resolveLevel1 {MSCquartets} | R Documentation |
Resolve Tree of Blobs to Level-1 network
Description
Given a Tree of Blobs and qcCF information, resolve all multifurcations to cycles. Resolution is performed by finding a least-squares best-fit of an empirical distance to an expected distance related to the cycle, as described in Allman et al. (2024).
Usage
resolveLevel1(
ToB,
pTable,
test = "T3",
alpha,
beta,
distance = "NANUQ",
hdegree = 10,
plot = 2,
delta = 10^-6,
fullResMax = 10
)
Arguments
ToB |
an unrooted tree of blobs (phylo object) as determined by TINNIK or another method |
pTable |
a table of qcCFs, with columns p_star and p_test |
test |
either "T3" or "cut", indicating test to use for determining what qcCFs indicate hybridization |
alpha |
test level for p_test |
beta |
test level value for p_star |
distance |
cycle resolution distance to be used ("NANUQ" or "modNANUQ") |
hdegree |
resolve a multifurcation of this degree or larger by a heuristic method; must be at least 5 |
plot |
if 0, no plots; if 1, plot only possible root locations on ToB and full resolution; if 2, include plots of each individual blob resolution, if 3 include histograms of measure of fit for all hybrid/orders considered in choosing best |
delta |
cutoff for relative difference in squared residuals and smallest, (RSS-minRSS)/minRSS, for determining near ties as "best" fit resolutions |
fullResMax |
maximum number of full resolutions (all multifurcations at once)
to form; if the product of the number of resolutions of individual multifurcations
exceeds this, no full resolutions are produced, although |
Details
Possible distances to use are the NANUQ distance and a modified NANUQ distance that weights quartet trees differently, but from which the cycle structure is still identifiable.
For multifucations of degree less than a designated cutoff, all possible circular orders and choices of hybrid nodes are considered in choosing the best. Above that cutoff, a heuristic method is used to obtain a small number of orders likely to be good fits, with the least-squares fitting applied only to those.
Value
a list of resolutions and squared residuals:
[[1]] is a list of Newick resolutions of entire network, with all edge lengths 1 (NULL if one cannot be produced or
fullResMax
is exceeded),[[2]]-[[n]] are individual resolutions of each multifurcation on
ToB
, each given as a list as output fromresolveCycle
.
References
Allman ES, BaƱos H, Rhodes JA, Wicke K (2024).
“NANUQ^+
: A divide-and-conquer approach to network estimation.”
draft.
See Also
TINNIK
, labelIntNodes
, resolveCycle
,
combineCycleResolutions
Examples
data(pTableYeastRokas)
out=TINNIK(pTableYeastRokas, alpha=.01, beta=.05)
ToB=labelIntNodes(out$ToB)
resolveLevel1(ToB, pTable=out$pTable, alpha=.01, beta=.05, distance="NANUQ")