Settings for the classes that choose between the two tiers

The share of hybrids in each early class is part of the summaries the clock learns from, and it decides whether a population is dated by its individual classes or by the clock (see estimate_history()). Those classes must be made the same way in the simulated reference and in the data, so the settings are given once, to build_reference(), and are then used for both.

Usage

class_settings(
  error = 0.005,
  het_dropout = 0,
  effective_markers = NULL,
  markers = NULL,
  alpha = 0.01
)

Arguments

error

Genotyping error rate assumed by the classes.

het_dropout

Share of heterozygotes called homozygous (see classify_hybrids()); for RAD or GBS data where F1s show clearly less than full heterozygosity.

effective_markers

Optional effective number of independent markers (see effective_markers()), for many linked markers.

markers

Optional output of diagnostic_markers() (columns freq1, freq2) for markers that are not fixed; with it, animals are classified from their genotype counts at the markers.

alpha

Significance level of the fit test for "later".

Value

A list of class hybridclock_class_settings.

Details

With markers that are not fixed, class probabilities are averaged over markers using the reference allele frequencies, which needs only a few summary moments of the frequencies and keeps the classification fast enough to run on every simulated sample.

Examples

class_settings(het_dropout = 0.2)
#> class settings: error 0.005  het_dropout 0.2  effective markers none