relltest {scaleboot} | R Documentation |
Performing RELL test for finding the largest item. This calculates AU p-values for each item via the multiscale bootstrap resampling. Particularly useful for phylogenetic analysis to test tree topologies.
relltest(dat,nb=10000,sa=10^seq(-2,2,length=13),ass=NULL, cluster=NULL,nofit=FALSE,models=NULL,seed=100)
dat |
a matrix. Row vectors are to be resampled. Each column
vector gives score values to be evaluated for a item. For the
phylogenetic analysis, dat[i,j] is the site-wise log-likelihood value
at site-i for tree-j, and we are to find the tree with the largest
expected value of sum(dat[,j]) . |
nb |
Number of replicates for each scale. |
sa |
Scales in sigma squared (σ^2). |
ass |
A list of association vectors for testing edges as well as
trees. If ass=NULL , results for only trees are returned. |
cluster |
snow cluster object which may be generated by
function makeCluster . |
nofit |
logical. Passed to sbfit . |
models |
character vectors. Passed to sbfit . |
seed |
If non NULL, random seed is set. Specifying a seed is
particularly important when cluster is non NULL, in which
case seed + seq(along=cluster) are set to cluster nodes. |
relltest
performs the resampling of estimated log-likelihoods
(RELL) method of Kishino et al. (1990). For resampling indices stored
in a vector i
, the resampled log-likelihood for tree-j is
approximately calculated by sum(dat[i,j])
. This approximation
avoids time-consuming recalculation of the maximum likelihood
estimates of tree parameters, which are to be calculated by an
external phylogenetic software such as PAML as described in
mam15
. In the implementation of relltest
, the
resampled log-likelihood is calculated by
nrow(dat)*sum(dat[i,j])/length(i)
so that the statistic is
comparable to that of the case n'=n.
relltest
calls scaleboot
internally for
multiscale bootstrap resampling, and then calls sbfit
for fitting models to the bootstrap probabilities. The AU p-values
(named "k.3") obtained by the summary
method is an improvement
of the third-order p-value calculated by CONSEL software (Shimodaira
and Hasegawa 2001). In addition,
relltest
calls scaleboot
with sa=1
for
calculating p-values via the Shimodaira-Hasegawa test (SH-test) of
Shimodaira and Hasegawa (1999).
See mam15
for details through an example.
relltest
returns an object of class "relltest"
inheriting from class
"scalebootv"
by adding extra two attribute components "stat"
and "shtest". "stat" is a vector of the test statistics of
SH-test (i.e., the log-likelihood differences), and
"shtest" is a list with two components "pv", a vector of p-values of
SH-test, and "pe", a vector of standard errors of the
p-values. The results of multiscale bootstrap resampling are stored
in the "scalebootv"
components returned by a call to
sbfit
.
Hidetoshi Shimodaira
Kishino, H., Miyata, T. and Hasegawa, M. (1990). Maximum likelihood inference of protein phylogeny and the origin of chloroplasts., J. Mol. Evol., 30, 151-160.
Shimodaira, H. and Hasegawa, M. (1999). Multiple comparisons of log-likelihoods with applications to phylogenetic inference, Molecular Biology and Evolution, 16, 1114-1116.
Shimodaira, H. and Hasegawa, M. (2001). CONSEL: for assessing the confidence of phylogenetic tree selection, Bioinformatics, 17, 1246-1247; available from http://www.is.titech.ac.jp/~shimo/prog/consel/.
Luke Tierney, A. J. Rossini, Na Li and H. Sevcikova. snow: Simple Network of Workstations. R package version 0.2-1.
## Not run: ## An example from data(mam15). ## It may take 20 mins to run relltest below. mam15.mt <- read.mt("mam15.mt") # site-wise log-likelihoods mam15.trees <- relltest(mam15.mt) # resampling and fitting summary(mam15.trees) # AU p-values ## End(Not run)