scaleboot (version 1.0-1)

sbphylo: Tables for phylogenetic inference

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 sbphylo
summary(object, k = 2,...)
# S3 method for sbphylo
print(x,...)
# S3 method for 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.

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.

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).

See Also

relltest, read.ass, read.mt

Examples

# NOT RUN {
## 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
# }