docs/source/content/Doc_Function_Scripts/getTreeClades.R

In BobLiterman/Rboretum: Compare Phylogenetic Trees and Alignment Support Values

library(Rboretum)
sourceRboretum()

# Read in trees with two topologies (1=2, 1!=3)
myTree_1 <- readRooted(rb_tree1_path,root_taxa = c('Species_C','Species_H'))
myTree_2 <- readRooted(rb_tree2_path,root_taxa = c('Species_C','Species_H'))
myTree_3 <- readRooted(rb_tree4_path,root_taxa = c('Species_C','Species_H'))

# Topology A
getTreeClades(myTree_1)
getTreeClades(myTree_2)

# Topology B
getTreeClades(myTree_3)

# Get splits from a multiPhylo
myMultiPhylo <- c(myTree_1,myTree_2,myTree_3) %>% treeNamer()
  
getTreeClades(myMultiPhylo)

# Return all identified splits, but exclude root split
getTreeClades(myMultiPhylo,include_root = FALSE)

# Return only splits present in all trees
getTreeClades(myMultiPhylo,return_shared = TRUE)

# Return a table of results
getTreeClades(myMultiPhylo,return_counts = TRUE)

# Return clades, but print counts to console
getTreeClades(myMultiPhylo,print_counts = TRUE)