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#' Stability analysis based on Plaisted and Peterson (1959)
#' @description
#' `r badge('stable')`
#'
#' The function computes the stability as the arithmetic mean of the variance
#' component of the genotype-environment interaction between environment pairs
#' that includes a given genotype
#'
#'
#' @param .data The dataset containing the columns related to Environments,
#' Genotypes, replication/block and response variable(s).
#' @param env The name of the column that contains the levels of the
#' environments.
#' @param gen The name of the column that contains the levels of the genotypes.
#' @param rep The name of the column that contains the levels of the
#' replications/blocks.
#' @param resp The response variable(s). To analyze multiple variables in a
#' single procedure use, for example, `resp = c(var1, var2, var3)`.
#' @param verbose Logical argument. If `verbose = FALSE` the code will run
#' silently.
#' @return An object of class `plaisted_peterson` containing the results for each
#' variable used in the argument `resp`.
#' @author Tiago Olivoto \email{tiagoolivoto@@gmail.com}
#' @references Plaisted, R.L., and L.C. Peterson. 1959. A technique for
#' evaluating the ability of selections to yield consistently in different
#' locations or seasons. American Potato Journal 36(11): 381–385.
#' \doi{10.1007/BF02852735}
#' @export
#' @examples
#' \donttest{
#' library(metan)
#' plaisted_peterson(data_ge, ENV, GEN, REP, GY)
#'}
#'
plaisted_peterson <- function(.data, env, gen, rep, resp, verbose = TRUE) {
factors <-
.data %>%
select({{env}}, {{gen}}, {{rep}}) %>%
mutate(across(everything(), as.factor))
vars <-
.data %>%
select({{resp}}, -names(factors)) %>%
select_numeric_cols()
factors %<>% set_names(c("ENV", "GEN", "REP"))
listres <- list()
nvar <- ncol(vars)
if (verbose == TRUE) {
pb <- progress(max = nvar, style = 4)
}
for (var in 1:nvar) {
data <- factors %>%
mutate(Y = vars[[var]])
if(has_na(data)){
data <- remove_rows_na(data)
has_text_in_num(data)
}
joint_an <- anova_joint(data, ENV, GEN, REP, Y, verbose = FALSE)
r <- nlevels(data$REP)
nenv <- nlevels(data$ENV)
ngen <- nlevels(data$GEN)
qmr <- joint_an$Y$anova[nrow(joint_an$Y$anova) - 3, 4]
combs <- combn(ngen, 2)
df2 <- make_mat(data, GEN, ENV, Y)
gens <- rownames(df2)
dists <- NULL
for (j in 1:ncol(combs)) {
gens_sel <- df2[c(combs[1, j], combs[2, j]), ]
tmp <- dist(gens_sel) ^ 2
dif <- diff(apply(gens_sel, 1, sum))
tmp2 <- (r / 2) * (tmp - 1 / nenv * (dif ^ 2))
dists[j] <- (tmp2 / (nenv - 1) - qmr) / r
}
mat <- matrix(NA, nrow = ngen, ncol = ngen)
mat[lower.tri(mat)] <- dists
mat <- make_sym(mat)
mat_res <-
as.data.frame(mat) |>
mutate(theta = apply(mat, 1, mean, na.rm = TRUE),
theta_perc = theta / sum(theta) * 100)
rownames(mat_res) <- c(gens)
colnames(mat_res) <- c(gens, "theta", "theta_prop")
if (verbose == TRUE) {
run_progress(pb,
actual = var,
text = paste("Evaluating trait", names(vars[var])))
}
listres[[paste(names(vars[var]))]] <- mat_res
}
return(structure(listres, class = "plaisted_peterson"))
}
#' Print an object of class plaisted_peterson
#'
#' Print the `plaisted_peterson` object in two ways. By default, the results
#' are shown in the R console. The results can also be exported to the directory
#' into a *.txt file.
#'
#'
#' @param x The `plaisted_peterson` x
#' @param export A logical argument. If `TRUE`, a *.txt file is exported to
#' the working directory.
#' @param file.name The name of the file if `export = TRUE`
#' @param digits The significant digits to be shown.
#' @param ... Options used by the tibble package to format the output. See
#' [`tibble::print()`][tibble::formatting] for more details.
#' @author Tiago Olivoto \email{tiagoolivoto@@gmail.com}
#' @method print plaisted_peterson
#' @export
#' @examples
#' \donttest{
#' library(metan)
#' eco <- ecovalence(data_ge2,
#' env = ENV,
#' gen = GEN,
#' rep = REP,
#' resp = PH)
#' print(eco)
#' }
print.plaisted_peterson <- function(x, export = FALSE, file.name = NULL, digits = 3, ...) {
opar <- options(pillar.sigfig = digits)
on.exit(options(opar))
if (export == TRUE) {
file.name <- ifelse(is.null(file.name) == TRUE, "plaisted_peterson print", file.name)
sink(paste0(file.name, ".txt"))
}
for (i in 1:length(x)) {
var <- x[[i]]
cat("Variable", names(x)[i], "\n")
print(var)
}
cat("\n\n\n")
if (export == TRUE) {
sink()
}
}
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