taxmap: Taxmap class

In metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Taxmap class

Description

A class designed to store a taxonomy and associated information. This class builds on the [taxonomy()] class. User defined data can be stored in the list 'obj$data', where 'obj' is a taxmap object. Data that is associated with taxa can be manipulated in a variety of ways using functions like [filter_taxa()] and [filter_obs()]. To associate the items of lists/vectors with taxa, name them by [taxon_ids()]. For tables, add a column named 'taxon_id' that stores [taxon_ids()].

Usage

taxmap(..., .list = NULL, data = NULL, funcs = list(), 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 '...'.
data	A list of tables with data associated with the taxa.
funcs	A named list of functions to include in the class. Referring to the names of these in functions like [filter_taxa()] will execute the function and return the results. If the function has at least one argument, the taxmap object is passed to it.
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.

Details

To initialize a 'taxmap' object with associated data sets, use the parsing functions [parse_tax_data()], [lookup_tax_data()], and [extract_tax_data()].

on initialize, function sorts the taxon list based on rank (if rank information is available), see [ranks_ref] for the reference rank names and orders

Value

An 'R6Class' object of class [taxmap()]

See Also

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

Examples

# The code below shows how to contruct a taxmap object from scratch.
# Typically, taxmap objects would be the output of a parsing function,
#  not created from scratch, but this is for demostration purposes.

notoryctidae <- taxon(
name = taxon_name("Notoryctidae"),
rank = taxon_rank("family"),
id = taxon_id(4479)
)
notoryctes <- taxon(
  name = taxon_name("Notoryctes"),
  rank = taxon_rank("genus"),
  id = taxon_id(4544)
)
typhlops <- taxon(
  name = taxon_name("typhlops"),
  rank = taxon_rank("species"),
  id = taxon_id(93036)
)
mammalia <- taxon(
  name = taxon_name("Mammalia"),
  rank = taxon_rank("class"),
  id = taxon_id(9681)
)
felidae <- taxon(
  name = taxon_name("Felidae"),
  rank = taxon_rank("family"),
  id = taxon_id(9681)
)
felis <- taxon(
  name = taxon_name("Felis"),
  rank = taxon_rank("genus"),
  id = taxon_id(9682)
)
catus <- taxon(
  name = taxon_name("catus"),
  rank = taxon_rank("species"),
  id = taxon_id(9685)
)
panthera <- taxon(
  name = taxon_name("Panthera"),
  rank = taxon_rank("genus"),
  id = taxon_id(146712)
)
tigris <- taxon(
  name = taxon_name("tigris"),
  rank = taxon_rank("species"),
  id = taxon_id(9696)
)
plantae <- taxon(
  name = taxon_name("Plantae"),
  rank = taxon_rank("kingdom"),
  id = taxon_id(33090)
)
solanaceae <- taxon(
  name = taxon_name("Solanaceae"),
  rank = taxon_rank("family"),
  id = taxon_id(4070)
)
solanum <- taxon(
  name = taxon_name("Solanum"),
  rank = taxon_rank("genus"),
  id = taxon_id(4107)
)
lycopersicum <- taxon(
  name = taxon_name("lycopersicum"),
  rank = taxon_rank("species"),
  id = taxon_id(49274)
)
tuberosum <- taxon(
  name = taxon_name("tuberosum"),
  rank = taxon_rank("species"),
  id = taxon_id(4113)
)
homo <- taxon(
  name = taxon_name("homo"),
  rank = taxon_rank("genus"),
  id = taxon_id(9605)
)
sapiens <- taxon(
  name = taxon_name("sapiens"),
  rank = taxon_rank("species"),
  id = taxon_id(9606)
)
hominidae <- taxon(
  name = taxon_name("Hominidae"),
  rank = taxon_rank("family"),
  id = taxon_id(9604)
)
unidentified <- taxon(
  name = taxon_name("unidentified")
)

tiger <- hierarchy(mammalia, felidae, panthera, tigris)
cat <- hierarchy(mammalia, felidae, felis, catus)
human <- hierarchy(mammalia, hominidae, homo, sapiens)
mole <- hierarchy(mammalia, notoryctidae, notoryctes, typhlops)
tomato <- hierarchy(plantae, solanaceae, solanum, lycopersicum)
potato <- hierarchy(plantae, solanaceae, solanum, tuberosum)
potato_partial <- hierarchy(solanaceae, solanum, tuberosum)
unidentified_animal <- hierarchy(mammalia, unidentified)
unidentified_plant <- hierarchy(plantae, unidentified)

info <- data.frame(stringsAsFactors = FALSE,
                   name = c("tiger", "cat", "mole", "human", "tomato", "potato"),
                   n_legs = c(4, 4, 4, 2, 0, 0),
                   dangerous = c(TRUE, FALSE, FALSE, TRUE, FALSE, FALSE))

abund <- data.frame(code = rep(c("T", "C", "M", "H"), 2),
                    sample_id = rep(c("A", "B"), each = 2),
                    count = c(1,2,5,2,6,2,4,0),
                    taxon_index = rep(1:4, 2))

phylopic_ids <- c("e148eabb-f138-43c6-b1e4-5cda2180485a",
                  "12899ba0-9923-4feb-a7f9-758c3c7d5e13",
                  "11b783d5-af1c-4f4e-8ab5-a51470652b47",
                  "9fae30cd-fb59-4a81-a39c-e1826a35f612",
                  "b6400f39-345a-4711-ab4f-92fd4e22cb1a",
                  "63604565-0406-460b-8cb8-1abe954b3f3a")

foods <- list(c("mammals", "birds"),
              c("cat food", "mice"),
              c("insects"),
              c("Most things, but especially anything rare or expensive"),
              c("light", "dirt"),
              c("light", "dirt"))

reaction <- function(x) {
  ifelse(x$data$info$dangerous,
         paste0("Watch out! That ", x$data$info$name, " might attack!"),
         paste0("No worries; its just a ", x$data$info$name, "."))
}

ex_taxmap <- taxmap(tiger, cat, mole, human, tomato, potato,
                    data = list(info = info,
                                phylopic_ids = phylopic_ids,
                                foods = foods,
                                abund = abund),
                    funcs = list(reaction = reaction))

metacoder documentation built on April 4, 2023, 9:08 a.m.