Nothing
utils::globalVariables(c("Bi", "Bi1", "Bi2", "E", "Environment", "Genotype", "Mean.Yield", "Mj", "X", "Xi.bar", "Xj.bar", "Xj.max", "corrected.X", "corrected.rank", "dev", "deviation", "mean.rank", "s2d1", "s2d2", "s2di", "s2xi", "sqr", "sqr1", "wi"))
#' @title Genotypic superiority measure
#'
#' @description
#' \code{genotypic_superiority_measure} calculate variance of a genotype across environments.
#'
#' @keywords dynamic stability
#'
#' @details
#' Genotypic superiority measure (Lin and Binns, 1988) is calculatd based on means square distance between maximum value of environment j and genotype i.
#' Variety with low genotypic superiority measure is considered as stable.
#' Equation of genotypic superiority measure can be found in vignette file.
#'
#' @param data a dataframe containing trait, genotype and environment.
#' @param trait colname of a column containing a numeric vector of interested trait to be analysized.
#' @param genotype colname of a column containing a character or factor vector labeling different genotypic varieties
#' @param environment colname of a column containing a character or factor vector labeling different environments
#' @param unit.correct logical, default is \code{FALSE}, returning the stability index with unit equals to squared unit of trait; when \code{TRUE}, returning stability index with the unit as same as unit of trait.'
#' @return a data table with genotypic superiority measure
#'
#' @author Tien-Cheng Wang
#'
#' @references
#' \insertRef{lin1988}{toolStability}
#'
#' @importFrom dplyr group_by summarise mutate mutate_at rename
#' @importFrom data.table data.table
#' @importFrom Rdpack reprompt
#'
#' @export
#'
#' @examples
#' data(Data)
#' res <- genotypic_superiority_measure(
#' data = Data,
#' trait = "Yield",
#' genotype = "Genotype",
#' environment = "Environment",
#' unit.correct = FALSE)
genotypic_superiority_measure <- function(data, trait, genotype, environment, unit.correct = FALSE) {
if (!is.numeric(data[[trait]])) {
stop("Trait must be a numeric vector")
}
# combine vectors into data table
if (length(environment) == 1){
Data <- data.table(X = data[[trait]] ,
Genotype = data[[genotype]],
Environment = data[[environment]])
}else { # if input is the vector containing the name that are going to combine in one column
data$Environment <- interaction(data[,environment],sep = '_')
Data <- data.table(X = data[[trait]] ,
Genotype = data[[genotype]],
Environment = data[['Environment']])
}
varnam <- paste0("Mean.",trait)
res <-summarise(
mutate(
group_by(
mutate(
group_by(Data, Environment), # for each environment
Xj.max = max(X, na.rm = TRUE)
), # first calculate environmental mean
Genotype
), # for each genotype
Mj = (X - Xj.max)^2 / (2 * length(X))
),
Mean.trait = mean(X),
genotypic.superiority.measure = (sum(Mj)))
if (unit.correct==TRUE){
res <- mutate_at(res,"genotypic.superiority.measure", sqrt)
}
names(res)[names(res) == "Mean.trait"] <- sprintf("Mean.%s", trait)
return(res)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.