match_phylo_comm compares taxa (species, labels, tips) present in a phylogeny with a community matrix. Pruning, sorting and trying to add missing species on genus level if possible to match in subsequent analysis.
match_phylo_comm(phy, comm, delete_empty_rows = TRUE)A phylogeny
A (sparse) community data matrix
delete rows with no observation
A list containing the following elements, pruned and sorted to match one another:
A phylogeny object of class phylo
A (sparse) community data matrix
Based on the function of the same name in picante but allows sparse matrices and with taxa addition.
data(africa)
tree <- africa$phylo
x <- africa$comm
subphy <- match_phylo_comm(tree, x)$phy
submat <- match_phylo_comm(tree, x)$com