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Aggregate species data to given taxonomic rank

Source: R/tax_agg.R
tax_agg.Rd

Aggregate species data to given taxonomic rank

Usage

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

# S3 method for class 'tax_agg'
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). If using ncbi we recommend getting an API key; see taxize-authentication

messages

(logical) If FALSE (Default) suppress messages

...

Other arguments passed to get_tsn() or get_uid()

Value

A list of class tax_agg with the following items:

  • x Community data matrix with aggregated data.

  • by A lookup-table showing which taxa were aggregated.

  • n_pre Number of taxa before aggregation.

  • rank Rank at which taxa have been aggregated.

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

if (FALSE) { # \dontrun{
if (requireNamespace("vegan", quietly = TRUE)) {
  # use dune dataset
  data(dune, package='vegan')
  species <- c("Achillea millefolium", "Agrostis stolonifera",
    "Aira praecox", "Alopecurus geniculatus", "Anthoxanthum odoratum",
    "Bellis perennis", "Bromus hordeaceus", "Chenopodium album",
    "Cirsium arvense", "Comarum palustre", "Eleocharis palustris",
    "Elymus repens", "Empetrum nigrum", "Hypochaeris radicata",
    "Juncus articulatus", "Juncus bufonius", "Lolium perenne",
    "Plantago lanceolata", "Poa pratensis", "Poa trivialis",
    "Ranunculus flammula", "Rumex acetosa", "Sagina procumbens",
    "Salix repens", "Scorzoneroides autumnalis", "Trifolium pratense",
    "Trifolium repens", "Vicia lathyroides", "Brachythecium rutabulum",
    "Calliergonella cuspidata")
  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(x=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')
} # }