Biodiverse analysis software: November 2022

Saturday 26 November 2022

Biodiverse version 4.0 has been released

We are pleased to announce the release of Biodiverse version 4.0.

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 4.0 represents 52 issues closed across 752 source code commits. 260 files have been changed.

Highlights of the changes since version 3.1 are at https://github.com/shawnlaffan/biodiverse/wiki/ReleaseNotes#version-40, and the related blog posts can be accessed via https://biodiverse-analysis-software.blogspot.com/search/label/Version4

A more detailed listing of the closed issues is at https://github.com/shawnlaffan/biodiverse/milestone/17?closed=1

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Shawn Laffan

26-Nov-2022

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

Friday 25 November 2022

Export cluster groups to shapefile

Biodiverse Version 4 allows users to export their cluster analyses using the same grouping process as is used to colour the branches.

This can be convenient to reconstruct the clusters in a GIS or other graphics system.

One issue is that only the cluster polygons (or points) are exported. If you want to attached data from the clusters then you can export them to delimited text using the Table Grouped method (with the same grouping parameters) and use a database join to attach them to the shapefile. The main reason for this is that shapefiles have a limit of 11 characters for field names, and many indices in Biodiverse exceed this (as well as sometimes containing characters other than letters, numbers and the underscore).

Another point to be aware of is that each group (cell) is a separate polygon so use a dissolve to merge them if you want to remove the internal boundaries.

Pictures are better than words so here are some screenshots.

An example cluster analysis, in this case with six clusters coloured.

The export option is in the usual place. It can also be accessed through the outputs tab.

In this case the export is set to use six clusters to match the display, but you can choose whatever you like. Other options include selecting by depth or by distance from the root (by length or depth).

And here we have a plot of the clusters. The colours differ but the clusters themselves are the same (and one can always update the colours).

If you want to use the grouped clusters in a spatial condition then it is easier to do so directly - see more details here.

If you just want to replicate the display then it is better to export the spatial data to an RGB geotiff and the tree to nexus with the colours embedded - see geotiff details here and the tree details here.

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Shawn Laffan

25-Nov-2022

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

To see what else 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

Trees: Merge single-child branches with their children

When Biodiverse is used to trim a tree to a subset of branches, for example to match the selected BaseData object, any branch with no remaining descendants is removed from the tree. All other branches are retained.

What this means is that some internal branches (nodes) can be left with only one child branch (node),. These can be referred to as single-child nodes and also knuckles. Retaining such nodes can be useful if some of the structure of the original tree needs to be kept, for example to indicate that there is phylogenetic data but that it has been removed from the tree. The counter to this is that most phylogenetic trees are samples and so are likely to be missing many branches anyway.

In the spirit of letting the user decide, Biodiverse version 4 supports the merger of internal branches with their children if they have only one child.

Names are important, and like many systems any node can be named in Biodiverse. In fact, all nodes have names but internal nodes default to a number with three trailing underscores (so "1___", "35___" etc). This allows many of the branch and clade level indices such as the phylogenetic endemism clade contributions and PD clade loss.

The general rule when merging is that the name of the merged node is whichever node had a non-default name to begin with. If both have non-default names then a child that is a terminal wins. Otherwise the parent name is used.

The process is best demonstrated using images.

An example tree plotted using depth instead of length to show the individual branches. The black branches are not in the basedata.

The tree trimming interface includes the option to merge single child nodes. In this case it is not selected.

The black branches from the previous screenshot have been deleted but one can see several branches that appear twice as long as the others. These are actually pairs of branches.

Repeating the process above but this time merging the single child (knuckle) nodes.

In this case all the branches are the same length because all single child branches have been merged with their children.

The examples above all use the tree trimming process, but if you have a tree that already has knuckles or forget to merge them then you can also merge the nodes directly from the tree menu.