Comments (3)
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.
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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.
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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.
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Related Issues (17)
- Single colour gradient PD and richness HOT 1
- Intervals and gradients mixed HOT 3
- Filter for establishment means HOT 1
- Percentages vs absolute PD
- Feature request HOT 3
- Is it possible to query the Open Tree directly? HOT 5
- Support for Nexus format as input in PhyloNext HOT 1
- OToL fetching: Implement informative help messages for missing taxa
- [feature] Implement notifications for coordinate precision and uncertainty
- Known issues
- indices and leaflet_var params HOT 2
- To do
- pandoc document conversion failed with error 137 HOT 6
- Add list of contributing GBIF datasets to output directory HOT 4
- Identification of title on execution report
- Intervals of legend change unexpectedly HOT 1
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