1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
|
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/treeConcordance.R
\name{treeConcordance}
\alias{treeConcordance}
\title{Tree concordance}
\usage{
treeConcordance(catTree, indTree, df)
}
\arguments{
\item{catTree}{object of class phylo}
\item{indTree}{object of class phylo}
\item{df}{data frame specifying to which category each individual belongs. Each row gives an individual (column 2) and its corresponding category (column 1)}
}
\description{
This function calculates the concordance between a category tree and an individuals tree
}
\examples{
# create an example category tree
catTree <- read.tree(text="(C:1,(B:1,A:1):1);")
plot(catTree)
# make individuals tree with complete concordance:
indTree1 <- read.tree(text="(((c4,c3),(c2,c1)),((b1,b2),((a3,a2),a1)));")
plot(indTree1)
# create data frame linking categories with individuals
df <- cbind(c(rep("A",3),rep("B",2),rep("C",4)),sort(indTree1$tip.label))
treeConcordance(catTree,indTree1,df)
# make a less concordant tree:
indTree2 <- read.tree(text="((((c4,c3),(c2,c1)),b2),(b1,((a3,a2),a1)));")
plot(indTree2)
treeConcordance(catTree,indTree2,df)
# simulate larger example:
catTree <- rtree(10)
indTree3 <- simulateIndTree(catTree, tipPercent=10)
df <- cbind(sort(rep(catTree$tip.label,5)),sort(indTree3$tip.label))
plot(indTree3)
treeConcordance(catTree,indTree3,df)
}
\seealso{
\code{\link{simulateIndTree}} \code{\link{makeCollapsedTree}}
}
|
