sumstatMCMCbf: Phylogenetic Stochastic Mapping for a 2x2 unknown rate matrix...
In vnminin/phylomap: Phylogenetic Stochastic Mapping

Creates an MCMC chain of substitution histories conditional on a phylogenetic tree, and observed states at the tips of the tree. Returns summary statisitics of each sampled substitution history.

1	sumstatMCMCbf(z,Q,pid,Omega,N,prior)

`z`	a phylogenetic tree in phytools format (a list). One of the list elements, "mapnames", must be added to the phylosim format. "mapnames" is a list of vectors. Each vector is composed of integers that are the names in phylosim's "maps" list. The "mapnames" list has a vector for each branch composed of the states visited along each branch (in order).
`Q`	a 2x2 rate matrix, the rows sum to zero
`pid`	a probability vector containing the prior probabilities that the root is in each state
`Omega`	a positive real number, the absolute value of each diagonal element of Q will be less than Omega
`N`	a positive integer: the number of substitution histories to be sampled
`prior`	a vector of length 4. The first two elements are the shape and rate parameters for the prior on Q[1,2]. The second two elements are the shape and rate parameters for the prior on Q[2,1].

sumstatMCMCbf returns a matrix, each row contains summary statistics of one of the N sampled substitution histories. The first column contains the amount of time spent in state 1 over the entire tree. The second column contains the amount of time spent in state 2 over the entire tree. The third column contains the number of virtual transitions from state 1 to state 1. The fourth column contains the number of real transitions from state 1 to state 2. The fifth column contains the number of real transitions from state 2 to state 1. The sixth column contains the number of virtual transitions from state 2 to state 2. The seventh column contains the transition rate from state 1 to state 2, l01 (also called Q[1,2]). The eighth column contains the transition rate from state 2 to state 1, l10 (also called Q[2,1]). The nineth column contains the state of the root (starting with state 0, sorry for the lack of consistency).

vnminin/phylomap documentation built on May 3, 2019, 6:38 p.m.