Imports: stats, utils, ecd, optimx, xts (>= 0.10-0), zoo, moments,
parallel, graphics, scales, ggplot2, grid, methods

Title: LD LASSO Regression for SNP Association Study
Description: ldlasso requires data be of class gwaa.data from the the
Depends: R (>= 2.6.0), GenABEL, quadprog

Maintainer: Samuel G. Younkin <samuel.younkin@gmail.com>

Title: Methods for likelihood-based dimension reduction in regression
Depends: R (>= 2.10), GrassmannOptim, Matrix
Author: Kofi Placid Adragni, Andrew Raim
Description: Functions, methods, and datasets for fitting
likelihood-based dimension reduction in regression, using
principal fitted components (pfc), likelihood acquired
directions (lad), covariance reducing models (core).

Depends: R (>= 3.0.0), GrassmannOptim, Matrix
Description: Functions, methods, and data sets for fitting likelihood-based dimension reduction in regression, using principal fitted components (pfc), likelihood acquired directions (lad), covariance reducing models (core).

Description: Functions, methods, and datasets for fitting likelihood-based dimension reduction in regression, using principal fitted components (pfc), likelihood acquired directions (lad), covariance reducing models (core).

Title: Linkage Disequilibrium Shrinkage Estimation for Polyploids
Description: Estimate gametic or composite pairwise linkage disequilibrium
(LD) in polyploids, using either genotypes or genotype likelihoods.
Support is provided to estimate the popular measures of LD: the LD
coefficient D, the standardized LD coefficient D', and the Pearson
correlation coefficient r. All estimates are returned with corresponding
standard errors. These estimates and standard errors can then be used
for shrinkage estimation. The main functions are ldest(), mldest(),
sldest(), plot.lddf(), format_lddf(), and ldshrink().
Imports: Rcpp, foreach, doParallel, ashr, corrplot, lpSolve
Suggests: testthat, covr, knitr, rmarkdown, updog (>= 2.0.2)
Author: David Gerard [aut, cre] (<https://orcid.org/0000-0001-9450-5023>)

Description: Estimate haplotypic or composite pairwise linkage disequilibrium
sldest(), plot.lddf(), format_lddf(), and ldshrink(). Details of the methods
Suggests: testthat, covr, knitr, rmarkdown, updog (>= 2.0.2),