sbphylo function

Tables for phylogenetic inference

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

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).

Returns

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