ArtificialExtinction {TreeTools}

Artificial Extinction

Description

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).

Details

Further details are provided in Asher and Smith (2022).

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

Value

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

Author(s)

Martin R. Smith ([e-mail])

References

Asher R, Smith MR (2022). “Phylogenetic signal and bias in paleontology.” Systematic Biology, 71(4), 986–1008. doi:10.1093/sysbio/syab072.

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")