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Export fossil records as PyRate input

Source: R/pyrate.R
export_pyrate.Rd

Writes fossil occurrences in the input format of PyRate (Silvestro et al. 2014), the Bayesian estimator of speciation and extinction rates from fossil occurrences: a Python file holding, per replicate, one array of occurrence ages per taxon, and a tab-separated list of the taxa with their status. An extant taxon gets an extra age of 0. Each record's age is drawn uniformly from its range (random = TRUE) or set to the range's midpoint; a minimum age of 0 is set to 0.001.

Usage

export_pyrate(
  x,
  file,
  status,
  columns = occ_columns(),
  trait = NULL,
  replicates = 1,
  random = TRUE,
  seed = NULL
)

Arguments

x

A data frame of fossil records, for example the kept records of a flagged table.

file

Path prefix of the output: <file>_PyRate.py and <file>_TaxonList.txt are written.

status

"extinct" or "extant": one value for all records, one per record, or the name of a column of x holding them. A taxon must have a single status.

columns

Field names, see occ_columns(); the taxon is read from species and the ages from min_age and max_age.

trait

Optional numeric trait, one value per record or the name of a column; the taxon mean is written as a continuous trait.

replicates

Number of age replicates (data sets) in the file.

random

Draw ages from the ranges (TRUE) or use the midpoints. Replicates of midpoint ages are identical.

seed

Seed for the age draws; the caller's random-number stream is left unchanged. NULL draws from the current stream.

Value

The paths of the two files, invisibly.

Details

The records are exported as given, so the cleaning rule is applied first: x[!has_flag(x$flags, rule), ].

References

Silvestro, D., Schnitzler, J., Liow, L. H., Antonelli, A. and Salamin, N. (2014). Bayesian estimation of speciation and extinction from incomplete fossil occurrence data. Systematic Biology 63:349-367. doi:10.1093/sysbio/syu006

See also

flag_occurrences(), test_age_equal

Examples

x <- data.frame(accepted_name = c("Equus caballus", "Equus caballus", "Hipparion sp"),
                min_ma = c(0.5, 1.2, 5), max_ma = c(1, 2.6, 11))
paths <- export_pyrate(x, file.path(tempdir(), "horses"), status = c("extant", "extant", "extinct"),
                       columns = occ_columns(species = "accepted_name"), random = FALSE)
cat(readLines(paths[1]), sep = "\n")