Biodiversity mapping functions for R (4): Phylogenetic Endemism (test against expectation)

Phylogenetic endemism – non-parametric tests

I am sequentially posting some self-contained functions for mapping biodiversity metrics in R, this one is:

pe.null.test.R [see full code at https://raw.githubusercontent.com/GregGuerin/biomap/master/pe.null.test.R]

Description --
Taking the outputs from the 'phylogenetic.endemism' function, tests whether observed phylogenetic diversity/endemism is higher than expected, using non-parametric methods

Details --
With the outputs from the 'phylogenetic.endemism' function, performs the following tests:

1) non-parametric significance test as to whether observed phylogenetic diversity/endemism is higher or lower than expected, given species richness (and observed species frequencies)

2) identifies and maps outliers (i.e. in terms of map grid cells that have higher or lower PD/PE) based on quantiles. As categorical: whether score lies more than 1.5 (or other user-defined amount) times outside the interquartile range; as continuous: the factor of the interquartile by which observed values differ from the median / 50% quantile). Returns vectors of values plus raster maps.

Usage --
An example:

mite.PE <- phylogenetic.endemism(mite, records="site", site.coords=mite.xy, sep.comm.spp="none", phylo.tree=mite.tree, sep.phylo.spp="none", weight.type="geo")

pe.mite.test <- pe.null.test(mite.PE)


And an example of the raster outputs from phylogenetic.endemism.R and pe.null.test.R: