R: Artificial Extinction

ArtificialExtinction {TreeTools} | R Documentation

## 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 (martin.smith@durham.ac.uk)

### References

Asher R, Smith MR (2022). “Phylogenetic signal and bias in paleontology.” Systematic Biology, Online ahead of print, syab072. 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')

[Package TreeTools version 1.7.2 Index]