R/add_anova.R

In stability: Stability Analysis of Genotype by Environment Interaction (GEI)

#' @name    add_anova
#' @aliases add_anova
#' @title Additive ANOVA for Genotypes by Environment Interaction (GEI) model
#' @description Additive ANOVA for Genotypes by Environment Interaction (GEI) model
#'
#' @param .data  data.frame
#' @param .y     Response Variable
#' @param .rep   Replication Factor
#' @param .gen   Genotypes Factor
#' @param .env   Environment Factor
#'
#' @return Additive ANOVA
#'
#' @author
#' \enumerate{
#'          \item Muhammad Yaseen (\email{myaseen208@@gmail.com})
#'          \item Kent M. Edkridge (\email{keskridge1@@unl.edu})
#'          }
#'
#' @references
#'  Singh, R. K. and Chaudhary, B. D. (2004) \emph{Biometrical Methods in Quantitative Genetic Analysis}.
#'              New Delhi: Kalyani.
#'
#' @import rlang
#' @importFrom stats anova as.formula ave coef confint formula lm pf terms
#'
#' @export
#'
#' @examples
#' data(ge_data)
#' YieldANOVA <-
#'      add_anova(
#'             .data = ge_data
#'           , .y    = Yield
#'           , .rep  = Rep
#'           , .gen  = Gen
#'           , .env  = Env
#'       )
#' YieldANOVA
#'
add_anova <- function(.data, .y, .rep, .gen, .env) {
  UseMethod("add_anova")
}

#' @export
#' @rdname add_anova

add_anova.default <-
  function(.data, .y, .rep, .gen, .env){

    Y   <- deparse(substitute(.y))
    Rep <- deparse(substitute(.rep))
    G   <- deparse(substitute(.gen))
    E   <- deparse(substitute(.env))


    fm1 <- lm(formula = terms(.data[[Y]] ~ .data[[E]] + .data[[Rep]]:.data[[E]] +
                                 .data[[G]] + .data[[G]]:.data[[E]], keep.order = TRUE))
    fm1ANOVA <- anova(fm1)
    rownames(fm1ANOVA) <- c("Env", "Rep(Env)", "Gen", "Gen:Env",
                            "Residuals")
    fm1ANOVA[1, 4] <- fm1ANOVA[1, 3]/fm1ANOVA[2, 3]
    fm1ANOVA[2, 4] <- NA
    fm1ANOVA[1, 5] <- 1 - pf(as.numeric(fm1ANOVA[1, 4]), fm1ANOVA[1,
                                                                  1], fm1ANOVA[2, 1])
    fm1ANOVA[2, 5] <- 1 - pf(as.numeric(fm1ANOVA[2, 4]), fm1ANOVA[2,
                                                                  1], fm1ANOVA[5, 1])
    class(fm1ANOVA) <- c("anova", "data.frame")
    return(list(
      anova = fm1ANOVA
      ))

  }