quartetTreeErrorProb {MSCquartets}

Bayesian posterior probability of error in 4-taxon unrooted species tree topology estimate

Description

From a gene quartet count concordance factor (qcCF), computes Bayesian posterior probabilities of the three 4-taxon species tree topologies and the Bayesian posterior probability that the assumed topology is incorrect, under the assumption that the counts arise from the MSC on some species tree.

Usage

quartetTreeErrorProb(obs, model = "T3")

Arguments

obs

vector of counts for 3 topologies

model

"T3" or "T1", for the models of Mitchell et al. (2019) describing an unspecified species tree topology ("T3"), or the topology whose count is the first entry of obs ("T1")

Details

The Jeffreys prior is used for internal branch length, along with the uniform prior on the resolved topology.

Value

(error.prob, top.probs) where error.prob is the species tree error probability and top.probs is a vector of the three species tree topology probabilities in the order of obs; for model "T1" the species tree used is the one corresponding to the first count; for model "T3" the species tree is the one corresponding to the largest count

References

Mitchell J, Allman ES, Rhodes JA (2019). “Hypothesis testing near singularities and boundaries.” Electron. J. Statist., 13(1), 2150-2193. doi:10.1214/19-EJS1576.

Examples

obs <- c(28,32,30)
quartetTreeErrorProb(obs,model="T1")
quartetTreeErrorProb(obs,model="T3")