R/area_func.r

In MethodOpt: Advanced Method Optimization for Spectra-Generating Sampling and Analysis Instrumentation

# area of peak function

#' @title Computes areas of peaks
#'
#' @description
#' Computes the areas beneath the specified maxima.
#'
#' @param data dataframe of time versus intensity.
#' @param hts heights of peaks in chronological order.
#' @param tms time locations of peaks in chronological order.
#'
#' @return area for each peak

area <- function(data, hts, tms){
  ar <- c()
  frame <- data
  colnames(frame) <- c("time", "TIC")

  for (i in 1:length(hts)) {
    if (is.na(tms[i])) {
      ar <- append(ar,NA)
    }
    else {
      loc <- which(frame$time == tms[i])
      a <- hts[i]
      st <- loc-10
      if (loc < 10) {
        st <- 1
      }
      time <- frame$time[st:(loc+10)]
      y <- frame$TIC[st:(loc+10)]
      b <- tms[i]
      if (a == 0) {
        ar <- append(ar,0)
      }
      else {
        suppressWarnings({
          fitting <- stats::nls(y ~ gauss(a,b,c,time),
                                start = list(b = b, c = .01),
                                control = stats::nls.control(maxiter = 300, warnOnly = TRUE))
        })
        b <- as.numeric(abs(fitting$m$getPars()[1]))
        c <- as.numeric(abs(fitting$m$getPars()[2]))
        integrand <- function(x) {a*exp(-(x-b)^2/(2*(c)^2))}
        result <- stats::integrate(integrand, b-2,b+2)$value # area under the gaussian for +-2 s.d.
        ar <- append(ar, as.numeric(result))
      }
    }
  }
  return(ar)
}


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