SPACoDi

Written by Olivier Hardy

Description

SPACoDi (Spatial & Phylogenetic Analysis of Community Diversity) is primarily designed to characterise the structure of communities using inventory data in the form of a presence/absence or abundance species-plot matrix. The structure can be interpreted according to the spatial position of plots (subcommunities) and/or according to the phylogenetic or functional relationships between species (community phylogenetic structure), following methods described in Hardy & Senterre (2007) and Hardy (2008). SPACoDi can also characterise the phylogenetic structure of species traits using phylogenetic autocorrrelograms.

SPACoDi is conceptually very similar to SPAGeDi («Spatial Pattern Analysis of Genetic Diversity»; Hardy & Vekemans 2002), a software designed to characterise the genetic structure of populations. Hence, many methods of data analysis are inspired by population genetics theory and practice, bridging a link between community ecology and population genetics.

To describe community structure, SPACoDi can compute various statistics describing (phylogenetic) diversity of plots and (phylogenetic) distances between plots in a pairwise fashion. To analyse how values of pairwise comparisons are related to geographical distances, SPACoDi computes 1°) average values for a set of predefined distance intervals, 2°) linear regressions of pairwise statistics on geographical distances (or their logarithm). The slopes of these regressions provide a synthetic measure of the strength of spatial structuring. SPACoDi can also treat data without spatial information, providing global estimates of plot differentiation and/or matrices of pairwise statistics between plots.

Different permutation procedures allow testing if there is significant plot differentiation, spatial structure, or if phylogenetic (or functional) distance between species carries relevant information about community structure (i.e. significant community phylogenetic structure).

Currently the version is still a beta release (0.10). It is possible that particular data sets cause a program crash. If you encounter such problems, please first check that data files are correctly formatted and that you use the last available version. If the problem persists, send me an e-mail describing it and I will try to solve it if I find time (sorry if you have to wait).

How to run SPACoDi

SPACoDi runs under Microsoft Windows but has no fancy windowing features. You can launch the program in two ways: 1. by a double click on the program which will ask you questions defining the instructions (an instruction file will be produced); 2. using a preset instruction file by dragging the icon of this file onto the icon of the SPACoDi program.

The instruction file is a simple text file specifying: 1. the types of data available and the names of files containing them, 2. the statistical analyses to perform. Each type of instruction is defined by a command (in uppercase letters) starting a new line followed by specific details (e.g. name of a file, computation parameters…).

1. SpaCoDi program for Windows (no installation required) with manual and example of data files
   

How to cite SPACoDi

Hardy OJ (2010) SPACoDi 0.10: a program for Spatial & Phylogenetic Analysis of Community Diversity. http://ebe.ulb.ac.be/ebe/Software.html