ordersHeuristicmodNANUQ {MSCquartets} | R Documentation |
Choose cycle orders heuristically from empirical modNANUQ distance
Description
Find candidates for best hybrid node and circular order fitting the modNANUQ distance.
Usage
ordersHeuristicmodNANUQ(M, delta = 10^-6)
Arguments
M |
an empirical modNANUQ distance table |
delta |
cutoff for relative difference in distances for determining near ties for "best" orders |
Details
Candidadte orders are obtained by first picking the hybrid node (from the minimum column sum of the distance matrix), then ordering nodes by distance from the hybrid, and for each consecutive pair picking nodes in the cycle closest to the previous node. This constructs one or more orders since ties may occur. For more details, see Allman et al. (2024).
This function is used by NANUQ+ commands to resolve multifurcations in a tree of blobs of high degree.
Value
a list of circular orders
References
Allman ES, BaƱos H, Mitchell JD, Rhodes JA (2024). “TINNiK: Inference of the Tree of Blobs of a Species Network Under the Coalescent.” bioRxiv. doi:10.1101/2024.04.20.590418, https://www.biorxiv.org/content/10.1101/2024.04.20.590418v1.
See Also
expmodNANUQCycleDist
resolveCycle
resolveLevel1