Tuesday 19 September 2017

Export lists to Newick format

In version 2 of Biodiverse you can now export any lists that are stored on a tree to the Nexus format.

A useful example of this is when you run calculations for each node of a cluster tree, thereby using the terminal nodes (branches) below each branch as the neighbourhood units in a spatial analysis.  An example of this in practice is in Gonz├ílez-Orozco et al. (2014)  where the environmental parameters of each biogeographic region were summarised (see table 4 in that paper).

In a previous post I described how you can export the colours from the Biodiverse display to Nexus format to more easily generate figures for publication.  Now you can also export the values of the results to Nexus, which means you can use them for further analysis or alternate display methods using tools such as FigTree or Mesquite.

Below are images showing the general process in practice.

Note that the Nexus format does not support a hierarchy of names, so the lists need to be flattened.  Given that it is possible to have items with the same value within different lists in Biodiverse (e.g. for list indices that generate a result per label in a set), the exported names use the list name followed by the item name, joined by two underscores e.g. SPATIAL_RESULTS__ENDC_CWE.

Setting up a cluster analysis where a set of endemism indices will be calculated for each branch in the cluster tree.

Displaying the results, in this case the Corrected Weighted Endemism (CWE) for the set of branches intercepted by the blue slider bar on the dendrogram

The exported tree, but with default display settings.  

And now with thicker branches, and the colours set to show the CWE results using a divergent red-blue colour scheme.

And with the Richness index plotted using the HSB spectrum.

And here is a video of the process in Biodiverse (partly as a test to see if it works):

Shawn Laffan

For more details about Biodiverse, see http://purl.org/biodiverse 

For the full list of changes in the 1.99 series (leading to version 2) see https://purl.org/biodiverse/wiki/ReleaseNotes (for all issues addressed or being targeted to fix for version 2, see https://github.com/shawnlaffan/biodiverse/milestone/4 ).

To see what else Biodiverse has been used for, see https://purl.org/biodiverse/wiki/PublicationsList

You can also join the Biodiverse-users mailing list at http://groups.google.com/group/Biodiverse-users

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