Given a Tree of Blobs and quartet Concordance Factor data, resolve a specific polytomy to a cycle. 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 ABRW24;textualMSCquartets.
resolveCycle(
ToB,
node,
pTable,
test = "T3",
alpha,
beta,
distance = "NANUQ",
hdegree = 10,
plot = TRUE,
delta = 10^-6
)a list of resolution information, given as a list of:
$node node number,
$cycleRes list [[1]]-[[k]] of best resolutions,
$RSSs RSSs from all cycle resolutions considered in choosing best.
Each resolution is itself a 5-element list with entries:
$cycleNet Newick network with 1 cycle (with all edge lengths 1)
$cycleRSS RSS for cycle,
$taxonGroups taxon groups for cycle,
$order order of groups around cycle,
$nonRootEdges logical vector indicating edges of ToB
where root cannot be.
(Items $taxonGroups,$order,$nonRootEdges are
needed to combine resolutions to form networks with multiple cycles using
combineCycleResolutions, and otherwise may not be of interest to users).
an unrooted tree of blobs (phylo object), as determined by TINNIK
or another method, with multifurcations labelled by labelIntNodes
number of an internal node to be resolved
a table of qcCFs, with columns p_star and p_test
either "T3" or "cut", indicating the test to use for determining what qcCFs indicate hybridization
test level for p_test
test level for p_star
cycle resolution distance to be used; one of "NANUQ" or "modNANUQ"
resolve a multifurcation of this degree or larger by a heuristic method; must be at least 5
if FALSE (0), no plots; if TRUE (>0), make plots of resolved cycle(s) considered best and histogram of measure of fit for all hybrid/orders considered
cutoff for relative difference in squared residuals and smallest, (RSS-minRSS)/minRSS, for determining near ties as "best" fit resolutions
Possible distances to use are the NANUQ distance and a modified NANUQ distance that weights quartet trees differently, but from which the cycle structure is still identifiable.
For multifucations of degree less than a designated cutoff, all possible circular orders and choices of hybrid nodes are considered in choosing the best. Above that cutoff, a heuristic method built on the modified NANUQ distance is used to obtain a small number of orders likely to be good fits, with the least-squares fitting applied only to those.
ABRW24MSCquartets
TINNIK, labelIntNodes, combineCycleResolutions,
resolveLevel1
data(pTableYeastRokas)
out=TINNIK(pTableYeastRokas, alpha=.01, beta=.05)
ToB=labelIntNodes(out$ToB)
resolveCycle(ToB, node=9, pTable=out$pTable, alpha=.01, beta=.05, distance="NANUQ")
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