Measuring Morphological Diversity and Evolutionary Tempo


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Documentation for package ‘Claddis’ version 0.3.0

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Claddis-package Measuring Morphological Diversity and Evolutionary Tempo
AncStateEstMatrix Ancestral Character State Estimation
ChangesInBins Counts the changes in a series of time bins
ChronoPhyloMorphospacePlot Chronophylomorphospace Plot
Claddis Measuring Morphological Diversity and Evolutionary Tempo
CompactifyMatrix Collapses matrix to unique character state distributions
CorrectRootTime Corrects root.time after taxa have been pruned from a tree
Day2016 Character-taxon matrix from Day et al. 2016
DiscreteCharacterRate Discrete character rates across trees, time, and character types
DolloSCM Stochastic Character Map For Dollo Character
EdgeLengthsInBins Edge-lengths present in time-bins
EdgeMatch Edge matching function
FindAncestor Find ancestor
FindLinkedEdges Find linked edges for a tree
Gauthier1986 Character-taxon matrix from Gauthier 1986
GetAllStateChanges Finds all state changes on a tree using stochastic character mapping
GetDescendantEdges Gets descendant edges of an internal node
GetNodeAges Returns node ages for a time-scaled tree
MakeMorphMatrix Creates a morphological data file from a matrix
MatrixPruner Prunes a character matrix of characters or taxa
Michaux1989 Character-taxon matrix from Michaux 1989
MinSpanTreeEdges Get edges of minimum spanning tree
MorphDistMatrix Get distance matrices from a cladistic matrix
MorphMatrix2PCoA Principal Coordinates on a Cladistic Matrix
MorphospacePlot Plot Morphopace
MultiMorphospacePlot Plot Multiple Morphopaces
PhyloCharCompletenessInBins Phylogenetic character completeness in time-bins
PlotCharacterChanges Plots character changes on branches
ReadMorphNexus Reads in a morphological #NEXUS data file
SafeTaxonomicReduction Safe Taxonomic Reduction
SafeTaxonomicReinsertion Reinsert Safely Removed Taxa Into A Tree
StackPlot Plot Stacked Ordination Spaces
TrimMorphDistMatrix Trims a morphological distance matrix
WriteMorphNexus Writes out a morphological #NEXUS data file
WriteMorphTNT Writes out a morphological TNT data file