Description Usage Arguments Details Value References See Also
Simulates the number of substitutions on a phylogeny conditional on the observed tip states.
1 2 | phylojumps.sim(tree, rate.mat, root.dist, scale = FALSE,
states = c("a","c","g","t"), seq.data, N)
|
tree |
A tree object of class |
rate.mat |
A continuous-time Markov chain (CTMC) rate matrix. |
root.dist |
A numeric vector defining the root distribution of the evolutionary process on the tree. If this process starts at stationarity (as is commonly assumed), then the root distribution is equal to the CTMC stationary distribution. |
scale |
A logical indicating whether to scale the time dimension. If
|
states |
A character or integer vector denoting the CTMC state space.
Defaults to the set of DNA nucleotides |
seq.data |
A character or integer matrix representing the observed
sequence alignment with rows (columns) that correspond to the sequences
(sites) under study. All elements of |
N |
An integer specifying the number of samples to draw. |
This simulation function follows the procedure outlined in Nielsen (2002).
More information on phylogenetic tree objects of class "phylo"
can be
found at http://ape-package.ird.fr/misc/FormatTreeR_24Oct2012.pdf.
An integer matrix with dimensions c(N, ncol(seq.data))
, where
the i'th column contains N
independent samples of
substitution counts for the i'th site in seq.data
.
Nielsen R (2002) “Mapping mutations on phylogenies”, Systematic Biology, 51(5):729-739.
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