Calculates the time since admixture, given unphased ancestry data.
estimate_time_diploid(
ancestry_information,
analysis_type = "individuals",
phased = FALSE,
pop_size = 1000,
freq_ancestor_1 = 0.5,
lower_lim = 2,
upper_lim = 2000,
num_threads = 1,
verbose = FALSE
)a matrix with five columns: column 1) indicator of individual, column 2) indicator of chromosome, 3) location of marker in Morgan, 4) ancestry at chromosome 5) ancestry at chromosome 2.
how should the data be broken down? there are multiple options: "individuals" - time is inferred for each individual separately, grouping all chromosomes together that belong to the same individual. "chromosomes" - time is inferred for each chromosome separately, grouping chromosomes together belonging from separate individuals. "separate" - time is inferred for each chromosome from each individual separately, "all" - time is inferred jointly for all chromosomes and individuals, grouping all chromosomes and individuals together.
is the data phased?
population size
Frequency of ancestor 1 at t = 0
lower limit of the optimization algorithm. Increase if the expected admixture time is relatively ancient
upper limit of hte optimization algorithm. If set too large, recent admixture events can be overlooked - best to set as low as possible.
num_threads, default is all threads. 5 threads is recommended.
display intermediate output? Default = FALSE