getFactoredEdges: Returns edges from a phylofactor

In reptalex/phylofactor: phylofactor

Returns edges from a phylofactor

Description

Returns edges from a phylofactor

Usage

getFactoredEdges(v = NULL, tree, M = NULL, grp1 = NULL,
  grp2 = NULL)

Arguments

v	Optional input of an ILR-style partition vector, which automatically extracts grp1 and grp2
tree	Phylo object
M	Most recent common ancestor matrix of tree, the output from mrca
grp1	Vector of the indexes for tips contained in group1 (also the nodes corresponding to the tips in group1)
grp2	same as grp1, but must be a disjoint group from grp1.

Examples

#Case 1: mrca1>root:
set.seed(1)
tree <- rtree(12)
grp1 <- c(9:12)
grp2 <- c(1:8) #correct answer: 16
getFactoredEdges(tree=tree,grp1=grp1,grp2=grp2)

#Case 2: mrca2>root:
grp1 <- c(1:8)
grp2 <- c(9:12) #correct answer:16
getFactoredEdges(tree=tree,grp1=grp1,grp2=grp2)

grp1 <- c(1:8,12)
grp2 <- c(9:11) #correct answer: 17
getFactoredEdges(tree=tree,grp1=grp1,grp2=grp2)
#Case 3: mrca1>root & mrca2 >root - nodepath passing trough root
grp1 <- c(9:11)
grp2 <- c(2:3) #correct answer: c(17,16,6,1,3)
getFactoredEdges(tree=tree,grp1=grp1,grp2=grp2)
#Case 4: mrca1>root & mrca2 >root - nodepath NOT passing trough root
grp1 <- c(9:11)
grp2 <- c(5,6) #correct answer: c(17,16,7,8,10,11)
getFactoredEdges(tree=tree,grp1=grp1,grp2=grp2)

reptalex/phylofactor documentation built on Feb. 28, 2024, 3:19 p.m.