R/iqr.evaluate.core.R

In EvaluateCore: Quality Evaluation of Core Collections

### This file is part of 'EvaluateCore' package for R.

### Copyright (C) 2018-2022, ICAR-NBPGR.
#
# EvaluateCore is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
# EvaluateCore is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
#  A copy of the GNU General Public License is available at
#  https://www.r-project.org/Licenses/


#' Interquartile Range
#'
#' Compute the Interquartile Range (IQR)
#' \insertCite{upton_general_1996}{EvaluateCore} to compare quantitative traits
#' of the entire collection (EC) and core set (CS).
#'
#' @inheritParams snk.evaluate.core
#'
#' @return A data frame with the IQR values of the EC and CS for the traits
#'   specified as \code{quantitative}.
#'
#' @seealso \code{\link[stats]{IQR}}
#'
#' @importFrom stats IQR
#' @export
#'
#' @references
#'
#' \insertAllCited{}
#'
#' @examples
#'
#' data("cassava_CC")
#' data("cassava_EC")
#'
#' ec <- cbind(genotypes = rownames(cassava_EC), cassava_EC)
#' ec$genotypes <- as.character(ec$genotypes)
#' rownames(ec) <- NULL
#'
#' core <- rownames(cassava_CC)
#'
#' quant <- c("NMSR", "TTRN", "TFWSR", "TTRW", "TFWSS", "TTSW", "TTPW", "AVPW",
#'            "ARSR", "SRDM")
#' qual <- c("CUAL", "LNGS", "PTLC", "DSTA", "LFRT", "LBTEF", "CBTR", "NMLB",
#'           "ANGB", "CUAL9M", "LVC9M", "TNPR9M", "PL9M", "STRP", "STRC",
#'           "PSTR")
#'
#' ec[, qual] <- lapply(ec[, qual],
#'                      function(x) factor(as.factor(x)))
#'
#' iqr.evaluate.core(data = ec, names = "genotypes",
#'                   quantitative = quant, selected = core)
#'
iqr.evaluate.core <- function(data, names, quantitative, selected) {
  # Checks
  checks.evaluate.core(data = data, names = names,
                       quantitative = quantitative,
                       selected = selected)

  if (any(c("tbl_dataf", "tbl") %in% class(data))) {
    warning('"data" is of type tibble\nCoercing to data frame')
    data <- as.data.frame(data)
  }

  dataf <- data[, c(names, quantitative)]

  datafcore <- dataf[dataf[, names] %in% selected, ]

  dataf$`[Type]` <- "EC"
  datafcore$`[Type]` <- "CS"

  dataf <- rbind(dataf, datafcore)
  rm(datafcore)


  outdf <- data.frame(`Trait` = quantitative,
                      `EC_IQR` = unlist(lapply(dataf[dataf$`[Type]` == "EC",
                                                     quantitative],
                                               stats::IQR)),
                      `CS_IQR` = unlist(lapply(dataf[dataf$`[Type]` == "CS",
                                                     quantitative],
                                               stats::IQR)))
  return(outdf)
}