This file describes the installation of SpeciesGeoCoder on Mac OSX, GNU/Linux and Windows systems.

For the impatient

Download the latest version from https://github.com/mtop/speciesgeocoder/releases

unzip speciesgeocoder-x.x.x.zip
cd speciesgeocoder-x.x.x
./geocoder.py -l example_data/localities.csv -p example_data/polygons.txt -t example_data/*.tif

Dependencies

The following package is required for SpeciesGeoCoder to run:

• argparse (Module included in python v2.7. Available at https://pypi.python.org/pypi/argparse)

The following packages are optional and will depend on which kind of analyses you will do:

• osgeo (The GDAL library available at https://pypi.python.org/pypi/GDAL/). Required for altitudinal coding
• R (Available from http://www.r-project.org/). Required if you want to use the plot functions or do stochastic mapping
• R-packages: rgeos, maptools, maps, mapdata, raster, optparse, ape, geiger, phytools (R will prompt you for the missing packages)

Installing on Mac OSX

Download the latest version from https://github.com/mtop/speciesgeocoder/releases

1. Unzip the file by double-clicking on it.
2. Open a terminal window and use the command "cd" to move into the directory "speciesgeocoder-x.x.x" (where "x.x.x" will indicate the version number of the latest release; tips: instead of writing the path, you can just 'drag' the folder to your terminal window)
3. Copy and paste the following command into your terminal window to make sure everything works as expected:

./geocoder.py -l example_data/localities.csv -p example_data/polygons.txt -t example_data/*.tif

Installing on Windows

1. Download and install the Latest Python 2 Release from https://www.python.org/downloads/windows/
2. Direct your browser to http://www.lfd.uci.edu/~gohlke/pythonlibs/ and then download and install GDAL for python 2.7
3. Download and install R from http://cran.r-project.org/bin/windows/base/

In addition, you'll also have to add the R executables to your PATH (in order for SpeciesGeoCoder to find it).

1. Find the directory that the R program is installed in (e.g "C:\Program Files\R\R-3.1.1")
2. From the desktop, right-click My Computer and click Properties.
3. In the System Properties window, click on the Advanced tab.
4. In the Advanced section, click the Environment Variables button.
5. Click the Environment Variables button, highlight the Path variable in the Systems Variable section and click the Edit button.
6. Add ";C:\Program Files\R\R-3.1.1\bin" (if that is where the R executables are found, don't forget the preceding ";" character) to the end of line and click "Ok".

Change permissions to the R "library" directory in the following way: (this is nessesary as SpeciesGeoCoder will have to automatically install additional R packages).

1. Right click on "C:\Program Files\R\R-3.1.1\library" and select properties -> Security.
2. Click "Edit".
3. In "Group our user names" select your name.
4. Mark the "Full control" checkbox.
5. Click "Ok".

Installing on GNU/Linux

Download the latest version from https://github.com/mtop/speciesgeocoder/releases

unzip speciesgeocoder-x.x.x.zip
cd speciesgeocoder-x.x.x
./geocoder.py -l example_data/localities.csv -p example_data/polygons.txt -t example_data/*.tif

Optionally you can make a symbolic link from a directory in your PATH to the file "speciesgeocoder" in the "speciesgeocoder-x.x.x" directory.

Installing and running the development version

git clone [email protected]:mtop/speciesgeocoder.git
cd speciesgeocoder/
./geocoder.py -l example_data/localities.csv -p example_data/polygons.txt -t example_data/*.tif