taxmap: 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())

Arguments

...

Any number of object of class hierarchy() or character vectors. Cannot be used with .list.

.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.

Value

An R6Class object of class taxmap()

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

Examples

Run this code

# NOT RUN {
# 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(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))
# }

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