atlantis_directory: Open an Atlantis output directory

In mareframe/mfdbatlantis: MareFrame Atlantis Interface

Description

Open Atlantis output directory, find required files

Usage

atlantis_directory(path,
        bgm_area = first_file(path, '*.bgm'),
        nc_catch = first_file(path, "*CATCH.nc"),
        nc_out = first_file(path, "*.nc"),
        nc_prod = first_file(path, "*PROD.nc"),
        txt_diet = first_file(path, "*DietCheck.txt"),
        xml_bio = first_file(path, '*[Bb]io*.xml'),
        xml_fg = first_file(path, '*Groups*.xml'),
        xml_fisheries = first_file(path, '*Fisheries*.xml'),
        xml_opt = first_file(path, '*[rR]un*.xml'),
        start_year = 1948)

Arguments

path	Directory containing model output
bgm_area	The BGM file that defines model boxes
nc_catch	The .nc file containing catch data
nc_out	The .nc file containing count and StructN
nc_prod	The .nc file containing Eat
txt_diet	The diet matrix
xml_bio	XML biology file
xml_fg	XML functional group definitions
xml_fisheries	XML fisheries definitions
xml_opt	XML run options
start_year	The year the model is assumed to start at

Details

All aguments apart from path are optional. If not supplied then it makes a best guess of the filename and errors if it can't be found.

Value

The path to the directory, annotated with filenames

mareframe/mfdbatlantis documentation built on May 21, 2019, 11:45 a.m.