However, it did not calculate the super class when first implemented. Now it does.
From version 5, Biodiverse calculates all CANAPE classes when a randomisation is run for an analysis that includes phylogenetic endemism and relative phylogenetic endemism.
Note that the CANAPE classed are only updated after at least one randomisation iteration has been run. If you have an existing randomisation then you can run one more iteration to trigger the calculation. Otherwise you can run a new randomisation with the same settings. This should not take long for most analyses, assuming they are consistent with the sizes of data sets in existing publications.
If you are wondering why it was not plotted in the first place, it was largely because the plotting system needed some re-engineering to allow for additional legend labels. This was done when the z-score and p-rank plotting was implemented, a little while after the initial CANAPE plotting.
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Shawn Laffan
02-Dec-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
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