# The Breakdown of Genomic Ancestry Blocks in Hybrid Lineages

## Documentation for package ‘junctions’ version 2.1.1

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

## 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