Example BGM Files for the Atlantis Ecosystem Model.

BGM files for Atlantis

A raw-data package with example .bgm files (box geometry model) for Atlantis ecosystem model.

Atlantis is a deterministic, biogeochemical, whole-of-ecosystem model: http://atlantis.cmar.csiro.au/.

PLEASE NOTE: this is not an official source of BGM for use in Atlantis.

See https://github.com/mdsumner/rbgm for an R package to read these files and work with the box geometry.

See https://github.com/AustralianAntarcticDivision/box-geometry-models for the project that collects the files used in this package.

Installation

Install from CRAN:

install.packages("bgmfiles")

Install the develop version from Github using devtools.

# install.packages("devtools")
devtools::install_github("AustralianAntarcticDivision/bgmfiles")

Usage

List the available raw files available in this package.

library(bgmfiles)
files <- bgmfiles()
print(basename(files))
#>  [1] "AEEC_poly_projETRS89_LAEA_snapped0p002.bgm"
#>  [2] "ams71.bgm"                                 
#>  [3] "antarctica_28.bgm"                         
#>  [4] "antarctica_99.bgm"                         
#>  [5] "CalCurrentV3_utm.bgm"                      
#>  [6] "Final_CAM_Boxes_8.bgm"                     
#>  [7] "GOM_BGM.bgm"                               
#>  [8] "Guam_utm1.bgm"                             
#>  [9] "JFRE_ll.bgm"                               
#> [10] "JFRE_xy.bgm"                               
#> [11] "NGOM.bgm"                                  
#> [12] "Nordic02.bgm"                              
#> [13] "VMPA_setas.bgm"

If needed filter based on a specific string with the pattern argument:

afiles <- bgmfiles(pattern = "^antarc")
print(basename(afiles))
#> [1] "antarctica_28.bgm" "antarctica_99.bgm"

This package exists as a data package to install example files, there is just one function bgmfiles that runs file finding functions:

list.files(system.file("extdata", package = "bgmfiles"), pattern = NULL, full.names = TRUE, recursive = TRUE)

We don't need to load or attach the package to find these files, but using the installation mechanism is very convenient for R use.

Contribute!

If you would like to contribute example BGM files or to the package:

• contribute to the repository of example files https://github.com/AustralianAntarcticDivision/box-geometry-models
• submit a suggestion or issue for this package https://github.com/AustralianAntarcticDivision/bgmfiles/issues

or just get in touch directly via email.