edgeProbs

<p>an object of class <code>"multiSimmap"</code> containing a sample of trees that are identical in topology &amp; branch lengths with different stochastically mapped character histories.</p>

trees

<p>This function computes the relative frequencies of character state changes along edges from a sample of stochastically mapped character histories. This function assumes that all trees in the sample differ only in their mapped histories &amp; not at all in topology or branch lengths. Note that it only asks whether the starting and ending states of the edge differ in a particular way, and thus ignores multiple-hits along a single edge.</p>

phylogenetics

plotting

discrete character

ancestral states

A wide range of functions for phylogenetic analysis. Functionality is concentrated in phylogenetic comparative biology, but also includes numerous methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees and data. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, simulation of phylogenies and data, and multivariate analysis. There are a broad range of plotting methods for phylogenies and comparative data which include, but are not restricted to, methods for mapping trait evolution on trees, for projecting trees into phenotypic space or a geographic map, and for visualizing correlated speciation between trees. Finally, there are a number of functions for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data not covered by other packages. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for estimating supertrees or consensus phylogenies from a set, for simulating trees and phylogenetic data under a range of models, and for a wide variety of other manipulations and analyses that phylogenetic biologists might find useful in their research.

edgeProbs: Compute the relative frequencies of state changes along edges

Description

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References

See Also