The Breakdown of Genomic Ancestry Blocks in Hybrid Lineages
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Documentation for package ‘junctions’ version 2.1.3
Help Pages
| 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 |