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Artificial Extinction

Source: R/ArtificialExtinction.R
ArtificialExtinction.Rd

Remove tokens that do not occur in a fossil "template" taxon from a living taxon, to simulate the process of fossilization in removing data from a phylogenetic dataset.

Usage

ArtificialExtinction(
  dataset,
  subject,
  template,
  replaceAmbiguous = "ambig",
  replaceCoded = "original",
  replaceAll = TRUE,
  sampleFrom = NULL
)

# S3 method for class 'matrix'
ArtificialExtinction(
  dataset,
  subject,
  template,
  replaceAmbiguous = "ambig",
  replaceCoded = "original",
  replaceAll = TRUE,
  sampleFrom = NULL
)

# S3 method for class 'phyDat'
ArtificialExtinction(
  dataset,
  subject,
  template,
  replaceAmbiguous = "ambig",
  replaceCoded = "original",
  replaceAll = TRUE,
  sampleFrom = NULL
)

ArtEx(
  dataset,
  subject,
  template,
  replaceAmbiguous = "ambig",
  replaceCoded = "original",
  replaceAll = TRUE,
  sampleFrom = NULL
)

Arguments

dataset

Phylogenetic dataset of class phyDat or matrix.

subject

Vector identifying subject taxa, by name or index.

template

Character or integer identifying taxon to use as a template.

replaceAmbiguous, replaceCoded

Character specifying whether tokens that are ambiguous (?) or coded (not ?) in the fossil template should be replaced with:

  • original: Their original value; i.e. no change;

  • ambiguous: The ambiguous token, ?;

  • binary: The tokens 0 or 1, with equal probability;

  • uniform: One of the tokens present in sampleFrom, with equal probability;

  • sample: One of the tokens present in sampleFrom, sampled according to their frequency.

replaceAll

Logical: if TRUE, replace all tokens in a subject; if FALSE, leave any ambiguous tokens (?) ambiguous.

sampleFrom

Vector identifying a subset of characters from which to sample replacement tokens. If NULL, replacement tokens will be sampled from the initial states of all taxa not used as a template (including the subjects).

Value

A dataset with the same class as dataset in which entries that are ambiguous in template are made ambiguous in subject.

Details

Further details are provided in Asher2020;textualTreeTools.

Note: this simple implementation does not account for character contingency, e.g. characters whose absence imposes inapplicable or absent tokens on dependent characters.

References

Author

Martin R. Smith (martin.smith@durham.ac.uk)

Examples

set.seed(1)
dataset <- matrix(c(sample(0:2, 4 * 8, TRUE),
                    "0", "0", rep("?", 6)), nrow = 5,
                    dimnames = list(c(LETTERS[1:4], "FOSSIL"),
                                    paste("char", 1:8)), byrow = TRUE)
artex <- ArtificialExtinction(dataset, c("A", "C"), "FOSSIL")