This method merges species that have the same taxonomy at a certain
Its approach is analogous to
tip_glom, but uses categorical data
instead of a tree. In principal, other categorical data known for all taxa
could also be used in place of taxonomy,
but for the moment, this must be stored in the
of the data. Also, columns/ranks to the right of the rank chosen to use
for agglomeration will be replaced with
because they should be meaningless following agglomeration.
A character string specifying the taxonomic level
that you want to agglomerate over.
Should be among the results of
(Optional). Logical, length equal to one. Default is
(Optional). Character vector. Default:
A taxonomically-agglomerated, optionally-pruned, object with class matching
the class of
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# data(GlobalPatterns) # ## print the available taxonomic ranks # colnames(tax_table(GlobalPatterns)) # ## agglomerate at the Family taxonomic rank # (x1 <- tax_glom(GlobalPatterns, taxrank="Family") ) # ## How many taxa before/after agglomeration? # ntaxa(GlobalPatterns); ntaxa(x1) # ## Look at enterotype dataset... # data(enterotype) # ## print the available taxonomic ranks. Shows only 1 rank available, not useful for tax_glom # colnames(tax_table(enterotype))
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