Biodiverse version 6 contains new spatial conditions and visualisation options to work with polygons of label and tree node ranges.
Three polygon types are supported, convex hulls, concave hulls and circumcircles. Convex hulls and circumcircles are best avoided when modelling geographic ranges given they are sensitive to outliers, do not model arcuate shapes such as ranges that follow coastlines, and in the circumcircle case are gross generalisations. They are also not constrained by other factors, so a terrestrial taxon range can easily span oceans. However, they do represent useful models of regions that can be used in randomisations to define things such as the set of locations with which to swap labels, or to define dispersal extents in spatially constrained randomisations.
When used as a spatial condition, the range polygons can be applied either for a single label at a time, for the labels subtending a tree node, or for all labels in a groups' assemblage. In each of the latter two aggregate cases, the system uses the union of the component polygons rather than the polygons spanning the component groups. This produces multipart polygons that allow for gaps in the distributions, for example an internal node in a tree might have some tips on one side of a continent, and others on the opposite side. Or even across continents.
The spatial conditions also support arguments for the concave hulls to allow holes and to define the degree of concavity (a value of 1 matches the convex hull, 0 is maximum concavity).
Pictures are better than text, so here are some examples of the visualisations. The first few screen shots below are for the Labels tab but they also apply to Spatial Outputs.
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| Assemblage range polygons can be added via the Map menu. |
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| Tree range polygons are added through the Tree menu. |
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| Check the boxes to select which ones you want. You can also set the map or tree highlights to be the same, and set the values to match the other highlighting. This save a few mouse clicks and windows. |
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| Now when you hover on a cell, the selected polygons are shown. In this case it is the circumcircle and convex hull for each label in a group in the south west of Western Australia. |
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| And for contrast, here are the circumcircle and convex hull unions for the same assemblage. (It also shows why one should be cautious about using concave hulls to model taxon ranges). |
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| The same process applies to tree nodes (branches) when they are hovered over. |
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| The polygons for an ancestral branch of the previous plot. |
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| And the convex hulls. The shapes can get pretty weird, which is why one would normally use a concavity parameter greater than zero. |
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| This plot shows both that the visualisations work in the spatial outputs tab, and also why one generally wants to use the union of the polygons when many labels are being plotted. |
The plots above are all static but the system is dynamic. The set of polygons changes as you hover over a different branch or cell. If you want to hold a plot constant then right click on the branch or cell and Biodiverse will stop updating things. Remember to right click in the same pane again to bring back the dynamic updates.
An important point is the the spatial conditions use the cell centroids to define the polygons, where the visualisations use the cell polygons. This can lead to slightly different results in some cases. We can add an option to use polygons in the spatial conditions if there is a need.
As noted at the start, this functionality will be in Version 6. if you want to try it now then it is also part of the 5.99_001 development release.
