tracts.legacy

Functions

eprint(*args, **kwargs)
optimize(p0, bins, Ls, data, nsamp, model_func)	Optimizes parameters to fit model to data using the BFGS method.
optimize_bfgs(p0, bins, Ls, data, nsamp, ...)	Optimizes parameters to fit model to data using the BFGS method.
optimize_brute_fracs2(bins, Ls, data, nsamp, ...)	Optimizes params to fit model to data using the brute force method.
optimize_brute_multifracs(bins, Ls, ...[, ...])	Optimizes params to fit model to data using the brute force method.
optimize_cob(p0, bins, Ls, data, nsamp, ...)	Optimizes params to fit model to data using the cobyla method.
optimize_cob_fracs(p0, bins, Ls, data, ...)	Optimizes params to fit model to data using the COBYLA method.
optimize_cob_fracs2(p0, bins, Ls, data, ...)	Optimizes params to fit model to data using the cobyla method.
optimize_cob_multifracs(p0, bins, Ls, ...[, ...])	Optimizes params to fit model to data using the cobyla method.
optimize_slsqp(p0, bins, Ls, data, nsamp, ...)	Optimizes params to fit model to data using the slsq method.
plotmig(mig[, colordict, order])
test_model_func(model_func, parameters[, ...])	Given a demographic model function, run a few debugging tests to ensure that it behaves as expected, namely: (i) that migration matrices sum to less than one (exactly one for the last generation, (ii) that it behaves continuously realtive to time parameters.

Classes

Chrom([ls, auto, label, tracts])	A chromosome wraps a list of tracts, which form a paritition on it.
Chropair([chroms, len, auto, label])	A pair of chromosomes.
CompositeDemographicModel(model_function, ...)	The class of demographic models that account for variance in the number of ancestors of individuals of the underlying population.
DemographicModel(mig[, ...])
Haploid([Ls, lschroms, fname, selectchrom, ...])
Indiv([Ls, label, fname, labs, selectchrom, ...])	The class of diploid individuals.
Population([list_indivs, names, fname, ...])
Tract(start, end, label[, bpstart, bpend])	A tract is the lower-level object of interest.