Saturday 22 December 2018

Visualise matrices of spatial turnover

A long standing feature in Biodiverse is the ability to interactively visualise spatial patterns of turnover.  This was described in Laffan (2011), but without detailed instructions for how to generate the data.

This blog post provides a few more details, as well as a video showing how to visualise and export the data.  Exported data can be used in, for example, NMDS analyses to relate turnover to environmental patterns (see González-Orozco et al. 2013 and González-Orozco et al. 2014).

One thing to note is that if you have a phylogeny selected then you can view which branches of the tree are shared or differ between the index and neighbour group (cell).  This is evident in the video, and is described in an earlier blog post: 

1.  Generate the data

If you only want to build the matrix (or matrices) then select this option. 

2.  View the matrices

[Update 2019-01-29]  The matrix can be viewed by opening it from the Outputs tab.  The default display from the cluster analysis is the dendrogram and its associated spatial plot.

Notice the regions that become evident depending on which cells are selected.  For example, cells in South-West Western Australia are strongly related to other cells in that region, cells in Northern Australia are related across part of the top-end, while those in Tasmania extend into Victoria.

3.  Export the data

Exporting of the data is via the Export menu at the left.  It can also be done using the export button in the Outputs tab when the matrix is selected.

Currently only delimited text is supported, but you can choose whether to use normal, sparse or GDM compatible output formats.  Hovering over the options gives more details about what they do.  

Shawn Laffan


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