taxonomy {metacoder}

Taxonomy class

Description

Stores a taxonomy composed of [taxon()] objects organized in a tree structure. This differs from the [hierarchies()] class in how the [taxon()] objects are stored. Unlike [hierarchies()], each taxon is only stored once and the relationships between taxa are stored in an [edge list](https://en.wikipedia.org/wiki/Adjacency_list).

Usage

taxonomy(..., .list = NULL, named_by_rank = FALSE)

Arguments

...

Any number of object of class [hierarchy()] or character vectors.

.list

An alternate to the '...' input. Any number of object of class [hierarchy()] or character vectors in a list. Cannot be used with '...'.

named_by_rank

('TRUE'/'FALSE') If 'TRUE' and the input is a list of vectors with each vector named by ranks, include that rank info in the output object, so it can be accessed by 'out$taxon_ranks()'. If 'TRUE', taxa with different ranks, but the same name and location in the taxonomy, will be considered different taxa.

Value

An 'R6Class' object of class 'Taxonomy'

See Also

Other classes: hierarchies(), hierarchy(), taxa(), taxmap(), taxon(), taxon_database(), taxon_id(), taxon_name(), taxon_rank()

Examples

# Making a taxonomy object with vectors
taxonomy(c("mammalia", "felidae", "panthera", "tigris"),
         c("mammalia", "felidae", "panthera", "leo"),
         c("mammalia", "felidae", "felis", "catus"))

# Making a taxonomy object from scratch
#   Note: This information would usually come from a parsing function.
#         This is just for demonstration.
x <- taxon(
  name = taxon_name("Notoryctidae"),
  rank = taxon_rank("family"),
  id = taxon_id(4479)
)
y <- taxon(
  name = taxon_name("Notoryctes"),
  rank = taxon_rank("genus"),
  id = taxon_id(4544)
)
z <- taxon(
  name = taxon_name("Notoryctes typhlops"),
  rank = taxon_rank("species"),
  id = taxon_id(93036)
)

a <- taxon(
  name = taxon_name("Mammalia"),
  rank = taxon_rank("class"),
  id = taxon_id(9681)
)
b <- taxon(
  name = taxon_name("Felidae"),
  rank = taxon_rank("family"),
  id = taxon_id(9681)
)

cc <- taxon(
  name = taxon_name("Puma"),
  rank = taxon_rank("genus"),
  id = taxon_id(146712)
)
d <- taxon(
  name = taxon_name("Puma concolor"),
  rank = taxon_rank("species"),
  id = taxon_id(9696)
)

m <- taxon(
  name = taxon_name("Panthera"),
  rank = taxon_rank("genus"),
  id = taxon_id(146712)
)
n <- taxon(
  name = taxon_name("Panthera tigris"),
  rank = taxon_rank("species"),
  id = taxon_id(9696)
)

(hier1 <- hierarchy(z, y, x, a))
(hier2 <- hierarchy(cc, b, a, d))
(hier3 <- hierarchy(n, m, b, a))

(hrs <- hierarchies(hier1, hier2, hier3))

ex_taxonomy <- taxonomy(hier1, hier2, hier3)