| ldsep-package | Linkage Disequilibrium Shrinkage Estimation for Polyploids |
| 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 |
| 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_gam | Estimate gametic pair-wise LD using either genotypes or genotype likelihoods. |
| ldsep | 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()' |
| 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. |