_harvest.prm", fishing_para)

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