Package index
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dimoose - A dichotomous key
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keyFromSpreadsheet() - Build a key from a spreadsheet
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keyFromLeads() - Build a dimoose key from a table of leads
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keyFromRpart() - Build a dimoose key from a classification tree
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generateTree() - Generate a tree from a feature matrix
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keyDiagram() - Draw a key as a box diagram
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exportWizard() - Export an interactive dichotomous key
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toNewick() - Write a key as Newick, with safe labels or node annotations
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toIgraph() - Convert a key to an igraph directed graph
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toTreedata() - Convert a key to a tidytree treedata (for ggtree)
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toAuspiceJSON() - Export a key as Auspice (Nextstrain) JSON v2
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sharkKey()arachnidaKey()vibrioKey()montanaKey() - Example keys
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montana - Key to the native broadleaf trees of Montana
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arachnida - Key to the Orders of Arachnida
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vibrio - Vibrio consensus identification matrix
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phylotree17 - PhyloTree Build 17: the human mitochondrial DNA phylogeny
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phylotree17_mutations - PhyloTree Build 17 mutations, one per row
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phylotreeKey() - Build an identification key from PhyloTree Build 17
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importFishbase() - Import a dichotomous key from FishBase
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parseFishbase() - Build a dimoose object from FishBase key pages
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rawhtml - Raw FishBase key tables
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visionModel() - Load a vision model for embedding images
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modelMeta() - Model details as metadata rows
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embedImages() - Embed images
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embedTexts() - Embed texts
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imageSet() - A set of labelled images
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imageMeta() - Embed images in a key's metadata
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imageMime() - MIME type of an image file from its first bytes
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discoverSniglets()discoverTerms() - Discover sniglets by clustering patch embeddings
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snigletScores()termScores() - Score images against sniglets
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snigletNames() - Names of a key's sniglets
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renameSniglets() - Rename sniglets
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inventNames() - Invent pronounceable names
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keyFromSniglets()keyFromTerms() - Build a key from sniglet scores
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vocabularyPrompts() - Prompts for a vocabulary of visual features
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keyFromClusters() - Build a key by clustering classes and describing each split
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patchExemplars() - Add example crops to a sniglet key
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scoreImages() - Score new images against a key's features
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featureTable() - A table of machine-computable features
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featureScores() - Compute a key's feature scores from embeddings
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classify() - Follow a key by machine
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evaluateKey() - Accuracy of a key followed by machine
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looKey() - Leave-one-out evaluation of a key builder
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keyFromAlignment() - Build a key from a multiple sequence alignment
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alignmentScores() - Score aligned sequences against a key built from an alignment
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readHaplogrep() - Read a Haplogrep / PhyloTree tree XML
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haplotypeMatrix() - Which mutations each haplogroup carries
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macroHaplogroup() - Macrohaplogroup of a haplogroup
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recurrentPositions() - Recurrent (homoplasic) mutation sites
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mecit() - Mixed-effects conditional inference trees
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keyFromMecit() - Turn a mixed-effects tree into a key
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simulateExpression() - Simulate expression data on PhyloTree
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splitVariables() - Variables a fitted tree splits on