partitions: function partitions applied to objects of class bsd

In sebastianduchene/ClockstaR: ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis

Description

This is the definition of method partitions for bsd objects. See partitions.bsd for more details.

Usage

partitions(bsd.object, ...)

Arguments

bsd.object

An object of class bsd, obtained with bsd.matrix or bsd.matrix.para

Author(s)

Sebastian Duchene

See Also

partitions.bsd

Examples

## Not run: 

tr.fix <- rtree(10)

set.seed(12345)
rates1 <- abs(rnorm(18, sd = 0.1))
set.seed(123456)
rates2 <- abs(rnorm(18, sd = 0.1))
set.seed(1234567)
rates3 <- abs(rnorm(18, sd = 0.1))
set.seed(12345678)
rates4 <- abs(rnorm(18, sd = 0.1))

trees.list <- list()

for(i in 1:20){
      trees.list[[i]] <- tr.fix
      if(i <= 5){
      	   trees.list[[i]]$edge.length <- abs(rates1 + rnorm(18, 0, 0.01)) 
      }else if(i > 5 && i <= 10){
      	    trees.list[[i]]$edge.length <- abs(rates2 + rnorm(18, 0, 0.01)) 
      }else if(i >= 10 && i < 15){
      	    trees.list[[i]]$edge.length <- abs(rates3 + rnorm(18, 0, 0.01))  
      }else{
	    trees.list[[i]]$edge.length <- abs(rates4 + rnorm(18, 0, 0.01)) 
      }
}

names(trees.list) <- paste0("tree", 1:20)
class(trees.list) <- "multiPhylo"

# Estimate sBSDmin distance for all pairs of trees:
trees.bsd <- bsd.matrix(trees.list)

partitions(trees.bsd)



## End(Not run)

## The function is currently defined as
function (bsd.object, ...) 
UseMethod("partitions")

sebastianduchene/ClockstaR documentation built on May 29, 2019, 4:57 p.m.