Description Usage Arguments Value Author(s) References See Also
This function performs an analitic stochastic character mapping on a phylogenetic tree (algorithym proposed by Minin and Suchard).
1 | sfreemapr.map(tree, tip_states, Q, ...)
|
tree |
a phylogenetic tree as an object of class |
tip_states |
Two formats are accepted:
|
Q |
The transition rate matrix. Can be given as a matrix or estimated by the program, according to the following options:
|
... |
Optional parameters listed below:
When
|
Returns a modified object of class "phylo", adding the following data:
mapped.edge |
a matrix containing the total time spent in each state along each edge of the tree |
mapped.edge.lmt |
a matrix containing the number of labelled markov transitions for each state along each edge of the tree |
Q |
the given or estimated value of Q |
logL |
The likelihood of given or sampled Q |
Diego Pasqualin dpasqualin@inf.ufpr.br
Vladimir N Minin e Marc A Suchard. Fast, accurate and simulation-free stochastic mapping. Philosophical Transactions of the Royal Society B: Biological Sciences, 363 (1512): 3985-3995, 2008.
See Also
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