Package index • hybridclock

Markers and scores

diagnostic_markers(): Find diagnostic markers between two reference groups
shared_loci(): Find loci shared by both species
orient_genotypes(): Count species-2 alleles at diagnostic markers
marker_information(): Information carried by a set of markers
check_markers(): Check that markers are diagnostic in the parents that actually bred
microsat_markers(): Microsatellite markers
hybrid_scores_microsat(): Hybrid index and heterozygosity from microsatellites
classify_hybrids_microsat(): Classify recent hybrids from microsatellites
hybrid_scores(): Hybrid index and interspecies heterozygosity
plot_triangle(): Plot animals on the hybrid triangle

simulate_hybrid_zone(): Simulate a hybrid population forward in time
random_map(): Random marker map
sample_summaries(): Summarize a population sample of hybrid scores
build_reference(): Simulate a reference set of hybrid histories
class_settings(): Settings for the classes that choose between the two tiers
train_clock(): Train the hybrid clock on a reference set
estimate_history(): Estimate the hybrid history of sampled populations
predict(<hybridclock_model>): Predict histories from sample summaries

marker_power() markers_needed(): Chance that a backcrossed hybrid looks pure
classification_power(): Expected accuracy of individual classification