#' Frequentist and Bayesian methods for breeders, quantitative geneticists and
#' forest genetic resources analysts.
#'
#' This package provides statistical tools to build predictive models for the
#' breeders, quantitative genetists and forest genetic resources analysts
#' communities. It aims to assess the genetic value of individuals under a
#' number of situations, including spatial autocorrelation, genetic/environment
#' interaction and competition. It is under active development as part of the
#' Trees4Future project, particularly developed having forest genetic trials in
#' mind. But can be used for animals or other situations as well.
#'
#' The package functionality builds up on a wrapping up of Ignacy Misztal's
#' progsf90 suite of Fortran programs. Particularly, the function \code{reml}
#' performs classical Restricted-Maximum Likelihood inference by interfacing
#' Misztal's programs with several high-level options such as spatial
#' components, etc. The Fortran back-end allows for fast inference on rather
#' large datasets (hundreds of thousands of individuals) with complex pedigrees.
#'
#' @name breedR-package
#' @aliases breedR-package breedR
#' @docType package
#' @seealso \code{\link[pedigreemm]{pedigreemm}}
#' @references Most functionality in the package is based on Ignacy Misztal's
#' suite of Fortran programs for mixed model computations in breeding.
#' \url{http://nce.ads.uga.edu/wiki/doku.php}
#'
#' M. Lynch \& B. Walsh (1998). \emph{Genetics and Analysis of Quantitative
#' Traits}. Sinauer Associates, Inc.
#' @keywords package
#' @examples
#'
#' # Load, summarize and visualize data
#' data(m4)
#' summary(m4)
#' plot(m4)
#'
#' # Fit Mixed Model using REML
#' res.f90 <- remlf90(fixed = phe_X ~ gen,
#' genetic = list(model = 'add_animal',
#' pedigree = get_pedigree(m4),
#' id = 'self'),
#' data = as.data.frame(m4))
#'
#' # Summary of results
#' summary(res.f90)
#'
#' # Observed phenotypes vs. Fitted values
#' library(ggplot2)
#' qplot(phe_X, fitted(res.f90), color=gen, data = as.data.frame(m4)) +
#' geom_abline(intercept=0, slope=1)
#'
NULL
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