Meaning of randomisations values given by Biodiverse

[sonqollay]

Hi everyone! I'm making a lot of analysis of PD from microbiome data. I calculated de PD of two different vegetation units (shcrubland and forest) and the value of PD is higher in the forest. However when I calculated some randomisations indexes, like PD random, Relative PD and random RPD there is no a clear pattern. So I'm asking what is the meaning of each value given by the algorithm? If I want to analyze a particular site where the oberved PD is higher or lower than expected by chance, what kind of information gives me the value of the PD randomized (i.e. 0.7). Is this meaning that the PD is higher in a 0.7 rate or something like that?

Thank you in advance!

[shawnlaffan]

For the randomisations, the easiest way to interpret them is to use the p-rank lists that are generated. This needs a more recent version that 4.3. There is not yet a full release of version 5 but you can use 4.99_010. The analyses are stable, it's just the GUI that needs testing.
https://biodiverse-analysis-software.blogspot.com/2023/04/changes-to-randomisation-results-p-rank.html

Some more info is on the help system https://github.com/shawnlaffan/biodiverse/wiki/AnalysisTypes#where-do-the-randomisation-results-go-and-what-do-they-mean

And also in a series of blog posts: https://biodiverse-analysis-software.blogspot.com/search/label/randomisations

The help system does need a lot of work, so for anyone reading this: contributions are always welcome.

[shawnlaffan]

(I'll also shift this to the discussion system as it's not a bug per se).