Tools for 'Box Geometry Model' (BGM) Files and Topology for the Atlantis Ecosystem Model

Facilities for working with Atlantis box-geometry model (BGM) files. Atlantis is a deterministic, biogeochemical, whole-of-ecosystem model. Functions are provided to read from BGM files directly, preserving their internal topology, as well as helper functions to generate 'Spatial' objects. This functionality aims to simplify the creation and modification of box and geometry as well as the ability to integrate with other data sources.


rbgm - R tools for Box Geometry model files


rbgm allows reading of geometry from BGM files, either in raw coordinate form or as Spatial objects. The aim is to make all of the following straightforward:

  • read of the BGM format, maintaining all topology and attributes
  • use of the BGM specification for visualization and data extraction
  • creation of BGM from from shapefiles, R spatial objects and whatever else

Install from CRAN:

install.packages("rbgm")

Install the development version from Github using devtools.

devtools::install_github("mdsumner/rbgm")

Install, use, test the package, and let me know!

Please use the Issues tab on GitHub to add feature requests and bug reports: https://github.com/AustralianAntarcticDivision/rbgm/issues/

use Pull Requests if you have changes you'd like to contribute.

  • mfdbatlantis MareFrame Atlantis routines
  • atlantistools data processing and visualisation tool for R
  • shinyrAtlantis
  • ratlantis R code for interfacing with Atlantis ecosystem modeling software
  • vat Visualizing Atlantis Tool (vat)
  • EastAntarctica_Atlantis Project work at Australian Antarctic Division and the Antarctic Climate and Ecosystems CRC
  • AtlantisNEUS_R R code (scripts and functions) to interact with and analyze output from the Atlantis NEAU End-2-end marine ecosystem model

See the package vignettes for examples.

News

rbgm 0.0.4

  • added vignettes, examples, more doc

  • removed some old functions

  • cleaned up for CRAN

  • fixed a gnarly bug due to lexicographic sorting on a list! Lines from faceSpatial were coming out in the sorted order of "face0", "face1", "face10", "face30" etc.

  • renamed "leftbox" and "rightbox" to "left" and "right"

  • readme includes all example files in bgmfiles

  • new example files added

  • added functions pointSpatial and nodeSpatial

  • new function bgmfile to replace deprecated read_bgm

  • new tests and changes to capture Guam_utm1 variant

rbgm 0.0.2

  • First fully working build ready for check.

Reference manual

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