Description Usage Arguments Details Value References See Also
This function calculates the means, variances, and covariance of the posterior mean of labeled substitution counts over two prespecified sets of branches on a phylogeny using a simulation-free dynamic programming algorithm and Monte Carlo sampling.
1 2 3 4 |
tree |
A tree object of class |
rate.mat |
A reversible continuous-time Markov chain (CTMC) rate matrix. |
label.mat |
A 0-1 matrix of the same size as |
edge.set1, edge.set2 |
Two integer vectors of branch indices specifying the branch sets over which the joint posterior moments will be calculated. |
subtree |
An integer denoting a node index in the tree. If provided,
then |
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
|
N |
An integer specifying the number of Monte Carlo samples to draw. |
The means obtained in this function are computed exactly, while the variances and covariance are partially approximated using Monte Carlo simulations.
More information on phylogenetic tree objects of class "phylo"
can be
found at http://ape-package.ird.fr/misc/FormatTreeR_24Oct2012.pdf.
A numeric vector holding the means, variances, and covariance of the posterior mean of labeled substitution counts.
Dhar A and Minin VN (2017) “Calculating Higher-Order Moments of Phylogenetic Stochastic Mapping Summaries in Linear Time”, Journal of Computational Biology, 24(5):377-399.
joint.prior.moments.phylojumps
,
joint.post.moments.phylojumps
,
postmean.moments.phylojumps
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