All functions

Dprime()

Get the standardized composite D'.

format_lddf()

Format an element of mldest() or sldest() into an upper-triangular matrix.

get_prob_array()

Obtain the distribution of genotypes given haplotype frequencies under HWE

gl_to_gp()

Normalize genotype likelihoods to posterior probabilities.

glike

Genotype log-likelihoods from uit

gp

Posterior probabilities from uit

is.lddf()

Tests if an argument is a lddf object.

ldest()

Pairwise LD estimation in polyploids.

ldest_comp()

Estimates of composite pairwise LD based either on genotype estimates or genotype likelihoods.

ldest_hap()

Estimate haplotypic pair-wise LD using either genotypes or genotype likelihoods.

ldfast()

Fast bias-correction for LD Estimation

ldsep-package

Linkage Disequilibrium Shrinkage Estimation for Polyploids

ldshrink()

Obtain shrinkage estimates of correlation from output of mldest() or sldest().

mldest()

Estimate all pair-wise LD's in a collection of SNPs using genotypes or genotype likelihoods.

pbnorm_dist()

Returns distribution of proportional bivariate normal.

plot(<lddf>)

Plot the output of mldest() or sldest() using corrplot()

pvcalc()

Calculate prior variances from a matrix of prior genotype probabilities.

slcor()

Sliding window correlation

sldest()

Sliding window LD estimation

uit

Updog fits on the data from Uitdewilligen et. al. (2013)

zshrink()

Shrinks Fisher-z transformed correlation estimates and returns resulting correlation estimates.