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dimoose 0.1.2

  • keyDiagram() also writes .png and .pdf files when the ‘rsvg’ package is installed.
  • With the ‘magick’ package installed, keyDiagram() shrinks thumbnails to 112 px and imageMeta() (and so keyFromSpreadsheet()) scales photos down to at most 1200 px (maxSize), so keys made from camera photos stay small. The Montana diagram drops from 1.2 MB to 83 KB.
  • keyDiagram() sets the part of a result in parentheses in italics only when it is a scientific name: parsed by gnparser when ‘rgnparser’ is installed, otherwise a capitalised genus and lower-case epithets. “Willows (several species)” stays upright.

dimoose 0.1.1

  • keyFromSpreadsheet() builds a key from a plain CSV spreadsheet (one row per lead, with optional questions and photos) and reports mistakes by spreadsheet row.
  • keyDiagram() draws any key as a top-down box diagram (SVG), with photos in the result boxes.
  • New vignette, “A photo key to Montana’s broadleaf trees”, including how to make your own key from a spreadsheet.
  • montanaKey() and the montana dataset: a key to the eleven native broadleaf trees of Montana with photos from Wikimedia Commons, kept as a spreadsheet template in inst/extdata/montana/.

dimoose 0.1.0

  • First release.
  • Renamed from moose, because CRAN has an unrelated package of that name. The key class is now dimoose (dimoose$new(), inherits(x, "dimoose")), the S3 classes are dimooseVisionModel, dimooseTerms and dimooseSniglets, the vision tests read DIMOOSE_CLIP_WEIGHTS, and the repository is https://github.com/leipzig/dimoose. The first argument of exportWizard() is now key.
  • Dichotomous keys as dimoose objects: build them from lead tables (keyFromLeads()), classification trees (keyFromRpart(), generateTree()) or FishBase (importFishbase(), parseFishbase()), then validate, summarise and convert them to data.tree, Newick, igraph, treedata and Auspice JSON.
  • Example keys and datasets: sharks (FishBase key 1), Arachnida orders, Vibrio (Noguerola & Blanch 2008) and PhyloTree Build 17.
  • exportWizard() writes a self-contained, mobile-friendly HTML key.
  • Automated key generation from photos: sniglets, recurring visual features given coined names (discoverSniglets(), keyFromSniglets()) that can be renamed afterwards (renameSniglets()); vocabulary questions (keyFromClusters()); machine classification and evaluation (classify(), evaluateKey(), looKey()); and an optional open_clip vision layer through reticulate (visionModel()), including BioCLIP.
  • Automated key generation from a multiple sequence alignment (keyFromAlignment()), with the tree built by ape, phangorn, FastTree or IQ-TREE.
  • Mixed-effects conditional inference trees (mecit(), keyFromMecit()) and simulated expression data on PhyloTree (simulateExpression()).