NANUQdist | R Documentation |
Computes the quartet distance tables for the NANUQ algorithm of \insertCiteABR19;textualMSCquartets, using precomputed p-values for quartets, for each of several levels specified. Distance tables are written to files, in nexus format.
NANUQdist(
pTable,
outfile = "NANUQdist",
alpha = 0.05,
beta = 0.95,
plot = TRUE
)
pTable |
a table of resolved quartets and p-values, as previously computed by |
outfile |
a character string giving an output file name stub for
saving a |
alpha |
a value or vector of significance levels for judging p-values testing a null hypothesis of no hybridization for each quartet; a smaller value applies a more liberal test for a tree (more trees), hence a stricter requirement for suspecting hybridization (fewer reticulations) |
beta |
a value or vector of significance levels for judging p-values testing
a null hypothesis of a star tree for each quartet; a smaller value applies a more liberal
test for a star tree (more polytomies), hence a stricter requirment for suspecting a resolved tree;
if vectors, |
plot |
|
If plots are produced, each point represents an empirical quartet concordance factor, color-coded to represent test results giving interpretation as network, resolved tree, or star tree.
If alpha
and beta
are vectors, they must be of the same length k. Then the i-th entries are
paired to produce k plots and k distance tables/output files. This is equivalent to k
calls to NANUQdist
with paired scalar values from the vectors of alpha
and beta
.
See the documentation for quartetNetworkDist
for an explanation of a small, rarely noticeable,
stochastic element of the algorithm.
a NANUQ distance table, or a list of such tables if alpha
and beta
are vectors (returned invisibly)
ABR19MSCquartets
NANUQ
, quartetTreeTestInd
, quartetStarTestInd
data(pTableYeastRokas)
dist=NANUQdist(pTableYeastRokas, alpha=.05, beta=.95, outfile = NULL)
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