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PhyloNext: Changelog

This project tries to adhere to Semantic Versioning.
For version numbering, we use the following convention: MAJOR.MINOR.PATCH.
Each element increases numerically (e.g., 1.9.0 -> 1.10.0 -> 1.11.0).

v1.5.0 - [dev]

  • Added support of phylogenetic trees in Nexus format;
  • Fixed geometry of World Geographical Regions (duplicated vertices, loop crosses, anti-meridian problem);

v1.4.0 - [July 21, 2023]

  • Added: Estimation of Hurlbert's ES index (a measure of species diversity that accounts for sample size);
  • Changes: The pseudo-abundance of species is now determined by the number of GBIF records per grid cell;
  • Fixed: The Open Tree has implemented significant updates to the API that disrupted existing integrations;

v1.3.0 - [May 25, 2023]

  • Biodiverse updated to v4.3 Biodiverse changelog:
  • Added: maxyear parameter for occurrence filtering based on the upper bound of collection year

v1.2.0 - [Apr 11, 2023]

  • Added: spatially-constrained randomizations;
  • Added: spatial filtering using user-supplied polygons;
  • Added: CANAPE output in tabular format from Biodiverse;
  • Added: leaflet_canapesuper parameter (for 3-class or 4-class endemism types in CANAPE);
  • Added: geographic coordinates of H3 cells to the output table;
  • Added: leaflet_mapshots script;
  • Changes: previously, the spatial unit was categorical (H3 grid cell); to spatially constrain records, now we use geographic coordinates of grid cells;
  • Changes: record counts, derived dataset, and additional filtering now re-use the same code base;
  • Changes: screen output is less verbose now;
  • Changes: PRNG randomization seeds are explicit now;
  • Fixed: Number of Biodiverse randomizations per thread;
  • Fixed: CANAPE index requirements;
  • Fixed: antimeridian issue in static visualization;
  • Fixed: record counts and derived dataset take polygon-filtering into account;

v.1.0.0 - [Feb 1, 2023]

First stable version.

  • Added: derived datasets;
  • Added: basis-of-record filtering;
  • Added: GeoPackage output;
  • Added: Newick tree output;
  • Added: maxage and phyloonly parameters for phylogenetic tree fetching from the Open Tree of Life;
  • Added: leaflet_sescolor parameter to adjust Z-score coloring scheme;
  • Added: CI tests;
  • Fixed: urban areas shapefile;

v.0.0.2 - [Dec 22, 2022]

Code refactoring targeting for the execution in a cloud environment (in particular, MS Azure Batch).

  • Added: Leaflet-based interactive visualization;
  • Added: redundancy index;
  • Added: removal of extinct species;
  • Added: removal of human records (genus Homo);
  • Fixed: correct usage of val and path for input file staging;
  • Changes: class is a reserved word in Nextflow; now we are using classis parameter to refer taxonomic rank of Class;

v.0.0.1 - [Jun 1, 2022]

The initial release of PhyloNext.
First commit - Feb 09, 2022.