FIDIMO Installation

Software Prerequisites

To run FIDIMO a working GRASS GIS installation, certain GRASS add-ons, Python and certain Python modules as well as the statistical software R are required.

1. Installing GRASS GIS

FIDIMO was initially built for GRASS GIS 6.4.2 or 6.5 so GRASS 7.0 is not tested yet. Further it is highly recommended to read the tutorial pages on the GRASS WIKI to get generally familiar with the GRASS GIS software.

2. Needed GRASS Add-ons

For using FIDIMO with GRASS GIS the GRASS AddOns r.stream.basins and r.stream.order have to be installed.

3. Python Installation

FIDIMO is entirely programmed in python and therefore needs an official python distribution and some additional python libraries. Following has to be installed:

4. R INSTALLATION

For the estimation of species-specific dispersal distances and to general the corresponing leptokurtic dispersal kernels FIDIMO depends on the statistical software R and its package “fishmove” which needs to be installed before installing FIDIMO.

5. FIDIMO Installation

In general, FIDIMO can be installed like any other GRASS GIS add-on using the built in g.extension. The FIDIMO package can be found here and includes besides the FIDIMO model also a manual.

In some cases, especially with certain operating systems the installation via g.extension can be tricky. Please have a look at the GRASS add-ons page for more details. Furthermore I can really recommend the GRASS mailing-lists to get a lot of useful help from the GRASS user community.

As an example here the installation procedure that can be run from within a fresh Ubuntu installation e.g. within a Virtualbox environment. This is a working setup that has been tested and approved to work:

### To run in the bash terminal to install following packages:
 sudo add-apt-repository ppa:grass/grass-devel
 sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable
 sudo apt-get update
 sudo apt-get install grass643 grass70 grass-gui grass70-gui
 sudo apt-get install python-scipy
 sudo apt-get install r-base
 sudo apt-get install python-rpy2
### start R and install fishmove
 R install.packages("fishmove",repos="http://cran.at.r-project.org/")
### Start Grass (grass64 or grass70) from the terminal
 # install GRASS add-ons from within a GRASS session
 g.extension extension=r.stream.order
 g.extension extension=r.stream.basins
 g.extension extension=r.fidimo

A FIDIMO sample dataset (GRASS GIS location and mapset including an extracted river network, same as used in Radinger et al. 2013, Ecological Informatics) is available via GitHub: https://github.com/jradinger/fidimo_example_mapset (can be used similar to other GRASS example locations, see http://grass.osgeo.org/download/sample-data/).