#' @name ge_ammi
#' @aliases ge_ammi
#' @title AMMI of Genotype by Environment Interaction Model
#' @description Performs Additive Main Effects and Multiplication Interaction Analysis of Genotype by Environment Interaction Model
#'
#' @param .data data.frame
#' @param .y Response Variable
#' @param .gen Genotypes Factor
#' @param .env Environment Factor
#' @param .rep Replication Factor
#'
#' @return Genotype by Environment Interaction Model
#'
#' @author
#' \enumerate{
#' \item Muhammad Yaseen (\email{myaseen208@@gmail.com})
#' }
#'
#' @references
#' Crossa, J., Perez-Elizalde, S., Jarquin, D., Cotes, J.M., Viele, K., Liu, G., and Cornelius, P.L. (2011)
#' Bayesian Estimation of the Additive Main Effects and Multiplicative Interaction Model
#' \emph{Crop Science}, \strong{51}, 1458–1469.
#' (\href{https://dl.sciencesocieties.org/publications/cs/abstracts/51/4/1458?access=0&view=pdf}{doi: 10.2135/cropsci2010.06.0343})
#'
#' @import lme4
#' @import rlang
#' @import tidyr
#' @importFrom dplyr select group_by count
#' @importFrom magrittr %>%
#' @importFrom stats sigma
#'
#' @export
#'
#' @examples
#'
#' data(Maiz)
#' fm1 <-
#' ge_ammi(
#' .data = Maiz
#' , .y = y
#' , .gen = entry
#' , .env = site
#' , .rep = rep
#' )
#'
#'
#'
#'
ge_ammi <- function(.data, .y, .gen, .env, .rep) {
UseMethod("ge_ammi")
}
#' @export
#' @rdname ge_ammi
ge_ammi.default <-
function(.data, .y, .gen, .env, .rep){
.y <- deparse(substitute(.y))
.gen <- deparse(substitute(.gen))
.env <- deparse(substitute(.env))
.rep <- deparse(substitute(.rep))
df1 <- tibble::as_tibble(data.frame(
Env = factor(.data[[.env]])
, Gen = factor(.data[[.gen]])
, Rep = factor(.data[[.rep]])
, Y = .data[[.y]]
))
g <- length(levels(df1$Gen))
e <- length(levels(df1$Env))
Rep <- length(levels(df1$Rep))
k <- min(g, e) - 1
ge_means <-
ge_mean(
.data = df1
, .y = Y
, .gen = Gen
, .env = Env
)
ge_effects <-
ge_eff(
.data = df1
, .y = Y
, .gen = Gen
, .env = Env
)
g_effects <-
g_eff(
.data = df1
, .y = Y
, .gen = Gen
, .env = Env
)
e_effects <-
e_eff(
.data = df1
, .y = Y
, .gen = Gen
, .env = Env
)
ge_model <-
ge_model(
.data = df1
, .y = Y
, .gen = Gen
, .env = Env
, .rep = Rep
)
return(list(
g = g
, e = e
, Rep = Rep
, k = k
, ge_means = ge_means
, mu = ge_means$grand_mean
, sigma2 = sigma(ge_model)^2
, tau = 1/sigma(ge_model)^2
, tao = g_effects
, delta = e_effects
, lambdas = ge_effects$ge_svd$d[1:k]
, alphas = ge_effects$ge_svd$u[,1:k]
, gammas = ge_effects$ge_svd$v[,1:k]
))
}
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