Taxonomic dictionary contains a taxonomic tree and NCBI taxonomy data for all taxonomic IDs.

# S4 method for TaxRec
as.character(x)

# S4 method for TaxRec
show(object)

# S4 method for TaxRec
print(x)

# S4 method for TaxRec
str(object, max.level = 2L, ...)

# S4 method for TaxRec
summary(object)

Arguments

x

TaxRec object

object

TaxRec object

max.level

Maximum level of nesting for str()

...

Further arguments for str()

Slots

id

Taxonomic ID

scnm

Scientific name

cmnm

Common name

rnk

Rank

lng

Lineage

prnt

Parent

See also

Examples

data('aotus') taxrec <- aotus@txdct@recs[[aotus@txdct@txids[[1]]]] # this is a TaxRec object # it contains NCBI's taxonomic information for a single node show(taxrec)
#> TaxRec [id 1263727 (Aotus zonalis)]
# you can access its different data slots with @ taxrec@id # taxonomic ID
#> [1] "1263727"
taxrec@scnm # scientific name
#> [1] "Aotus zonalis"
taxrec@cmnm # common name, '' if none
#> [1] "Panamanian night monkey"
taxrec@rnk # rank
#> [1] "species"
taxrec@lng # lineage information: list of IDs and ranks
#> $ids #> [1] "131567" "2759" "33154" "33208" "6072" "33213" "33511" #> [8] "7711" "89593" "7742" "7776" "117570" "117571" "8287" #> [15] "1338369" "32523" "32524" "40674" "32525" "9347" "1437010" #> [22] "314146" "9443" "376913" "314293" "9479" "376918" "9504" #> [29] "1263727" #> #> $rnks #> [1] "no rank" "superkingdom" "no rank" "kingdom" "no rank" #> [6] "no rank" "no rank" "phylum" "subphylum" "no rank" #> [11] "no rank" "no rank" "no rank" "superclass" "no rank" #> [16] "no rank" "no rank" "class" "no rank" "no rank" #> [21] "no rank" "superorder" "order" "suborder" "infraorder" #> [26] "parvorder" "family" "genus" "species" #>
taxrec@prnt # parent ID
#> [1] "9504"