vtree {EnvNJ} | R Documentation |
Builds a tree when species are encoded by n-dim vectors.
vtree(matrix, outgroup = 'any')
matrix |
either a dataframe or matrix where each column represents an OTU. |
outgroup |
when a rooted tree is desired, it indicates the species to be used as outgroup. |
The method is based on a distance matrix obtained after converting the cos between vector (similarity measurement) in a dissimilarity measurement.
A list with two objects, the first one is an inter-species distance matrix. The second one is an object of class 'phylo'.
svdgram
data(bovids) mymatrix <- ngraMatrix(bovids[, 6:11], k = 2)[[2]][, 2:7] vtree(mymatrix, outgroup = "Pseudoryx_nghetinhensis")