Tree concordance

This function calculates the concordance between a category tree and an individuals tree

treeConcordance(catTree, indTree, df)

Arguments

catTree

object of class phylo

indTree

object of class phylo

df

data frame specifying to which category each individual belongs. Each row gives an individual (column 2) and its corresponding category (column 1)

See also

simulateIndTree makeCollapsedTree

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)
#> [1] 1

# make a less concordant tree:
indTree2 <- read.tree(text="((((c4,c3),(c2,c1)),b2),(b1,((a3,a2),a1)));")
plot(indTree2)

treeConcordance(catTree,indTree2,df)
#> [1] 0.7307692

# 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)
#> [1] 0.6071111