scaleboot (version 1.0-1)

interface: Interface to External Packages

Description

Interface for other packages such as CONSEL (phylogenetic inference), and pvclust (hierarchical clustering)

Usage

read.mt(file,tlab="t")
read.ass(file,identity=TRUE,tlab="t",elab="e") 
read.cnt(file)

# S3 method for pvclust
sbfit(x,...)
sbpvclust(x,mbs,k=3,select="average",...)

Arguments

file

character of a file name to be read.

identity

logical. Should the identity association be included?

tlab

character for basename of tree labels.

elab

character for basename of edge labels.

x

an object of class "pvclust".

mbs

an object of class "scalebootv".

k

numeric of \(k\) for a AU p-value.

select

character of model name (such as "poly.3") or one of "average" and "best".

...

further arguments passed to or from other methods.

Value

read.mt returns a matrix of dimension sequence-length by tree-number. If identity=FALSE, then read.ass returns a list containing components x for edge->tree associations and y for tree\(\to\)edge associations. If identity=TRUE, read.ass returns a list vector of edge\(\to\)tree associations, where the identity associations for tree\(\to\)tree are included. read.cnt returns a list containing components bps, nb, and sa to be used for sbfit. The list also contains components cnt, id, and val.

sbfit.pvclust returns an object of class "scalebootv". sbpvclust returns an object of class "sbclust" added to the class "pvclust".

Details

CONSEL is a program package consisting of small programs written in the C language for assessing the confidence of phylogenetic tree selection. Some functions for interfacing with CONSEL are: read.mt, read.ass, and read.cnt for reading, respectively, mt, ass, and cnt format. Once mt file is read, we can calculate improved versions of approximately unbiased p-values by relltestin scaleboot instead of CONSEL.

pvclust is a R package for hierarchical clustering with p-values. Functions for interface to pvclust are: sbfit method for an object of class "pvclust" to convert it to "scalebootv" class, and sbpvclust for writing back the result to a "pvclust" object with additional class "sbclust". plot method for class "sbclust" overwrites that for "pvclust".

References

Shimodaira, H. and Hasegawa, M. (2001). CONSEL: for assessing the confidence of phylogenetic tree selection, Bioinformatics, 17, 1246-1247 (software is available from http://stat.sys.i.kyoto-u.ac.jp/prog/consel/).

Suzuki, R. and Shimodaira, H. (2006). pvclust: An R package for hierarchical clustering with p-values, Bioinformatics, 22, 1540-1542 (software is available from CRAN or http://stat.sys.i.kyoto-u.ac.jp/prog/pvclust/).

See Also

lung73, mam15, relltest

Examples

# NOT RUN {
## replace au/bp entries in pvclust object
## see help(lung73) for details
library(pvclust)
data(lung73)
plot(lung73.pvclust) # draw dendrogram of pvlcust object
pvrect(lung73.pvclust)
lung73.new <- sbpvclust(lung73.pvclust,lung73.sb) # au <- k.3
plot(lung73.new) # redraw dendrogram with the new au/bp values
pvrect(lung73.new)

# }
# NOT RUN {
## reading CONSEL files
## sample files are found in mam15 subdirectory
## see help(mam15) for details
mam15.mt <- read.mt("mam15.mt")
mam15.ass <- read.ass("mam15.ass")
mam15.cnt <- read.cnt("mam15.cnt")
# }
# NOT RUN {
# }