treeConcordance: Tree concordance

In treespace: Statistical Exploration of Landscapes of Phylogenetic Trees

Tree concordance

Description

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

Usage

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)

# 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)

treespace documentation built on Sept. 8, 2023, 6:04 p.m.