dcTreeConnectivity {dcGOR} | R Documentation |
dcTreeConnectivity
is supposed to calculate the sparse
connectivity matrix between parents and children from a phylo-formatted
phylogenetic tree. The matrix has internal nodes (in rows) and tips
plus internal nodes (in columns). For a row (an internal node; as a
parent), the non-zeros indicate all its descendants/children.
dcTreeConnectivity(phy, verbose = T)
phy |
an object of class 'phylo' |
verbose |
logical to indicate whether the messages will be displayed in the screen. By default, it sets to TRUE for display |
a sparse matrix of Nnode X Ntip+Nnode, where Ntip and Nnode are the number of tips and internal nodes. A non-zero entry indicates a pair of a parent and its child.
None
# a newick tree tree <- "(((t1:5,t2:5):2,(t3:4,t4:4):3):2,(t5:4,t6:4):6);" phy <- ape::read.tree(text=tree) # connectivity matrix res <- dcTreeConnectivity(phy) dim(res) # convert to a full Matrix as.matrix(res)