Biodiverse analysis software: February 2023

Tuesday, 7 February 2023

Biodiverse version 4.1 has been released

We are pleased to announce the release of Biodiverse version 4.1.

Versions for Windows, Mac and Linux (Ubuntu) are available and can be accessed via https://github.com/shawnlaffan/biodiverse/wiki/Downloads

Installation instructions are at https://github.com/shawnlaffan/biodiverse/wiki/Installation

Version 4.1 represents five issues closed across 96 source code commits.

Highlights of the changes since version 4.0 are at https://github.com/shawnlaffan/biodiverse/wiki/ReleaseNotes#version-41, and the related blog posts can be accessed via https://biodiverse-analysis-software.blogspot.com/search/label/Version41

A more detailed listing of the closed issues is at https://github.com/shawnlaffan/biodiverse/milestone/19?closed=1

The main user visible change is that z-score indices are now plotted using a divergent colour scale using z-score significance thresholds. More details are in this blog post.

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Shawn Laffan

07-Feb-2023

For more details about Biodiverse, see http://shawnlaffan.github.io/biodiverse/

For a list of some of the analyses Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList

You can also join the Biodiverse-users mailing list at https://groups.google.com/group/Biodiverse-users or start a discussion at https://github.com/shawnlaffan/biodiverse/discussions

Plotting z-score indices and randomisation results

From version 4.1, Biodiverse will plot indices it knows are z-scores using a divergent colour scheme, with values classified into intervals (adapted from the ArcGIS implementation). This makes it much easier to see which locations are potentially significant given the expected values.

This process applies to indices like the Net Relatedness Index and Net Taxon Index, all of the Gi* indices such as for group properties and label properties (more on such analyses here), as well as the z-scores generated by randomisation analyses. It also applies to branches of a cluster dendrogram when indices have been calculated for each node/branch.

You can export the coloured images to geotiff in the same way as for any data set.

There is not much more to it than that, so here are some images of what it looks like for a spatial analysis using the Acacia data set of Mishler et al. (2014).

The Net Relatedness Index

Z-scores for Phylogenetic Diversity after a spatial randomisation process

Net Relatedness Index calculated for the groups (cells) under each branch of a cluster analysis. Coloured cells are associated with the dendrogram branches that intersect the blue slider bar.

The spatial distribution of PD significance (left) with branches occurring in a cell in south-west Western Australia (black dot) coloured by clade score significance against the same randomisation process.