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release after first phylolink sprint
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@temi temi released this 06 Oct 03:54
· 116 commits to master since this release
0.3
ae9d413

Main enhancements include:

  • users can upload own occurrence data on Occurrences tab, and can switch between a custom dataset and ALA data there. The choice of occurrence dataset selected then applies across all tabs until/unless the user changes the selection.
  • users can upload a tree with tips that do not match to ALA taxonomy (e.g. OTU, infraspecies, lineage). Users are given an opportunity to match tips to ALA taxonomy or leave unmatched and/or resolve mismatches. The tree can then be visualised with a custom occurrence set and characters, provided the names of the tips of the trees match the names used in the occurrence or character custom datasets.
  • users can upload custom character data on the Character tab, and can select this or other relevant character matrices (comes from the ALA list tool).
  • users can trim an uploaded tree to include/exclude taxa from a choice of Australia, ALA, or a custom species list.
  • raw data used to create Analysis and Map tab visualisations can be exported
  • sample size and other statistical information are shown on the Analysis tab
  • a tree admin page has been added to promote and withdraw expert trees (we have sourced more expert trees which will be loaded progressively)
  • an info box top right of visualisation landing page displays selected data source and number of taxa in the selected clade
  • users can delete their visualisation and trees
  • PD can be calculated for multiple polygons in a layer (e.g. for all IBRA regions)

Usability improvements include:

  • improved user interface layout and explanations for menu and wizard options
  • improved labelling for charts on Analysis and Character tabs
  • link to the spatial portal is available from the Map tab
  • ‘colour by’ dropdown on the Map tab now has human readable text
  • only character lists relevant to the selected tree are shown in the dropdown on Character tab
  • remarkable improvement in time taken to load species characters on the Character tab
  • on the Analysis tab environmental layers are now grouped into categories for easier selection, and metadata for selected environmental layers is available
  • users can now align tree leaves in a vertical line
  • layout, content and readability of PD results table in the spatial portal PD tool improved
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