Description Usage Arguments Value Examples
This function modifies the taxa names in the @commdf@counts
slot
of epd.entity.df-class
objects. More specifically, this
function compares the taxa name with the taxonomy of the EPD to use
the higher taxa names. If these changes result in duplicated columns of
the same taxa their values are unified by summing them.
1 2 3 4 5 6 7 8 9 | taxa_to_highertaxa(x, epd.taxonomy, rm_null_mhvar = FALSE)
## S4 method for signature 'epd.entity.df,data.frame'
taxa_to_highertaxa(x, epd.taxonomy,
rm_null_mhvar = FALSE)
## S4 method for signature 'epd.entity,data.frame'
taxa_to_highertaxa(x, epd.taxonomy,
rm_null_mhvar = FALSE)
|
x |
epd.entity |
epd.taxonomy |
data.frame Data frame with the taxonomy from
the EPD as from the |
rm_null_mhvar |
logical Logical value indicating whether to remove or not those taxa that has no value for higher level taxa. |
Object of class epd.entity.df-class
with new
taxa names.
1 2 3 4 5 6 7 8 9 10 11 12 | ## Not run:
epd.connection <- connect_to_epd(host="localhost", database="epd",
user="epdr", password="epdrpw")
epd.1 <- get_entity(1, epd.connection)
epd.1 <- entity_to_matrices(epd.1)
epd.1@commdf@taxanames
colnames(epd.1@commdf@counts)
epd.1.hn <- taxa_to_highertaxa(epd.1, get_taxonomy_epd(epd.connection))
epd.1.hn@commdf@taxanames
colnames(epd.1.hn@commdf@counts)
## End(Not run)
|
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