Package: dimoose 0.2.0

dimoose: Tools to Reshape and Manipulate Dichotomous Keys Used in Taxonomic Identification

Transforms between dichotomous identification keys and a variety of phenotype formats, including feature matrices, and generates interactive dichotomous key wizards. Imports keys from 'FishBase' <https://www.fishbase.se/keys/allkeys.php> and includes PhyloTree Build 17, the human mitochondrial DNA phylogeny (van Oven 2015, <doi:10.1016/j.fsigss.2015.09.155>), as distributed by 'Haplogrep' 3.

Authors:Jeremy Leipzig [aut, cre]

dimoose_0.2.0.tar.gz
dimoose_0.2.0.zip(r-4.7-any)dimoose_0.2.0.zip(r-4.6-any)dimoose_0.2.0.zip(r-4.5-any)
dimoose_0.2.0.tgz(r-4.6-any)dimoose_0.2.0.tgz(r-4.5-any)
dimoose_0.2.0.tar.gz(r-4.7-any)dimoose_0.2.0.tar.gz(r-4.6-any)
dimoose_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
dimoose/json (API)

# Install 'dimoose' in R:
install.packages('dimoose', repos = c('https://leipzig.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/leipzig/dimoose/issues

Pkgdown/docs site:https://leipzig.github.io

Datasets:
  • arachnida - Key to the Orders of Arachnida
  • montana - Key to the native broadleaf trees of Montana
  • phylotree17 - PhyloTree Build 17: the human mitochondrial DNA phylogeny
  • phylotree17_mutations - PhyloTree Build 17 mutations, one per row
  • vibrio - Vibrio consensus identification matrix

On CRAN:

Conda:

biodiversitybotanydichotomous-keyidentification-keyphylogeneticsspecies-identificationtaxonomy

3.90 score 7 scripts 57 exports 26 dependencies

Last updated from:1831f440a6. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK153
source / vignettesOK453
linux-releaseOK175
macos-releaseOK165
macos-oldrelOK131
windows-develOK131
windows-releaseOK126
windows-oldrelOK122
wasm-releaseOK129

Exports:alignmentScoresarachnidaKeycheckNamesclassifydimoosediscoverSnigletsdiscoverTermsembedImagesembedTextsevaluateKeyexportWizardfeatureScoresfeatureTablegenerateTreehaplotypeMatrixidentifyPhotosimageMetaimageMimeimageSetimportFishbaseinventNameskeyDiagramkeyFromAlignmentkeyFromClusterskeyFromLeadskeyFromMecitkeyFromRpartkeyFromSnigletskeyFromSpreadsheetkeyFromTermslooKeymacroHaplogroupmecitmodelMetamontanaKeyparseFishbasepatchExemplarsphylotreeKeyrawhtmlreadHaplogreprecurrentPositionsrenameSnigletsscoreImagessharkKeysimulateExpressionsnigletNamessnigletScoressplitVariablessuggestSpeciestermScorestoAuspiceJSONtoIgraphtoNewicktoTreedatavibrioKeyvisionModelvocabularyPrompts

Dependencies:askpassbase64encclicurldata.treegluehttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigR6rlangrpartrvestselectrstringisystibbleutf8vctrswithrxml2

A photo key to Montana's broadleaf trees
Make your own key in three steps | The Montana key | A diagram of the key | An interactive key | Checking a photo against the key | Diagrams of other keys
Rendered frommontana-hardwoods.Rmdusingknitr::rmarkdown

Last update: 2026-10-19
Started: 2026-10-16

Automated key generation from a sequence alignment
What the command does | An example | Choosing the phylogeny program | Rooting | Numbering sites | When a fork has no clean difference | Identifying a sequence
Rendered fromalignment-keys.Rmdusingknitr::rmarkdown

Last update: 2026-10-06
Started: 2026-10-02

Automated key generation from photos
What you need | The short version | Setup | Step 1: say which photo shows what | Step 2: load a vision model | Step 3: embed the photos | Step 4: build the key | Sniglets | Questions in words | Step 5: look at the key and share it | Step 6: rename the sniglets | How good is the key? | Identifying a new photo | Any model, no Python | Choosing a model: CLIP or BioCLIP
Rendered fromvision-keys.Rmdusingknitr::rmarkdown

Last update: 2026-10-06
Started: 2026-10-01

Mixed-effects conditional inference trees on PhyloTree
The problem: same mutation, many clades | Simulated data with known truth | Fitting a MECIT | A MECIT is a key | Random slopes | References
Rendered frommecit.Rmdusingknitr::rmarkdown

Last update: 2026-10-06
Started: 2026-10-02

Readme and manuals

Help Manual

Help pageTopics
Score aligned sequences against a key built from an alignmentalignmentScores
Key to the Orders of Arachnidaarachnida
Check a key's species names against GBIFcheckNames
Follow a key by machineclassify
A dichotomous keydimoose
Discover sniglets by clustering patch embeddingsdiscoverSniglets discoverTerms
Embed imagesembedImages
Embed textsembedTexts
Accuracy of a key followed by machineevaluateKey
Example keysarachnidaKey exampleKeys montanaKey sharkKey vibrioKey
Export an interactive dichotomous keyexportWizard
Compute a key's feature scores from embeddingsfeatureScores
A table of machine-computable featuresfeatureTable
Generate a tree from a feature matrixgenerateTree
Which mutations each haplogroup carrieshaplotypeMatrix
Name what a photo shows, as precisely as the evidence allowsidentifyPhotos
Embed images in a key's metadataimageMeta
MIME type of an image file from its first bytesimageMime
A set of labelled imagesimageSet
Import a dichotomous key from FishBaseimportFishbase
Invent pronounceable namesinventNames
Draw a key as a box diagramkeyDiagram
Build a key from a multiple sequence alignmentkeyFromAlignment
Build a key by clustering classes and describing each splitkeyFromClusters
Build a dimoose key from a table of leadskeyFromLeads
Turn a mixed-effects tree into a keykeyFromMecit
Build a dimoose key from a classification treekeyFromRpart
Build a key from sniglet scoreskeyFromSniglets keyFromTerms
Build a key from a spreadsheetkeyFromSpreadsheet
Leave-one-out evaluation of a key builderlooKey
Macrohaplogroup of a haplogroupmacroHaplogroup
Mixed-effects conditional inference treesmecit
Model details as metadata rowsmodelMeta
Key to the native broadleaf trees of Montanamontana
Build a dimoose object from FishBase key pagesparseFishbase
Add example crops to a sniglet keypatchExemplars
PhyloTree Build 17: the human mitochondrial DNA phylogenyphylotree17
PhyloTree Build 17 mutations, one per rowphylotree17_mutations
Build an identification key from PhyloTree Build 17phylotreeKey
Raw FishBase key tablesrawhtml
Read a Haplogrep / PhyloTree tree XMLreadHaplogrep
Recurrent (homoplasic) mutation sitesrecurrentPositions
Rename snigletsrenameSniglets
Score new images against a key's featuresscoreImages
Simulate expression data on PhyloTreesimulateExpression
Names of a key's snigletssnigletNames
Score images against snigletssnigletScores termScores
Variables a fitted tree splits onsplitVariables
Suggest which of a key's species a photo showssuggestSpecies
Export a key as Auspice (Nextstrain) JSON v2toAuspiceJSON
Convert a key to an igraph directed graphtoIgraph
Write a key as Newick, with safe labels or node annotationstoNewick
Convert a key to a tidytree treedata (for ggtree)toTreedata
Vibrio consensus identification matrixvibrio
Load a vision model for embedding imagesvisionModel
Prompts for a vocabulary of visual featuresvocabularyPrompts