rbgmeriser: rbgmeriser function

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

Description

This function creates bgm file format needed for Atlantis

Usage

rbgmeriser(map_location = getwd(), map_name, boundary_boxes = NULL,
  get_bathymetry = TRUE, bathymetry_layer_location = getwd(),
  bathymetry_layer_name, bathymetry_cutoff = 0.9, bathymetry_levels = c(-10,
  -20, -50, -200, -1000, -2000, -4000), bgmeriser_location = getwd())

Arguments

map_location	location of gis layer stored in wgs84 format; defaults to working directory
map_name	name of map to be used for bgm creation. Must incude "box_id" column. Other columns may be included (horizmix, vertmix,boundary_code)
boundary_boxes	a list of boxes that boundary boxes in the model
get_bathymetry	Should function automatically add depths (T(rue) or F(alse)
bathymetry_layer_location	location of gis layer stored in wgs84 format; defaults to working directory.
bathymetry_layer_name	name of bathmetry shp layer. Must be in wgs84 format
bathymetry_cutoff	What quantile should be assigned to polygon. Defaults to 90th quantile (to avoid small number of canyons or slope biasing entire polygon)
bathymetry_levels	Depth layers for final Atlantis polygons
bgmeriser_location	location of bgmeriser.jar file (location also must include java.exe file and may not have spaces (e.g. not C:/Desktop/John Doe/bgm))

Details

This function creates bgm file format needed for Atlantis by calling java program. It also adds in depth data (if desired) using provided bathymetry layer. This functions as a wrapper for bgmeriser.jar, available from CSIRO, and adds in required information.

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