The functions of this package provide components for Metroplolis coupled Markov Chain Monte Carlo (
MC3) simulations in the inference of Sequential Markov Ancestral Recombination Trees (SMARTree) from SNP data.
nsq — Number of sequences/chromsomes.
nbp — Length of chromosomes in unit of base pair.
treels — Local trees along chromosomes T(x), represented as a matrix. Column 1 is the location of change-point, column 2 is the interval tree after (including) the change-point, column 3 is the total branch length of the tree, and the last column (column 4) is the transition probability between subsequent trees.
snpls — SNP data matrix. Column 1 is the location of SNP sites, column 2 is the alleles vector, column 3 is the vector of allele frequecy, and the last coclumn (column 4) is the log likelihood given the local tree.
theta — The scaled mutation rate. theta = 4 Ne mu, where Ne is the effective population size and mu is the mutation rate per generation per bp.
rho — The scaled recombiation rate. rho = 4 Ne r, where r is the recombation rate per generation per bp.
epsilon — The probability of an allelic typing error.
chainstate — The state of a MCMC chain consists of inverse temperature, log (full posterior), {theta, epsilon, rho}, treels, adpaptive parameters, snpls}.
mcstate — The matrix of chainstates, and the element
(mcstate)ij is the chainstate for the
jth chain of the
ith group.
initializeSMARTchain — initializes parameters for one MCMC chain
updateSMARTchain — updates chainstate for one MCMC chain
swapSMARTchain — swaps temperatures of two random chosen chains in a group.
permuteSMARTchain — permute temperaures of all chain of a group.
saveSMARTchain — save mcstate for all the chains.
TreeLogPriorProb — Log prior probability of the tree at first site.
TreeLogLikelihood — Log likelihood of SNP data given local trees.
PolymorphicProb — The probablity that the number of minor alleles ≥2.
TreeTransitionProb — Transition probability between two trees of distance ≤ 1.
TreeTransitionTypeI — Transtion type of two trees given their distance ≤ 1.
TreeTransitionTypeII — Transtion type of two trees given their distance ≤ 2.