TreeTools: ArtificialExtinction – R documentation

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ArtificialExtinction

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

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 (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')

TreeTools

Create, Modify and Analyse Phylogenetic Trees

v1.4.4

GPL (>= 3)

Authors

Martin R. Smith [aut, cre, cph] (<https://orcid.org/0000-0001-5660-1727>), Emmanuel Paradis [cph] (<https://orcid.org/0000-0003-3092-2199>)

Initial release