relltest {scaleboot}R Documentation

RELL Test for Phylogenetic Inference

Description

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.

Usage


relltest(dat,nb=10000,sa=10^seq(-2,2,length=13),ass=NULL,
         cluster=NULL,nofit=FALSE,models=NULL,seed=100)

Arguments

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.

Details

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.

Value

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.

Author(s)

Hidetoshi Shimodaira

References

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.

See Also

sbfit, scaleboot, mam15.

Examples


## 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)


[Package scaleboot version 0.1-2 Index]