> require(phytools)
> source("utilities.R")
> tree<-pbtree(n=100,scale=1)
> Q<-matrix(c(-2,1,1,1,-2,1,1,1,-2),3,3)
> colnames(Q)<-rownames(Q)<-LETTERS[1:nrow(Q)]
> tree<-sim.history(tree,Q)
> mtrees<-make.simmap(tree,tree$states,model="ER",nsim=10)
> XX<-countSimmap(mtrees)
> XX
$Tr
N A,A A,B A,C B,A B,B B,C C,A C,B C,C
[1,] 43 0 13 15 3 0 5 5 2 0
[2,] 35 0 13 12 3 0 4 1 2 0
[3,] 39 0 15 11 3 0 6 3 1 0
[4,] 46 0 12 15 3 0 6 3 7 0
[5,] 48 0 5 5 10 0 14 8 6 0
[6,] 45 0 14 12 5 0 7 5 2 0
[7,] 53 0 12 11 18 0 7 1 4 0
[8,] 46 0 5 5 9 0 7 11 9 0
[9,] 48 0 10 5 6 0 12 8 7 0
[10,] 49 0 16 8 15 0 6 3 1 0
$message
[1] "Column N is the total number of character changes on
the tree"
[2] "Other columns give transitions x,y from x->y"
> source("utilities.R")
> tree<-pbtree(n=100,scale=1)
> Q<-matrix(c(-2,1,1,1,-2,1,1,1,-2),3,3)
> colnames(Q)<-rownames(Q)<-LETTERS[1:nrow(Q)]
> tree<-sim.history(tree,Q)
> mtrees<-make.simmap(tree,tree$states,model="ER",nsim=10)
> XX<-countSimmap(mtrees)
> XX
$Tr
N A,A A,B A,C B,A B,B B,C C,A C,B C,C
[1,] 43 0 13 15 3 0 5 5 2 0
[2,] 35 0 13 12 3 0 4 1 2 0
[3,] 39 0 15 11 3 0 6 3 1 0
[4,] 46 0 12 15 3 0 6 3 7 0
[5,] 48 0 5 5 10 0 14 8 6 0
[6,] 45 0 14 12 5 0 7 5 2 0
[7,] 53 0 12 11 18 0 7 1 4 0
[8,] 46 0 5 5 9 0 7 11 9 0
[9,] 48 0 10 5 6 0 12 8 7 0
[10,] 49 0 16 8 15 0 6 3 1 0
$message
[1] "Column N is the total number of character changes on
the tree"
[2] "Other columns give transitions x,y from x->y"
That's it.
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