atlantis_checkf: Test if model uses fishing mortality.

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

Test if model uses fishing mortality.

Description

Test if the active fleet uses the fishing mortality parameter in Atlantis. Check in the harvest parameters file if the parameter XXX_effortmodel is equal to 0 (Fishing mortality option) for each active fleet.

Usage

atlantis_checkf(path, harvest_filename, fishing_para)

Arguments

path	The directory of the batch or shell 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 an extra column to indicate if the fleet is active (1) or not (0) named active_flt (output from the function atlantis_fleetopen).

Value

fishing_para The input dataframe fishing_para with an extra column named effortmodel containing the effortmodel option used for each fleet.

See Also

atlantis_openfile to open a parameters file and select a parameter, str_split_fixed to split a chain of characters, and ex_number to extract number from a chain of characters.

Examples

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

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