Arbor docs

Phylogenies collection

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Build trees

  • hclustDendrogram - build tree from distance matrix using hclust

    • Manipulate trees

  • collapseSingles - collapse all singleton nodes in a phylogenetic tree

  • congruify - calibrate a target tree based on a reference

  • convertNexusToApePhylo - convert nexus string to ape phylo

  • convertTreeToHierarchyTable - convert a phylogenetic tree into a table of monophyletic clades

  • copheneticDistanceMatrixFromTree - make a distance matrix from a tree

  • cophylo - make a cophlogenetic plot (tanglegram) connecting tips on two trees

  • extractGenusFromTreeTipNames - Extract just the genus from the tree tip names

  • getTipNames - pull tip names from phylogenetic tree

  • graftTreeOntoNamedNode - graft subtree on to named node in recipient tree

  • makeFakeBranchLengths - Make fake branch lengths for tree

  • makeTreeDataMatch - match data matrix and tree

  • multi2di - make tree bifurcating

    • Investigate trees

  • compareTrees - compare the topology of two phylogenetic trees

    • Investigate characters on trees

  • calculateKForAllCharacters - Calculate phylogenetic signal for all characters in a matrix

  • consistencyIndexAllChars - calculate consistence index across all characters in a matrix

  • fitContinuous - fit models of evolution to continuous characters

  • fitDiscrete - fit models of evolution to discrete characters

  • phylogeneticSignal - estimate and test for phylogenetic signal in discrete and continuous characters

    • Phylogenies datasets

  • anolis.csv - Data on anoles

  • anolis.phy - Phylogenetic tree of anoles

  • phelsuma.csv - Data for Phelsuma

  • phelsuma.phy - Phylogenetic tree of Phelsuma