How Long Have Hybrids Been Forming? Hybrid Population Histories from Diagnostic Markers

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Documentation for package ‘hybridclock’ version 0.1.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

bettongs	Burrowing bettongs: two subspecies mixed in a fenced reserve
build_reference	Simulate a reference set of hybrid histories
carp	Bighead and silver carp: an invasive hybrid zone
check_markers	Check that markers are diagnostic in the parents that actually bred
chickens	Chickens: an advanced intercross after eight generations
classification_power	Expected accuracy of individual classification
classify_hybrids	Classify recent hybrids individually
classify_hybrids_microsat	Classify recent hybrids from microsatellites
class_settings	Settings for the classes that choose between the two tiers
diagnostic_markers	Find diagnostic markers between two reference groups
effective_markers	Effective number of independent markers
estimate_history	Estimate the hybrid history of sampled populations
hybridclock_example	Example data set
hybrid_scores	Hybrid index and interspecies heterozygosity
hybrid_scores_microsat	Hybrid index and heterozygosity from microsatellites
markers_needed	Chance that a backcrossed hybrid looks pure
marker_information	Information carried by a set of markers
marker_power	Chance that a backcrossed hybrid looks pure
microsat_markers	Microsatellite markers
orient_genotypes	Count species-2 alleles at diagnostic markers
plot_triangle	Plot animals on the hybrid triangle
possums	Mountain pygmy possums: genetic rescue at 24 microsatellites
predict.hybridclock_model	Predict histories from sample summaries
random_map	Random marker map
sample_summaries	Summarize a population sample of hybrid scores
shared_loci	Find loci shared by both species
simulate_hybrid_zone	Simulate a hybrid population forward in time
train_clock	Train the hybrid clock on a reference set
wolves	Mexican wolves: crosses between two captive lineages