Different amount of PD between 2 runs about phylonext HOT 3 OPEN

If the reported PD index is PD_P then that is the proportion of the tree in each sample, calculated as the PD score divided by the sum of all branch lengths. This could explain the differences.

See https://github.com/shawnlaffan/biodiverse/wiki/Indices#phylogenetic-diversity for index names and formulae.

from phylonext.

I think I am not looking at PD_P because the index is showing the absolute values of PD, not the percentages. I attached 2 screenshots of the result we get when we run the mentioned phylogenies. The PD shows different values, although Wollemia nobilis does not occur there (see third screenshot). This is the case for many of the hexagons.

from phylonext.

I think I am not looking at PD_P because the index is showing the absolute values of PD, not the percentages.

The PD legend is in percentages, though, which suggests PD_P. @vmikk can you clarify?

In terms of the spatial distribution it would appear that the Wollemia data are not being cleaned correctly. Only one of the hexagons in the third plot should contain it. Several appear to be associated with capital cities and thus probably are herbaria and/or botanic gardens.

from phylonext.