Index

A

admix() (moments.LD.LDstats method) (moments.Spectrum method)

ancestral_misid() (moments.TwoLocus.TLSpectrum method) Anscombe_Poisson_residual() (in module moments.Inference)

B

bin_stats() (in module moments.LD.Inference) bootstrap() (in module moments.Misc) bootstrap_data() (in module moments.LD.Parsing) bottlegrowth() (in module moments.Demographics1D) (in module moments.Demographics2D) (in module moments.LD.Demographics1D) (in module moments.TwoLocus.Demographics)

bottlegrowth_split() (in module moments.Demographics2D) bottlegrowth_split_mig() (in module moments.Demographics2D) branch() (moments.Spectrum method)

C

compute_average_stats() (in module moments.LD.Parsing) compute_average_stats_between() (in module moments.LD.Parsing) compute_bin_stats() (in module moments.Demes.Inference)

compute_ld_statistics() (in module moments.LD.Parsing) compute_pairwise_stats() (in module moments.LD.Parsing) compute_pairwise_stats_between() (in module moments.LD.Parsing) count_data_dict() (in module moments.Misc)

D

D() (moments.TwoLocus.TLSpectrum method)

D2() (moments.TwoLocus.TLSpectrum method) Dz() (moments.TwoLocus.TLSpectrum method)

E

equilibrium() (in module moments.TwoLocus.Demographics)

F

f2() (moments.LD.LDstats method) (moments.Spectrum method) f3() (moments.LD.LDstats method) (moments.Spectrum method) f4() (moments.LD.LDstats method) (moments.Spectrum method) FIM_uncert() (in module moments.Godambe) (in module moments.LD.Godambe) fixed_size_sample() (moments.Spectrum method) fold() (moments.Spectrum method) (moments.TwoLocus.TLSpectrum method) fold_ancestral() (moments.Triallele.TriSpectrum method)

fold_major() (moments.Triallele.TriSpectrum method) from_angsd() (moments.Spectrum static method) from_data_dict() (moments.Spectrum static method) from_demes() (moments.LD.LDstats static method) (moments.Spectrum static method) from_file() (moments.LD.LDstats static method) (moments.Spectrum static method) (moments.Triallele.TriSpectrum static method) (moments.TwoLocus.TLSpectrum static method) from_ms_file() (moments.Spectrum static method) fromfile() (moments.Spectrum static method) Fst() (moments.Spectrum method)

G

genotype_matrix() (moments.Spectrum method) get_bootstrap_sets() (in module moments.LD.Parsing) get_genotypes() (in module moments.LD.Parsing) GIM_uncert() (in module moments.Godambe) (in module moments.LD.Godambe)

growth() (in module moments.Demographics1D) (in module moments.LD.Demographics1D) (in module moments.TwoLocus.Demographics)

H

H() (moments.LD.LDstats method)

H2() (moments.LD.LDstats method) het_names() (in module moments.LD.Util)

I

IM() (in module moments.Demographics2D) IM_pre() (in module moments.Demographics2D) integrate() (moments.LD.LDstats method) (moments.Spectrum method) (moments.Triallele.TriSpectrum method) (moments.TwoLocus.TLSpectrum method)

island_model() (in module moments.LD.Demographics2D)

L

LD() (in module moments.Demes) (moments.LD.LDstats method) ld_names() (in module moments.LD.Util) LDstats (class in moments.LD) left() (moments.TwoLocus.TLSpectrum method) linear_Poisson_residual() (in module moments.Inference)

ll() (in module moments.Inference) ll_multinom() (in module moments.Inference) ll_over_bins() (in module moments.LD.Inference) log() (moments.Spectrum method) (moments.Triallele.TriSpectrum method) LRT_adjust() (in module moments.Godambe)

M

make_data_dict_vcf() (in module moments.Misc) map_moment() (in module moments.LD.Util) marginalize() (moments.LD.LDstats method) (moments.Spectrum method) mask_corners() (moments.Spectrum method) mask_fixed() (moments.Triallele.TriSpectrum method) (moments.TwoLocus.TLSpectrum method) mask_infeasible() (moments.Triallele.TriSpectrum method) (moments.TwoLocus.TLSpectrum method) means_from_region_data() (in module moments.LD.Parsing) merge() (moments.LD.LDstats method) module moments.Demographics1D moments.Demographics2D moments.Demographics3D moments.Godambe moments.LD.Demographics1D moments.LD.Demographics2D moments.LD.Demographics3D moments.LD.Godambe moments.LD.Inference moments.LD.Parsing moments.LD.Util moments.TwoLocus.Demographics

moment_names() (in module moments.LD.Util) moments.Demographics1D module moments.Demographics2D module moments.Demographics3D module moments.Godambe module moments.LD.Demographics1D module moments.LD.Demographics2D module moments.LD.Demographics3D module moments.LD.Godambe module moments.LD.Inference module moments.LD.Parsing module moments.LD.Util module moments.TwoLocus.Demographics module

N

names() (moments.LD.LDstats method)

O

optimal_sfs_scaling() (in module moments.Inference) optimally_scaled_sfs() (in module moments.Inference) optimize() (in module moments.Demes.Inference) optimize_LD() (in module moments.Demes.Inference) optimize_log() (in module moments.Inference) optimize_log_fmin() (in module moments.Inference) (in module moments.LD.Inference)

optimize_log_lbfgsb() (in module moments.Inference) (in module moments.LD.Inference) optimize_log_powell() (in module moments.Inference) (in module moments.LD.Inference) out_of_Africa() (in module moments.Demographics3D) (in module moments.LD.Demographics3D)

P

perturb_params() (in module moments.LD.Util) (in module moments.Misc) pi() (moments.Spectrum method) (moments.Triallele.TriSpectrum method) pi2() (moments.TwoLocus.TLSpectrum method)

project() (moments.Spectrum method) (moments.Triallele.TriSpectrum method) (moments.TwoLocus.TLSpectrum method) pulse_migrate() (moments.LD.LDstats method) (moments.Spectrum method)

R

remove_nonpresent_statistics() (in module moments.LD.Inference) remove_normalized_data() (in module moments.LD.Inference) remove_normalized_lds() (in module moments.LD.Inference)

rescale() (in module moments.Demes.DemesUtil) rescale_params() (in module moments.LD.Util) right() (moments.TwoLocus.TLSpectrum method)

S

S() (moments.Spectrum method) (moments.Triallele.TriSpectrum method) (moments.TwoLocus.TLSpectrum method) sample() (moments.Spectrum method) scramble_pop_ids() (moments.Spectrum method) set_cache_path() (in module moments.TwoLocus.Demographics) SFS() (in module moments.Demes) sigmaD2() (in module moments.LD.Inference) slice() (in module moments.Demes.DemesUtil) snm() (in module moments.Demographics1D) (in module moments.Demographics2D) (in module moments.LD.Demographics1D) (in module moments.LD.Demographics2D)

Spectrum (class in moments) split() (moments.LD.LDstats method) (moments.Spectrum method) split_mig() (in module moments.Demographics2D) (in module moments.LD.Demographics2D) steady_state() (moments.LD.LDstats static method) subset_data() (in module moments.LD.Parsing) swap_axes() (moments.Spectrum method) swap_pops() (moments.LD.LDstats method) swipe() (in module moments.Demes.DemesUtil)

T

Tajima_D() (moments.Spectrum method) theta_L() (moments.Spectrum method) three_epoch() (in module moments.Demographics1D) (in module moments.LD.Demographics1D) (in module moments.TwoLocus.Demographics) TLSpectrum (class in moments.TwoLocus) to_file() (moments.LD.LDstats method) (moments.Spectrum method) (moments.Triallele.TriSpectrum method) (moments.TwoLocus.TLSpectrum method)

tofile() (moments.Spectrum method) TriSpectrum (class in moments.Triallele) two_epoch() (in module moments.Demographics1D) (in module moments.LD.Demographics1D) (in module moments.TwoLocus.Demographics)

U

uncerts() (in module moments.Demes.Inference) uncerts_LD() (in module moments.Demes.Inference) unfold() (moments.Spectrum method) (moments.Triallele.TriSpectrum method) (moments.TwoLocus.TLSpectrum method)

unmask_all() (moments.Spectrum method) unmask_corners() (moments.Spectrum method)

W

Watterson_theta() (moments.Spectrum method)

Z

Zengs_E() (moments.Spectrum method)