execute_atlantis: execute_atlantis function

In jsgosnell/ratlantis: R package for developing, executing, and assessing Atlantis ecosystem models

Description

This function calls the terminal and executes an Atlantis model

Usage

execute_atlantis(atlantis_location, atlantis_exe, biology_nc, output_file_nc,
  run_file_prm, forcing_time_series_prm, physics_prm, biology_prm, harvest_prm,
  functional_group_csv, fisheries_csv, econ_prm, output_folder,
  wait_for_response = T)

Arguments

atlantis_location	location of atlantis file (location may not have spaces (e.g. not C:/Desktop/John Doe/bgm))
atlantis_exe	name of Atlantis executable file (typically atlantismain but may differ based on build)
biology_nc	name of biology initial conditions file (needs to be in same location as the atlantis exe file)
output_file_nc	desired name for output file
run_file_prm	name of initial conditions run file (needs to be in same location as the atlantis exe file)
forcing_time_series_prm	name of file detailing initial forcings (needs to be in same location as the atlantis exe file)
physics_prm	name of initial physics file detailing eddies and scaling (needs to be in same location as the atlantis exe file)
biology_prm	name of biology parameter file (needs to be in same location as the atlantis exe file)
harvest_prm	name of harvest file (needs to be in same location as the atlantis exe file)
functional_group_csv	list of functional groups (needs to be in same location as the atlantis exe file)
fisheries_csv	list delimiting targeted fisheries (needs to be in same location as the atlantis exe file)
econ_prm	(optional) name of econ file (needs to be in same location as the atlantis exe file)
output_folder	name of folder (in same directory as atlantis.exe file) where should results be stored?
wait_for_response	Should R wait for Atlantis to run before proceeding? Defaults to True

Details

This function acts as a wrapper for the Atlantis C++ program.

See Also

rbgmeriser

jsgosnell/ratlantis documentation built on May 20, 2019, 2:08 a.m.