palaeoverse (version 1.4.0)

tax_unique: Filter occurrences to unique taxa

Description

A function to filter a list of taxonomic occurrences to unique taxa of a predefined resolution. Occurrences identified to a coarser taxonomic resolution than the desired level are retained if they belong to a clade which is not otherwise represented in the dataset (see details section for further information). This has previously been described as "cryptic diversity" (e.g. Mannion et al. 2011).

Usage

tax_unique(
  occdf = NULL,
  binomial = NULL,
  species = NULL,
  genus = NULL,
  ...,
  name = NULL,
  resolution = "species",
  append = FALSE
)

Value

A dataframe of taxa, with each row corresponding to a unique "species" or "genus" in the dataset (depending on the chosen resolution). The dataframe will include the taxonomic information provided into the function, as well as a column providing the 'unique' names of each taxon. If append is TRUE, the original dataframe (occdf) will be returned with these 'unique' names appended as a new column. Occurrences that are identified to a coarse taxonomic resolution and belong to a clade which is already represented within the dataset will have their 'unique' names listed as NA.

Arguments

occdf

dataframe. A dataframe containing information on the occurrences or taxa to filter.

binomial

character. The name of the column in occdf containing the genus and species names of the occurrences, either in the form "genus species" or "genus_species".

species

character. The name of the column in occdf containing the species-level identifications (i.e. the specific epithet).

genus

character. The name of the column in occdf containing the genus-level identifications.

...

character. Other named arguments specifying columns of higher levels of taxonomy (e.g. subfamily, order, superclass). The names of the arguments will be the column names of the output, and the values of the arguments correspond to the columns of occdf. The given order of the arguments is the order in which they are filtered. Therefore, these arguments must be in ascending order from lowest to highest taxonomic rank (see examples below). At least one higher level of taxonomy must be specified.

name

character. The name of the column in occdf containing the taxonomic names at mixed taxonomic levels; the data column "accepted_name" in a Paleobiology Database occurrence dataframe is of this type.

resolution

character. The taxonomic resolution at which to identify unique occurrences, either "species" (the default) or "genus".

append

logical. Should the original dataframe be returned with the unique names appended as a new column?

Developer(s)

Bethany Allen & William Gearty

Reviewer(s)

Lewis A. Jones & William Gearty

Details

Palaeobiologists usually count unique taxa by retaining only unique occurrences identified to a given taxonomic resolution, however this function retains occurrences identified to a coarser taxonomic resolution which are not already represented within the dataset. For example, consider the following set of occurrences:

• Albertosaurus sarcophagus

• Ankylosaurus sp.

• Aves indet.

• Ceratopsidae indet.

• Hadrosauridae indet.

• Ornithomimus sp.

• Tyrannosaurus rex

A filter for species-level identifications would reduce the species richness to two. However, none of these clades are nested within one another, so each of the indeterminately identified occurrences represents at least one species not already represented in the dataset. This function is designed to deal with such taxonomic data, and would retain all seven 'species' in this example.

Taxonomic information is supplied within a dataframe, in which columns provide identifications at different taxonomic levels. Occurrence data can be filtered to retain either unique species, or unique genera. If a species-level filter is desired, the minimum input requires either (1) binomial, (2) species and genus, or (3) name and genus columns to be entered, as well as at least one column of a higher taxonomic level. In a standard Paleobiology Database occurrence dataframe, species names are only captured in the 'accepted_name' column, so a species-level filter should use 'genus = "genus"' and 'name = "accepted_name"' arguments. If a genus-level filter is desired, the minimum input requires either (1) binomial or (2) genus columns to be entered, as well as at least one column of a higher taxonomic level.

Missing data should be indicated with NAs, although the function can handle common labels such as "NO_FAMILY_SPECIFIED" within Paleobiology Database datasets.

The function matches taxonomic names at face value, so homonyms may be falsely filtered out.

References

Mannion, P. D., Upchurch, P., Carrano, M. T., and Barrett, P. M. (2011). Testing the effect of the rock record on diversity: a multidisciplinary approach to elucidating the generic richness of sauropodomorph dinosaurs through time. Biological Reviews, 86, 157-181. tools:::Rd_expr_doi("10.1111/j.1469-185X.2010.00139.x").

Examples

#Retain unique species
occdf <- tetrapods[1:100, ]
species <- tax_unique(occdf = occdf, genus = "genus", family = "family",
order = "order", class = "class", name = "accepted_name")

#Retain unique genera
genera <- tax_unique(occdf = occdf, genus = "genus", family = "family",
order = "order", class = "class", resolution = "genus")

#Append unique names to the original occurrences
genera_append <- tax_unique(occdf = occdf, genus = "genus", family = "family",
order = "order", class = "class", resolution = "genus", append = TRUE)

#Create dataframe from lists
occdf2 <- data.frame(species = c("rex", "aegyptiacus", NA), genus =
c("Tyrannosaurus", "Spinosaurus", NA), family = c("Tyrannosauridae",
"Spinosauridae", "Diplodocidae"))
dinosaur_species <- tax_unique(occdf = occdf2, species = "species", genus =
"genus", family = "family")

#Retain unique genera per collection with group_apply
genera <- group_apply(occdf = occdf,
                     group = c("collection_no"),
                     fun = tax_unique,
                     genus = "genus",
                     family = "family",
                     order = "order",
                     class = "class",
                     resolution = "genus")