All functions

base

  • addColumns - find the sum of two columns in a data matrix

  • aggregateTableByAverage - Aggregate a table using some factor by averaging

  • aggregateTableByColumnInParameterTable - Aggregate a table using some factor by averaging

  • aggregateTableByMax - Aggregate a table using some factor by finding the maximum value for each category

  • anolis.csv - Data on anoles

  • appendColumnsAccoringToParameterValue - Append columns to a table based on a parameter value

  • extractSpeciesNamesFromMatrix - Extract species names from a data matrix

  • phylogeny

  • anolis.csv - Data on anoles

  • anolis.phy - Phylogenetic tree of anoles

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

  • collapseSingles - collapse all singleton nodes in a phylogenetic tree

  • compareTrees - compare the topology of two phylogenetic trees

  • congruify - calibrate a target tree based on a reference

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

  • 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

  • fitContinuous - fit models of evolution to continuous characters

  • fitDiscrete - fit models of evolution to discrete characters

  • getTipNames - pull tip names from phylogenetic tree

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

  • hclustDendrogram - build tree from distance matrix using hclust

  • makeFakeBranchLengths - Make fake branch lengths for tree

  • makeTreeDataMatch - match data matrix and tree

  • multi2di - make tree bifurcating

  • phelsuma.csv - Data for Phelsuma

  • phelsuma.phy - Phylogenetic tree of Phelsuma

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