matrix

[Rafael Becker]

Hello. I'm new to using Biodiverse. I would like to know more details about the matrix, "as they have relationships between pairs of labels or groups, for example, numbers of base pairs shared between pairs of labels." Where can I find this relationship? How is it calculated? Where?

[Shawn Laffan]

Hello Rafael,

Apologies for the slow response.

Matrices such as for genetic similarity are usually generated using other analyses outside Biodiverse.  For example, a phylogenetic tree is usually built using such a matrix.  In such cases you might be able to access the data associated with the tree.  An example of an analysis using such a matrix is Bickford et al. (2004, https://doi.org/10.1111/j.1365-2699.2004.01127.x ). 

There are not many examples of spatial analyses using such matrices, largely because phylogenetic methods are "cleaner" in the sense that there is no double-counting of shared base pairs between samples.  (With the usual caveat that the tree may also have errors).

The above cases compare relationships between sets of labels, e.g. species, genera, OTUs or whatever one happens to be working with.

Matrices are also calculated as part of the cluster and region grower analyses.  In these cases one is working with the groups (cells). These can be visualised in the GUI to see the relative relationships between a selected index group and each other group in the analysis.  See for example Laffan (2011, https://www.mssanz.org.au/modsim2011/E3/laffan.pdf ) and https://biodiverse-analysis-software.blogspot.com/2018/12/visualise-matrices-of-spatial-turnover.html


Regards,
Shawn.

On 9/01/2025 07:11, Rafael Becker wrote:

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Hello. I'm new to using Biodiverse. I would like to know more details about the matrix, "as they have relationships between pairs of labels or groups, for example, numbers of base pairs shared between pairs of labels." Where can I find this relationship? How is it calculated? Where? --
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