Biogeography (Donoghue & Smith)

Introduction

Running lagrange is simple if you have the correct python and SciPy. The instructions for doing this for various machines is found here, but will also be presented below along with a tutorial on getting input files correct and running an example.
(Figure 1).

Preparation and Installation

Ubuntu Linux

Simply type

sudo apt-get install python-scipy

This should work for other Linux derivatives that use the apt-get system.

MacOSX

10.5

For MacOSX users with version 10.5 you should be able to use the installer at Macinscience. Here you download this and run

sh superpack.sh

This will download install scipy and ipython (as well as some other programs). You will have to type your password at some point. Do this before you come to Bodega as the downloads are large. Once this is installed you will be able to run lagrange.

10.4

For MacOSX users with version 10.4 there are different downloads depending on whether you have a PPC or Intel machine. However, before installing SciPy, you will need to install the current version of python. You can find this here. You will have to go through the page to find the one for your machine, but it is free and should be self explanatory. If you have an Intel machine you will need this link. If you have a PPC machine you will need this link. Unzip them and run the installers. These are, of course, no longer support so beware.

Windows

You can download Python from here. There are installers for SciPy available here.

After installation

After you install SciPy (and Python depending on what you had to do) you will need to make sure that SciPy is correctly installed and will load. To do this go to your terminal and type

python

then type

import scipy

There should be no errors and it should just give you a new line. If this happens, you are good to go with lagrange.

Lagrange

Once the python and scipy preparation have been completed you can download lagrange from here. Unzip and untar the file (typically in Mac you do this by double clicking it). Now you should be able to run the example within lagrange just to make sure that it works. To do this, go back to your terminal and navigate to the lagrange folder, so for example if you downloaded and unzipped in the Downloads directory you can get there by typing

cd /Users/<yourusername>/Downloads/lagrange2.0.1/

Once you are there in the terminal, type

python psychotria.py

and you should see things running. If this is happening then you are good to proceed. If not, then you will be unable to run lagrange and please send me your errors (sasmith at nescent dot org).

Tutorial

Please download this package (datasets.zip) that contains a pdf and the example files that will be used.

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