Comments (3)
Do you mean PD for all taxa in a sample? If so then that's pretty simple to calculate.
BTW, you might also be interested in some of the per-branch indices for PD clade contribution and potential loss.
https://github.com/shawnlaffan/biodiverse/wiki/Indices#pd-clade-contributions
https://github.com/shawnlaffan/biodiverse/wiki/Indices#pd-clade-loss
https://github.com/shawnlaffan/biodiverse/wiki/Indices#pd-clade-loss-ancestral-component
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Yes, indeed: PD for all taxa in a sample. How should it be calculated then?
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There are several ways, but if it is to be done within the phylonext framework then it could be a case of generating a set of dummy spatial units, where each unit has the taxa of interest for each sample.
Another approach is to use text groups. So if you already have a field in your data to denote the sample name then you can set the cellsize to be -1. This is then treated as an exact match. Actually, this is how the phylonext system uses the H3 hexagons so it should be relatively straightforward. @vmikk is the authoritative source for the system, so hopefully can comment further here.
Mapping the data is then a case of using a database join to the spatial units based on the sample name, assuming the samples are spatial. Otherwise the table will likely be all that is needed for further calculations.
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Related Issues (17)
- 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
- Single colour gradient PD and richness HOT 1
- Intervals and gradients mixed HOT 3
- Filter for establishment means HOT 1
- Percentages vs absolute PD
- Different amount of PD between 2 runs 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
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