View source: R/atlantisfmsy_core.R
atlantisfmsy_inisimu | R Documentation |
In the directory folder_path
, it creates the folder
AtlantisMSY
and the sub-folder named after the functional group
func_grp
where all simulations will take place. The calibrated model
files from the directory model_path
is copied into this newly
created folder. Then a series of values of F between F = 0 to F =
fmax
with an incrementation of 0.4 y-1 are tested. When the stock
collapse, the function stop and return the directory of the simulation
folder.
atlantisfmsy_inisimu( func_grp, folder_path, model_path, exe_name, harvest_filename, run_time, f_prop, fmax, fmin, fishing_para, save_time = NULL, batch_file = NULL )
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 |
exe_name |
The name of the atlantis executable you used (ex: atlantismain, atlantisNew). |
harvest_filename |
The name of the harvest parameters file with its extension (ex: file.prm). |
run_time |
The total duration of the simulation in days
( |
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. |
fmax |
The maximal value of F the simulation is going to test in y-1.
WARNING: only work if |
fmin |
The minimum value of F to test in y-1 (only used when the simulation are restarted after an interruption). The default value is 0. |
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 |
save_time |
The number of days to save from the end of the simulation. Default: NULL. |
simu_path
The directory of the simulation folder, and run
first set of simulations that are stored in the output folder.
Only work if fmax < 10 y-1, see atlantis_bachchange
).
atlantisfmsy_modelcopy
to create the simulation
directory and copy the calibrated model inside it,
atlantis_runtime
to modify the runtime in the run parameters
file, atlantis_wsummary
to modify periodicity of summary
outputs, atlantis_fchange
to change the value of F in the
harvest pramaters file, atlantis_bachchange
to change output
names in the batch/shell file, and atlantis_avbiomsp
to
estimate the functional group biomass.
atlantisfmsy_inisimu("COD", "C:/Atlantis/AtlantisEEC/", "C:/Atlantis/AtlantisEEC/AtlantisEECF_v3", "atlantismain", "AEEC_harvest.prm", 18250, c(0.2, 0.45, 0.05, 0.12, 0.08, 0.1), 4, 0, fishing_para, "runAtlantis.bat") atlantisfmsy_inisimu("COD", "/home/Atlantis/AtlantisEEC/", "/home/Atlantis/AtlantisEEC/AtlantisEECF_v3", "atlantisNew", "AEEC_harvest.prm", 18250, c(0.2, 0.45, 0.05, 0.12, 0.08, 0.1), 4, 0, fishing_para, "runAtlantis.sh") ## Not run: atlantisfmsy_inisimu("COD", "C:/Atlantis/AtlantisEEC/", "C:/Atlantis/AtlantisEEC/AtlantisEECF_v3", "atlantismain", "AEEC_harvest.prm", 18250, c(0.2, 0.45, 0.05, 0.12, 0.08, 0.1), 10, 0, fishing_para) ## End(Not run)
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