Package index • junctions

All functions

calc_k(): Calculate the limit of the number of junctions

calculate_mat(): Function to calculate the maximum accurate time

estimate_time(): Estimate the time since the onset of hybridization, using the number of junctions

estimate_time_diploid(): estimates the time since admixture, given diploid ancestry data.

estimate_time_haploid(): estimate time using likelihood for a single chromosome

estimate_time_one_chrom(): Estimate the time since the onset of hybridization, using the observed number of junctions, taking into account the distribution of markers on a single chromosome

junctions-package junctions: Extending The Theory of Junctions

log_likelihood_diploid(): calculate the log likelihood of observing diploid ancestry data.

log_likelihood_haploid(): log likelihood of the time since admixture for a haploid genome

number_of_junctions(): Calculate the average number of junctions

number_of_junctions_backcross(): Calculate the average number of junctions during backcrossing

number_of_junctions_di(): Calculate the expected number of junctions between two markers separated by a given amount of recombination

number_of_junctions_markers(): Calculate the expected total number of junctions in a chromosome, given the distribution of markers

sim_backcrossing(): Function to simulate data using a back crossing scheme

sim_fin_chrom(): Individual Based Simulation of the accumulation of junctions

sim_inf_chrom(): Individual Based Simulation of the accumulation of junctions

sim_phased_unphased(): Individual Based Simulation of the accumulation of junctions

time_error(): Estimate the error in the time estimate