sbphylo: Tables for phylogenetic inference

In scaleboot: Approximately Unbiased P-Values via Multiscale Bootstrap

Description

Creating tables of p-values and tree/edge associaitons for phylogenetic inference. Trees and edges are sorted by the likelihood value.

Usage

sbphylo(relltest,ass,trees,edges,edge2tree,
                   treename=NULL,edgename=NULL,taxaname=NULL,mt=NULL,sort=TRUE) 

## S3 method for class 'sbphylo'
summary(object, k = 2,...)

## S3 method for class 'sbphylo'
print(x,...)

## S3 method for class 'summary.sbphylo'
print(x,...)

Arguments

relltest	relltest output.
ass	read.ass output.
trees	relltest output for trees.
edges	relltest output for edges.
edge2tree	read.ass output for "edge to tree" association.
treename	character vector for tree descriptions.
edgename	character vector for edge descriptions.
taxaname	character vector for taxa names.
mt	read.mt output for the site-wise log-likelhiood values.
sort	sorting trees and edges by likelhiood when TRUE.
object	output of sbphylo.
k	integer of k for calculating p-values.
x	sbphylo or summary.sbphylo objects.
...	further arguments passed to and from other methods.

Details

First, apply sbphylo to consel results, and summary will make tables. Output tables are suitable for publication. For the input of sbphylo, you should specify either of (relltest, ass) or (trees, edges, edge2tree).

Value

sbphylo returns a list of several information of multiscale bootstrap. It does not do actual computation, but only sort trees and edges in decreasing order of likelihood values. The compied information is then passed to summary method, which returns a list containing character tables and its numerical values of p-values.

Author(s)

Hidetoshi Shimodaira

See Also

relltest, read.ass, read.mt

Examples

## working with CONSEL outputs
data(mam15)
mam15.trees <- mam15.relltest[attr(mam15.ass,"trees")]  # 15 trees
mam15.edges <- mam15.relltest[attr(mam15.ass,"edges")]  # 10 edges
mam15.edge2tree <- mam15.ass[attr(mam15.ass,"edges")] # 10 edges
mam15 <- sbphylo(trees=mam15.trees,edges=mam15.edges,
                edge2tree=mam15.edge2tree) # sort trees and edges by likelihood
mam15 # print method for sbphylo
tab <- summary(mam15) # summary method for sbphylo
tab # prints character table

## plot (beta0,beta1)
a1 <- attr(summary(mam15$trees,k=2),"table")
a2 <- attr(summary(mam15$edges,k=2),"table")
beta <- rbind(a1$value,a2$value)[,c("beta0","beta1")]
sbplotbeta(beta) # for diagnostics of p-values

scaleboot documentation built on Dec. 4, 2019, 5:07 p.m.