junctions-package |
Extending The Theory of Junctions |
calculate_mat |
Function to calculate the maximum accurate time |
calc_k |
Calculate the limit of the number of junctions |
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 |
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 |