jiho / atlasr

Niche modelling code for the Biogeographic Atlast of the Southern Ocean

License and citation

This code is licensed under a Creative Commons Attribution 3.0 Unported license (CC BY 3.0, http://creativecommons.org/licenses/by/3.0/). It allows you to use, share and remix the code as long as you cite us in the following way:

J-O Irisson, S Mormede, B Raymond (alphabetical order). atlasr: R code for ecoregionalisation. https://github.com/jiho/atlasr.

The data layers downloaded automatically by this code are under a Polar Information commons license http://polarcommons.org/ethics-and-norms-of-data-sharing.php and copyright Ben Raymond. The PIC license have similar terms to the CC BY license.

The GDM computation functions (files gdmfuncs.1.1.R and gdmlib.dll) are downloaded from http://www.biomaps.net.au/gdm/, retain their original license and should be cited as advised on the original page.

How to get started

The scripts are all written in R and should work on all platforms, provided that you have the right setup.

Pre-requisites

Install R and associated tools

Go to the R download site and download R for your system.

• Mac OS X users, you should get the R-**.pkg as well as tcltk-**.pkg in the tools subdirectory further down the page. Installing is just a matter of double-clicking and saying OK to everything.

• Windows users, you should select the base subdirectory and then the main Download R ** for Windows link. Install with the default choices everywhere.

• Linux users, you should get it from your package management system rather than from the above site. The package is usually called R-cran.

We recommend using a specialized editor on top of R, which will become your only interface to R. Download and install RStudio; on the download page, select RStudio Desktop and it should detect your operating system and present the appropriate file for you on the next page.

Download the latest version of the scripts

These scripts are rapidly evolving (at times...) and the latest version is always kept on this page (https://github.com/jiho/atlasr). You can download a zip file using the ZIP button or directly at the address:

https://github.com/jiho/atlasr/zipball/master

Unzipping the file should create an atlasr directory with all the scripts.

Run an analysis

Double-click the atlasr.Rproj project file inside the atlasr directory. This will start RStudio and load R in the appropriate location. Load all functions and update the environemental data repository by typing the following command in the "Console" section:

source("initialize.R")

The first time you do this, it will be quite long (over an hour) because it will download all necessary R packages and all environment data layers (well over a Gb of data). In R's console type the command you want to run. These are for example:

do.bioreg()
do.brt()
do.gdm()

Read documentation

For some analyses, documentation is provided in the documentation directory.