taxize (version 0.7.9)

tax_agg: Aggregate species data to given taxonomic rank

Description

Aggregate species data to given taxonomic rank

Usage

tax_agg(x, rank, db = "ncbi", verbose = FALSE, ...)
"print"(x, ...)

Arguments

x

Community data matrix. Taxa in columns, samples in rows.

rank

character; Taxonomic rank to aggregate by.

db

character; taxonomic API to use, 'ncbi, 'itis' or both, see tax_name. Note that each taxonomic data source has their own identifiers, so that if you provide the wrong db value for the identifier you could get a result, but it will likely be wrong (not what you were expecting).

verbose

(loigical) If FALSE (Default) suppresss messages

...

Other arguments passed to get_tsn or get_uid.

Value

A list of class tax_agg with the following items: with the following items:

Details

tax_agg aggregates (sum) taxa to a specific taxonomic level. If a taxon is not found in the database (ITIS or NCBI) or the supplied taxon is on higher taxonomic level this taxon is not aggregated.

See Also

tax_name

Examples

## Not run: 
# if (requireNamespace("vegan", quietly = TRUE)) {
#   # use dune dataset
#   library("vegan")
#   data(dune, package='vegan')
#   species <- c("Bellis perennis", "Empetrum nigrum", "Juncus bufonius",
#   "Juncus articulatus",
#   "Aira praecox", "Eleocharis parvula", "Rumex acetosa", "Vicia lathyroides",
#   "Brachythecium rutabulum", "Ranunculus flammula", "Cirsium arvense",
#   "Hypochaeris radicata", "Leontodon autumnalis", "Potentilla palustris",
#   "Poa pratensis", "Calliergonella cuspidata", "Trifolium pratense",
#   "Trifolium repens", "Anthoxanthum odoratum", "Salix repens", "Achillea
#   millefolium",
#   "Poa trivialis", "Chenopodium album", "Elymus repens", "Sagina procumbens",
#   "Plantago lanceolata", "Agrostis stolonifera", "Lolium perenne", "Alopecurus
#   geniculatus", "Bromus hordeaceus")
#   colnames(dune) <- species
# 
#   # aggregate sample to families
#   (agg <- tax_agg(dune, rank = 'family', db = 'ncbi'))
# 
#   # extract aggregated community data matrix for further usage
#   agg$x
#   # check which taxa have been aggregated
#   agg$by
# }
# 
# # A use case where there are different taxonomic levels in the same dataset
# spnames <- c('Puma','Ursus americanus','Ursidae')
# df <- data.frame(c(1,2,3), c(11,12,13), c(1,4,50))
# names(df) <- spnames
# out <- tax_agg(df, rank = 'family', db='itis')
# out$x
# 
# # You can input a matrix too
# mat <- matrix(c(1,2,3, 11,12,13), nrow = 2, ncol = 3,
#  dimnames=list(NULL, c('Puma concolor','Ursus americanus','Ailuropoda melanoleuca')))
# tax_agg(mat, rank = 'family', db='itis')
# ## End(Not run)