quartetCutMLE {MSCquartets}

Maximum likelihood estimate of quartet tree of blobs topology and CF under Cut model

Description

Computes Maximum likelihood estimate of quartet tree of blobs topology and CF under the Cut model of Allman et al. (2024), Section 3. In case of ties, the topology and CF estimate are chosen randomly among those maximizing the likelihood. In particular, a resolved tree of blobs is always returned.

Usage

quartetCutMLE(qcCF)

Arguments

qcCF

a quartet count Concordance Factor (a 3-element vector)

Value

output with output$topology = 1, 2, or 3 indicating topology of tree of blobs in accord with ordering of qcCF entries, and output$CFhat the ML estimate for the CF

References

Allman ES, Baños H, Mitchell JD, Rhodes JA (2024). “TINNIK: Inference of the Tree of Blobs of Species Networks Under the Coalescent.” draft.

Examples

 quartetCutMLE(c(17,72,11))
 quartetCutMLE(c(48,11,41))
 quartetCutMLE(c(11,48,41))
 quartetCutMLE(c(48,41,11))