R/mtsi.R

Defines functions mtsi

Documented in mtsi

#' Multi-trait stability index
#' @description
#' `r badge('stable')`
#'
#' Computes the multi-trait stability index proposed by Olivoto et al. (2019)
#'
#'
#' @param .data An object of class `waasb` or `waas`.
#' @param index If `index = 'waasby'` (default) both stability and mean
#'   performance are considered. If `index = 'waasb'` the multi-trait index
#'   will be computed considering the stability of genotypes only.  More details
#'   can be seen in [waasb()] and [waas()] functions.
#' @param ideotype A vector of length `nvar` where `nvar` is the
#'   number of variables used to plan the ideotype. Use `'h'` to indicate
#'   the traits in which higher values are desired or `'l'` to indicate the
#'   variables in which lower values are desired. For example, `ideotype =
#'   c("h, h, h, h, l")` will consider that the ideotype has higher values for
#'   the first four traits and lower values for the last trait.
#' @param SI An integer (0-100). The selection intensity in percentage of the
#' total number of genotypes.
#' @param mineval The minimum value so that an eigenvector is retained in the
#' factor analysis.
#' @param verbose If `verbose = TRUE` (Default) then some results are
#' shown in the console.
#' @return An object of class `mtsi` with the following items:
#' * **data** The data used to compute the factor analysis.
#' * **cormat** The correlation matrix among the environments.
#' * **PCA** The eigenvalues and explained variance.
#' * **FA** The factor analysis.
#' * **KMO** The result for the Kaiser-Meyer-Olkin test.
#' * **MSA** The measure of sampling adequacy for individual variable.
#' * **communalities** The communalities.
#' * **communalities_mean** The communalities' mean.
#' * **initial_loadings** The initial loadings.
#' * **finish_loadings** The final loadings after varimax rotation.
#' * **canonical_loadings** The canonical loadings.
#' * **scores_gen** The scores for genotypes in all retained factors.
#' * **scores_ide** The scores for the ideotype in all retained factors.
#' * **MTSI** The multi-trait stability index.
#' * **contri_fac** The relative contribution of each factor on the MTSI
#' value. The lower the contribution of a factor, the close of the ideotype the
#' variables in such factor are.
#' * **contri_fac_rank, contri_fac_rank_sel** The rank for the contribution
#' of each factor for all genotypes and selected genotypes, respectively.
#' * **sel_dif_trait, sel_dif_stab, sel_dif_mps** A data frame containing the
#' selection differential (gains) for the traits, for the stability (WAASB
#' index) WAASB, and for the mean performance and stability (WAASBY indexes).
#' The following variables are shown.
#'   - `VAR`: the trait's name.
#'   - `Factor`: The factor that traits where grouped into.
#'   - `Xo`: The original population mean.
#'   - `Xs`: The mean of selected genotypes.
#'   - `SD` and `SDperc`: The selection differential and selection differential in
#'   percentage, respectively.
#'   - `h2`: The broad-sense heritability.
#'   - `SG` and `SGperc`: The selection gains and selection gains in percentage,
#'   respectively.
#'   - `sense`: The desired selection sense.
#'   - `goal`: selection gains match desired sense? 100 for yes and 0 for no.
#' * **stat_dif_var, stat_dif_stab, stat_dif_mps** A data frame with the
#' descriptive statistic for the selection gains for the traits, for the
#' stability (WAASB index) WAASB, and for the mean performance and stability
#' (WAASBY index).
#' The following variables are shown.
#'    - `sense`: The desired selection sense.
#'    - `variable`: the trait's name.
#'    - `min`: the minimum value for the selection gain.
#'    - `mean`: the mean value for the selection gain.
#'    - `ci`: the confidence interval for the selection gain.
#'    - `sd.amo`: the standard deviation for the selection gain.
#'    - `max`: the maximum value for the selection gain.
#'    - `sum`: the sum of the selection gain.
#' * **sel_gen** The selected genotypes.
#' @md
#' @importFrom purrr map_dfc
#' @author Tiago Olivoto \email{tiagoolivoto@@gmail.com}
#' @export
#' @references Olivoto, T., A.D.C. L{\'{u}}cio, J.A.G. da silva, B.G. Sari, and
#'   M.I. Diel. 2019. Mean performance and stability in multi-environment trials
#'   II: Selection based on multiple traits. Agron. J. 111:2961-2969.
#' \doi{10.2134/agronj2019.03.0220}
#' @seealso [mgidi()], [waasb()], [get_model_data()]
#' @examples
#' \donttest{
#' library(metan)
#' # Based on stability only, for both GY and HM, higher is better
#' mtsi_model <-
#'     waasb(data_ge,
#'     env = ENV,
#'     gen = GEN,
#'     rep = REP,
#'     resp = c(GY, HM))
#' mtsi_index <-
#'     mtsi(mtsi_model, index = 'waasb')
#'
#'
#' # Based on mean performance and stability (using pipe operator %>%)
#' # GY: higher is better
#' # HM: lower is better
#'
#'mtsi_index2 <-
#'  data_ge %>%
#'  waasb(ENV, GEN, REP,
#'        resp = c(GY, HM),
#'        mresp = c("h, l")) %>%
#'  mtsi()
#'}
mtsi <- function(.data,
                 index = "waasby",
                 ideotype = NULL,
                 SI = 15,
                 mineval = 1,
                 verbose = TRUE) {
  if(has_class(.data, "waasb_group")){
    bind <-
      .data %>%
      mutate(data = map(data, ~.x %>%
                          mtsi(index = index,
                                SI = SI,
                                mineval = mineval,
                                verbose)))
    return(set_class(bind, c("tbl_df",  "mtsi_group", "mgidi", "tbl",  "data.frame")))
  } else{
  if (!index %in% c("waasb", "waasby")) {
    stop("The argument 'index' must be of of the 'waasb' or 'waasby'.", call. = FALSE)
  }
  if (length(.data) == 1) {
    stop("The multi-trait stability index cannot be computed with one single variable.", call. = FALSE)
  }


  if (has_class(.data, c("waas", "waas_means"))){
    if (index == "waasb") {
      data <- gmd(.data, "WAAS", verbose = FALSE) %>% as.data.frame()
    }
    if (index == "waasby") {
      data <- gmd(.data, "WAASY", verbose = FALSE) %>% as.data.frame()
    }
  }
  if (class(.data) == "waasb") {
    if (index == "waasb") {
      data <- gmd(.data, "WAASB", verbose = FALSE) %>% as.data.frame()
    }
    if (index == "waasby") {
      data <- gmd(.data, "WAASBY", verbose = FALSE) %>% as.data.frame()
    }
  }
  if(has_na(data)){
    stop("Missing values for traits ")
  }
    if (index == "waasby") {
      if(is.null(ideotype)){
        rescaled <- rep(100, length(data) - 1)
        ideotype.D <- rep(100, length(data) - 1)
        names(ideotype.D) <- names(.data)
      } else{
        rescaled <- unlist(strsplit(ideotype, split="\\s*(\\s|,)\\s*")) %>% all_lower_case()
        if(length(rescaled) != ncol(data)-1){
          stop("Ideotype must have length ", ncol(data)-1, ", the number of traits in the model.")
        }
        if(!all(rescaled %in% c("h", "l", "m"))){
          stop("argument 'ideotype' must have 'h', 'l', or 'm' only", call. = FALSE)
        }
        # ideotype.D <- ifelse(rescaled == "m", 50, 100)
        ideotype.D <- case_when(
          rescaled == "h" ~ 100,
          rescaled == "m" ~ 50,
          rescaled == "l" ~ 0)
        names(ideotype.D) <- names(.data)
      }
      df_ideotype <-
        data.frame(ideotype.D) %>%
        rownames_to_column("VAR") %>%
        set_names("VAR", "sense")
    }

  if (is.null(SI)) {
    ngs <- NULL
  } else {
    ngs <- round(nrow(data) * (SI/100), 0)
  }
  observed <-
    gmd(.data, "Y", verbose = FALSE) %>%
    column_to_rownames("GEN")
  means <- data[, 2:ncol(data)]
  rownames(means) <- data[, 1]
  cor.means <- cor(means)
  eigen.decomposition <- eigen(cor.means)
  eigen.values <- eigen.decomposition$values
  eigen.vectors <- eigen.decomposition$vectors
  colnames(eigen.vectors) <- paste("PC", 1:ncol(cor.means), sep = "")
  rownames(eigen.vectors) <- colnames(means)
  if (length(eigen.values[eigen.values >= mineval]) == 1) {
    eigen.values.factors <- as.vector(c(as.matrix(sqrt(eigen.values[eigen.values >= mineval]))))
    initial_loadings <- cbind(eigen.vectors[, eigen.values >= mineval] * eigen.values.factors)
    A <- initial_loadings
  } else {
    eigen.values.factors <-
      t(replicate(ncol(cor.means), c(as.matrix(sqrt(eigen.values[eigen.values >= mineval])))))
    initial_loadings <- eigen.vectors[, eigen.values >= mineval] * eigen.values.factors
    A <- varimax(initial_loadings)[[1]][]
  }
  partial <- solve_svd(cor.means)
  k <- ncol(means)
  seq_k <- seq_len(ncol(means))
  for (j in seq_k) {
    for (i in seq_k) {
      if (i == j) {
        next
      } else {
        partial[i, j] <- -partial[i, j]/sqrt(partial[i, i] * partial[j, j])
      }
    }
  }
  KMO <- sum((cor.means[!diag(k)])^2)/(sum((cor.means[!diag(k)])^2) + sum((partial[!diag(k)])^2))
  MSA <- unlist(lapply(seq_k, function(i) {
    sum((cor.means[i, -i])^2)/(sum((cor.means[i, -i])^2) + sum((partial[i, -i])^2))
  }))
  names(MSA) <- colnames(means)
  colnames(A) <- paste("FA", 1:ncol(initial_loadings), sep = "")
  pca <- tibble(PC = paste("PC", 1:ncol(means), sep = ""),
                Eigenvalues = eigen.values,
                `Variance (%)` = (eigen.values/sum(eigen.values)) * 100,
                `Cum. variance (%)` = cumsum(`Variance (%)`))
  Communality <- diag(A %*% t(A))
  Uniquenesses <- 1 - Communality
  fa <- cbind(A, Communality, Uniquenesses) %>% as_tibble(rownames = NA) %>%  rownames_to_column("VAR")
  z <- scale(means, center = FALSE, scale = apply(means, 2, sd))
  canonical_loadings <- t(t(A) %*% solve_svd(cor.means))
  scores <- z %*% canonical_loadings
  colnames(scores) <- paste("FA", 1:ncol(scores), sep = "")
  rownames(scores) <- data[, 1]
  pos.var.factor <- which(abs(A) == apply(abs(A), 1, max), arr.ind = TRUE)
  var.factor <- lapply(1:ncol(A), function(i) {
    rownames(pos.var.factor)[pos.var.factor[, 2] == i]
  })
  names(var.factor) <- paste("FA", 1:ncol(A), sep = "")
  names.pos.var.factor <- rownames(pos.var.factor)
  if (index == "waasb") {
    ideotype.D <- apply(means, 2, min)
  } else {
    names(ideotype.D) <- colnames(means)
  }
  ideotypes.matrix <- t(as.matrix(ideotype.D))/apply(means, 2, sd)
  rownames(ideotypes.matrix) <- "ID1"
  ideotypes.scores <- ideotypes.matrix %*% canonical_loadings
  gen_ide <- sweep(scores, 2, ideotypes.scores, "-")
  MTSI <- sort(apply(gen_ide, 1, function(x) sqrt(sum(x^2))), decreasing = FALSE)
  contr.factor <- data.frame((sqrt(gen_ide^2)/apply(gen_ide, 1, function(x) sum(sqrt(x^2)))) * 100) %>%
    rownames_to_column("GEN") %>%
    as_tibble()
  means.factor <- means[, names.pos.var.factor]
  observed <- observed[, names.pos.var.factor]
  contri_long <- pivot_longer(contr.factor, -GEN)
  if (!is.null(ngs)) {
    selected <- names(MTSI)[1:ngs]
    sel_dif <- tibble(VAR = names(pos.var.factor[, 2]),
                      Factor = paste("FA", as.numeric(pos.var.factor[, 2])),
                      Xo = colMeans(means.factor),
                      Xs = colMeans(means.factor[names(MTSI)[1:ngs], ]),
                      SD = Xs - Xo,
                      SDperc = (Xs - Xo) / Xo * 100)
    stat_dif_mps <-
      desc_stat(sel_dif, SDperc, stats = c("min, mean, ci, sd.amo, max, sum"))
    sel_dif_mean <-
      tibble(VAR = names(pos.var.factor[, 2]),
             Factor = paste("FA", as.numeric(pos.var.factor[, 2])),
             Xo = colMeans(observed),
             Xs = colMeans(observed[names(MTSI)[1:ngs], ]),
             SD = Xs - colMeans(observed),
             SDperc = (Xs - colMeans(observed)) / colMeans(observed) * 100)
      if(missing(ideotype)){
        sel_dif_mean <-
          sel_dif_mean %>%
          left_join(
            gmd(.data, "details", verbose = FALSE) %>%
              pivot_longer(-Parameters) %>%
              subset(Parameters == "mresp") %>%
              remove_cols(Parameters) %>%
              set_names("VAR", "sense"),
            by = "VAR")
      } else{
        sel_dif_mean <- left_join(sel_dif_mean, df_ideotype, by = "VAR")
      }
    sel_dif_mean <-
      sel_dif_mean %>%
      mutate(sense = case_when(sense == 0 ~ "decrease",
                               sense == 50 ~ "average",
                               sense == 100 ~ "increase"),
             goal = case_when(
               sense == "decrease" & SDperc < 0 ~ 100,
               sense == "increase" & SDperc > 0 ~ 100,
               sense == "average" & SDperc == 0 ~ 100,
               TRUE ~ 0
             ))
    if (class(.data) == "waasb") {
      h2 <- gmd(.data, "h2", verbose = FALSE)
      sel_dif_mean <-
        left_join(sel_dif_mean, h2, by = "VAR") %>%
        add_cols(SG = SD * h2,
                 SGperc = SG / Xo * 100,
                 .after = "SDperc") %>%
        reorder_cols(h2, .after  = "SDperc")
    }
    stat_gain <-
      desc_stat(sel_dif_mean,
                by = sense,
                any_of(c("SDperc", "SGperc")),
                stats = c("min, mean, ci, sd.amo, max, sum"))
    what <- ifelse(has_class(.data, "waasb"), "WAASB", "WAAS")
    waasb_index <- gmd(.data, what, verbose = FALSE)
    waasb_selected <- colMeans(subset(waasb_index, GEN %in% selected) %>% select_numeric_cols())
    sel_dif_stab <-
      tibble(
        TRAIT = names(waasb_selected),
        Xo = colMeans(waasb_index %>% select_numeric_cols()),
        Xs = waasb_selected,
        SD = Xs - Xo,
        SDperc = (Xs - Xo) / Xo * 100)
    stat_dif_stab <-
      desc_stat(sel_dif_stab, SDperc,
                stats = c("min, mean, ci, sd.amo, max, sum"))
    contri_fac_rank_sel <-
      contri_long %>%
      subset(GEN %in% selected) %>%
      ge_winners(name, GEN, value, type = "ranks", better = "l") %>%
      split_factors(ENV) %>%
      map_dfc(~.x %>% pull())
  }
  if (is.null(ngs)) {
    stat_dif_stab <- NULL
    stat_dif_mps <- NULL
    sel_dif <- NULL
    sel_dif_stab <- NULL
    sel_dif_mean <- NULL
    selected <- NULL
    contri_fac_rank_sel <- NULL
  }
  if (verbose) {
    cat("\n-------------------------------------------------------------------------------\n")
    cat("Principal Component Analysis\n")
    cat("-------------------------------------------------------------------------------\n")
    print(pca)
    cat("-------------------------------------------------------------------------------\n")
    cat("Factor Analysis - factorial loadings after rotation-\n")
    cat("-------------------------------------------------------------------------------\n")
    print(fa)
    cat("-------------------------------------------------------------------------------\n")
    cat("Comunalit Mean:", mean(Communality), "\n")
    cat("-------------------------------------------------------------------------------\n")
    if (!is.null(ngs)) {
      cat("Selection differential for the ", index, "index\n")
      cat("-------------------------------------------------------------------------------\n")
      print(sel_dif)
      cat("-------------------------------------------------------------------------------\n")
      cat("Selection differential for the mean of the variables\n")
      cat("-------------------------------------------------------------------------------\n")
      print(sel_dif_mean)
      cat("------------------------------------------------------------------------------\n")
      cat("Selected genotypes\n")
      cat("-------------------------------------------------------------------------------\n")
      cat(selected)
      cat("\n-------------------------------------------------------------------------------\n")
    }
  }
  contri_fac_rank <-
    contri_long %>%
    ge_winners(name, GEN, value, type = "ranks", better = "l") %>%
    split_factors(ENV) %>%
    map_dfc(~.x %>% pull())

  return(structure(list(data = data,
                        cormat = as.matrix(cor.means),
                        PCA = pca,
                        FA = fa,
                        KMO = KMO,
                        MSA = MSA,
                        communalities = Communality,
                        communalities_mean = mean(Communality),
                        initial_loadings = data.frame(initial_loadings) %>% rownames_to_column("VAR") %>% as_tibble(),
                        finish_loadings = data.frame(A) %>% rownames_to_column("VAR") %>% as_tibble(),
                        canonical_loadings = data.frame(canonical_loadings) %>% rownames_to_column("VAR") %>% as_tibble(),
                        scores_gen = data.frame(scores) %>% rownames_to_column("GEN") %>% as_tibble(),
                        scores_ide = data.frame(ideotypes.scores) %>% rownames_to_column("GEN") %>% as_tibble(),
                        MTSI = as_tibble(MTSI, rownames = NA) %>% rownames_to_column("Genotype") %>% rename(MTSI = value),
                        contri_fac = contr.factor,
                        contri_fac_rank = contri_fac_rank,
                        contri_fac_rank_sel = contri_fac_rank_sel,
                        sel_dif_trait = sel_dif_mean,
                        stat_dif_trait = stat_gain,
                        sel_dif_stab = sel_dif_stab,
                        stat_dif_stab = stat_dif_stab,
                        sel_dif_mps = sel_dif,
                        stat_dif_mps = stat_dif_mps,
                        sel_gen = selected),
                   class = "mtsi"))
}
}







#' Plot the multi-trait stability index
#'
#' Makes a radar plot showing the multitrait stability index proposed by Olivoto
#' et al. (2019)
#'
#'
#' @param x An object of class `mtsi`
#' @param SI An integer (0-100). The selection intensity in percentage of the
#'   total number of genotypes.
#' @param type The type of the plot. Defaults to `"index"`. Use `type
#'   = "contribution"` to show the contribution of each factor to the MGIDI
#'   index of the selected genotypes.
#' @param position The position adjustment when `type = "contribution"`.
#'   Defaults to `"fill"`, which shows relative proportions at each trait
#'   by stacking the bars and then standardizing each bar to have the same
#'   height. Use `position = "stack"` to plot the MGIDI index for each
#'   genotype.
#' @param genotypes When `type = "contribution"` defines the genotypes to
#'   be shown in the plot. By default (`genotypes = "selected"` only
#'   selected genotypes are shown. Use `genotypes = "all"` to plot the
#'   contribution for all genotypes.)
#' @param title Logical values (Defaults to `TRUE`) to include
#'   automatically generated titles.
#' @param radar Logical argument. If true (default) a radar plot is generated
#'   after using `coord_polar()`.
#' @param arrange.label Logical argument. If `TRUE`, the labels are
#'   arranged to avoid text overlapping. This becomes useful when the number of
#'   genotypes is large, say, more than 30.
#' @param x.lab,y.lab The labels for the axes x and y, respectively. x label is
#'   set to null when a radar plot is produced.
#' @param size.point The size of the point in graphic. Defaults to 2.5.
#' @param size.line The size of the line in graphic. Defaults to 0.7.
#' @param size.text The size for the text in the plot. Defaults to 10.
#' @param width.bar The width of the bars if `type = "contribution"`.
#'   Defaults to 0.75.
#' @param n.dodge The number of rows that should be used to render the x labels.
#'   This is useful for displaying labels that would otherwise overlap.
#' @param check.overlap Silently remove overlapping labels, (recursively)
#'   prioritizing the first, last, and middle labels.
#' @param invert Logical argument. If `TRUE`, rotate the plot.
#' @param col.sel The colour for selected genotypes. Defaults to `"red"`.
#' @param col.nonsel The colour for nonselected genotypes. Defaults to `"black"`.
#' @param legend.position The position of the legend.
#' @param ... Other arguments to be passed from  [ggplot2::theme()].
#' @return An object of class `gg, ggplot`.
#' @author Tiago Olivoto \email{tiagoolivoto@@gmail.com}
#' @method plot mtsi
#' @export
#' @references Olivoto, T., A.D.C. L{\'{u}}cio, J.A.G. da silva, B.G. Sari, and M.I. Diel. 2019. Mean performance and stability in multi-environment trials II: Selection based on multiple traits. Agron. J. (in press).
#' @examples
#' \donttest{
#' library(metan)
#' mtsi_model <- waasb(data_ge, ENV, GEN, REP, resp = c(GY, HM))
#' mtsi_index <- mtsi(mtsi_model)
#' plot(mtsi_index)
#'}
#'
#'
plot.mtsi <- function(x,
                      SI = 15,
                      type = "index",
                      position = "fill",
                      genotypes = "selected",
                      title = TRUE,
                      radar = TRUE,
                      arrange.label = FALSE,
                      x.lab = NULL,
                      y.lab = NULL,
                      size.point = 2.5,
                      size.line = 0.7,
                      size.text = 10,
                      width.bar = 0.75,
                      n.dodge = 1,
                      check.overlap = FALSE,
                      invert = FALSE,
                      col.sel = "red",
                      col.nonsel = "black",
                      legend.position = "bottom",
                      ...) {
  if (!class(x) == "mtsi") {
    stop("The object 'x' is not of class 'mtsi'")
  }
  if(!type %in% c("index", "contribution")){
    stop("The argument index must be one of the 'index' or 'contribution'", call. = FALSE)
  }
  if(!genotypes %in% c("selected", "all")){
    stop("The argument 'genotypes' must be one of the 'selected' or 'all'", call. = FALSE)
  }
  if(type == "index"){
  data <- x$MTSI %>%
    add_cols(sel = "Selected")
  data[["sel"]][(round(nrow(data) * (SI/100), 0) + 1):nrow(data)] <- "Nonselected"
  cutpoint <- max(subset(data, sel == "Selected")$MTSI)
  p <-
    ggplot(data = data, aes(x = reorder(Genotype, -MTSI), y = MTSI)) +
    geom_hline(yintercept = cutpoint, col = col.sel, size = size.line) +
    geom_path(colour = "black", group = 1, size = size.line) +
    geom_point(size = size.point,
               stroke = size.point / 10,
               aes(fill = sel),
               shape = 21,
               colour = "black",
               ) +
    scale_x_discrete() +
    scale_y_reverse() +
    theme_minimal()  +
    theme(legend.position = legend.position,
          legend.title = element_blank(),
          axis.title.x = element_blank(),
          panel.border = element_blank(),
          panel.grid = element_line(size = size.line / 2),
          axis.text = element_text(colour = "black"),
          text = element_text(size = size.text),
          ...) +
    labs(y = "Multitrait stability index") +
    scale_fill_manual(values = c(col.nonsel, col.sel))
  if (radar == TRUE) {
    if(arrange.label == TRUE){
      tot_gen <- length(unique(data$Genotype))
      fseq <- c(1:(tot_gen/2))
      sseq <- c((tot_gen/2 + 1):tot_gen)
      fang <- c(90 - 180/length(fseq) * fseq)
      sang <- c(-90 - 180/length(sseq) * sseq)
      p <-
        p +
        coord_polar()  +
        theme(axis.text.x = suppressMessages(suppressWarnings(element_text(angle = c(fang, sang)))), ...)
    } else{
      p <- p + coord_polar()
    }
  }
  } else{
    x.lab <- ifelse(!missing(x.lab), x.lab, "Selected genotypes")
    y.lab <- ifelse(!missing(y.lab), y.lab, "Proportion")
    if(genotypes == "selected"){
      data <-
        x$contri_fac %>%
        subset(GEN %in% x$sel_gen) %>%
        droplevels()
    } else{
      data <- x$contri_fac
    }
    data %<>% pivot_longer(-GEN)
    if(radar == TRUE){
      p <-
      ggplot(data, aes(x = GEN, y = value)) +
        geom_polygon(aes(group = name, color = name),
                     fill = NA,
                     size = size.line) +
        geom_polygon(aes(group = 1, x = GEN, y = 100 / length(unique(name))),
                     fill = NA,
                     color = "black",
                     linetype = 2,
                     size = size.line,
                     show.legend = FALSE) +
        geom_line(aes(group = name, color = name), size = size.line) +
        theme_minimal()  +
        theme(strip.text.x = element_text(size = size.text),
              axis.text.x = element_text(color = "black", size = size.text),
              axis.ticks.y = element_blank(),
              panel.grid = element_line(size = size.line / 2),
              axis.text.y = element_text(size = size.text, color = "black"),
              legend.position = legend.position,
              legend.title = element_blank(),
              ...) +
        labs(x = NULL,
             y = "Contribution of each factor to the MTSI index") +
        {if(title)ggtitle("The strengths and weaknesses for genotypes")} +
        scale_y_reverse() +
        guides(color = guide_legend(nrow = 1)) +
        coord_radar()
      if(arrange.label == TRUE){
        tot_gen <- length(unique(data$GEN))
        fseq <- c(1:(tot_gen/2))
        sseq <- c((tot_gen/2 + 1):tot_gen)
        fang <- c(90 - 180/length(fseq) * fseq)
        sang <- c(-90 - 180/length(sseq) * sseq)
        p <- p  +
          theme(axis.text.x = suppressMessages(suppressWarnings(element_text(angle = c(fang, sang)))), ...)
      }
    } else{
    p <-
      ggplot(data, aes(GEN, value, fill = name))+
      geom_bar(stat = "identity",
               position = position,
               color = "black",
               size = size.line,
               width = width.bar) +
      scale_y_continuous(expand = expansion(0))+
      theme_metan()  +
      theme(legend.position = legend.position,
            axis.ticks = element_line(size = size.line),
            plot.margin = margin(0.5, 0.5, 0, 0, "cm"),
            panel.border = element_rect(size = size.line),
            ...)+
      scale_x_discrete(guide = guide_axis(n.dodge = n.dodge, check.overlap = check.overlap),
                       expand = expansion(0))+
      labs(x = x.lab,
           y = y.lab) +
      {if(title)ggtitle("The strengths and weaknesses for genotypes")} +
      guides(guide_legend(nrow = 1))
    if(invert == TRUE){
      p <- p + coord_flip()
    }
    }
  }
  return(p)
}



#' Print an object of class mtsi
#'
#' Print a `mtsi` object in two ways. By default, the results are shown in
#' the R console. The results can also be exported to the directory.
#'
#' @param x An object of class `mtsi`.
#' @param export A logical argument. If `TRUE|T`, 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 mtsi
#' @export
#' @examples
#' \donttest{
#' library(metan)
#' # Based on stability only
#' MTSI_MODEL <- waasb(data_ge,
#'   resp = c(GY, HM),
#'   gen = GEN,
#'   env = ENV,
#'   rep = REP
#' )
#'
#' MTSI_index <- mtsi(MTSI_MODEL)
#' print(MTSI_index)
#' }
print.mtsi <- function(x, export = FALSE, file.name = NULL, digits = 4, ...) {
  if (!class(x) == "mtsi") {
    stop("The object must be of class 'mtsi'")
  }
  if (export == TRUE) {
    file.name <- ifelse(is.null(file.name) == TRUE, "mtsi print", file.name)
    sink(paste0(file.name, ".txt"))
  }
  opar <- options(pillar.sigfig = digits)
  on.exit(options(opar))
  cat("-------------------- Correlation matrix used used in factor analysis -----------------\n")
  print(x$cormat)
  cat("\n")
  cat("---------------------------- Principal component analysis -----------------------------\n")
  print(x$PCA)
  cat("\n")
  cat("--------------------------------- Initial loadings -----------------------------------\n")
  print(x$initial_loadings)
  cat("\n")
  cat("-------------------------- Loadings after varimax rotation ---------------------------\n")
  print(x$finish_loadings)
  cat("\n")
  cat("--------------------------- Scores for genotypes-ideotype -----------------------------\n")
  print(rbind(x$scores_gen, x$scores_ide))
  cat("\n")
  cat("---------------------------- Multitrait stability index ------------------------------\n")
  print(x$MTSI)
  cat("\n")
  cat("------------------------- Selection differential (variables) --------------------------\n")
  print(x$sel_dif_trait)
  cat("\n")
  cat("-------------------------------- Selected genotypes -----------------------------------\n")
  cat(x$sel_gen)
  cat("\n")
  if (export == TRUE) {
    sink()
  }
}

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metan documentation built on Nov. 10, 2021, 9:11 a.m.