README.Rmd

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# 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: 

```{r,eval=FALSE}
install.packages("bgmfiles")
```

Install the develop version from Github using `devtools`. 

```{r,eval=FALSE}
# install.packages("devtools")
devtools::install_github("AustralianAntarcticDivision/bgmfiles")
```

## Usage 

List the available raw files available in this package. 

```{r}
library(bgmfiles)
files <- bgmfiles()
print(basename(files))
```

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

```{r}
afiles <- bgmfiles(pattern = "^antarc")
print(basename(afiles))

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

```{r, eval=FALSE}
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.