R/findStrainPeaks.R

In dloewenstein/straindys: A collection of tools to calculate different strain and dyssynchrony metrcis for CMR FT

#' Finds peaks and valleys in the strain dataframe
#'
#' @param straindata dataframe in longformat with separate column for each strain segment
#' @param position.firstStraincolumn the index position of the first strain column
#'
#' @return A dataframe with 2 new columns added for each strain segment indicating
#' whether the corresponding strain value is a peak/valley or not
#'
#' @importFrom magrittr %>%
#' @importFrom stats setNames
#'
#' @export
#'
#' @examples
#'
findStrainPeaks <- function (straindata, position.firstStraincolumn) {

  if (!requireNamespace("dplyr", quietly = TRUE)) {
    stop("dplyr needed for this function to work. Please install/load it.",
         call. = FALSE)
  }


  if (!requireNamespace("lazyeval", quietly = TRUE)) {
    stop("lazyeval needed for this function to work. Please install/load it.",
         call. = FALSE)
  }


  if (!requireNamespace("stringr", quietly = TRUE)) {
    stop("stringr needed for this function to work. Please install/load it.",
         call. = FALSE)
  }


  endrow <- c(NA, rep(0, ncol(straindata)-1))

  straindata <- rbind(straindata, endrow)

  strain_segments <- names(straindata[position.firstStraincolumn : ncol(straindata)])

  strain_segments <- stringr::str_extract(strain_segments, "(?:(?!_).)*")

  for (i in seq_along(strain_segments)) {
          strain_peak <- paste(strain_segments[i], "peak", sep = "_")

          strain_valley <- paste(strain_segments[i], "valley", sep = "_")

          strain_value <- paste(strain_segments[i], "strain", sep = "_")

          find_strain_valley <- lazyeval::interp(~ a %in% a[findValleys(a)-1],

                                       a = lazyeval::as_name(strain_value))

          find_strain_peak   <- lazyeval::interp(~ a %in% a[findPeaks(a)-1],

                                       a = lazyeval::as_name(strain_value))

          set_valley_false_time_zero <- lazyeval::interp(~ ifelse(time == 0,
                                                        FALSE,
                                                        a),

                                               a = lazyeval::as_name(strain_valley))

          set_peak_true_time_zero <- lazyeval::interp(~ ifelse(time == 0,
                                                      TRUE,
                                                     a),

                                            a = lazyeval::as_name(strain_peak))

          straindata <- straindata %>%
                  dplyr::mutate_(.dots = setNames(list(find_strain_valley,

                                                find_strain_peak,

                                                set_valley_false_time_zero,

                                                set_peak_true_time_zero),

                                           list(strain_valley,

                                                strain_peak,

                                                strain_valley,

                                                strain_peak)))
  }

return(straindata)

  }