R/irms_std.R

In henningte/elco: Handling Data on Chemical Element Contents and Isotope signatures

#' Creates an object of class `irms_std`
#'
#' `elco_new_irms_std` is the internal constructor function for objects of class
#' `irms_std`.
#' An object of class `irms` is an object of class [`irms`][elco::elco_new_irms], but
#' contains only measurements on standards. Objects of class `irms` are intended to be created
#' only internally.
#'
#' @param x A `data.frame` with a row for each measured sample or standard and the
#' following columns:
#' \describe{
#'   \item{file_id}{An integer increasing by 1 and starting from 1, representing a unique ID for each
#'   csv file that has been imported.}
#'   \item{measurement_id}{An integer increasing by 1 and starting from 1 for each imported file,
#'   representing a unique ID for each measurement per file.}
#'   \item{measurement_type}{A character vector representing the measurement type. One of "Sam" (the
#'   measurement is a measurement of a sample) or "Ref" (the measurement is a measurement of a
#'   standard/reference).}
#'   \item{sample_label}{A character vector with names for the samples. If `measurement_type == "Sam"`,
#'   this is a label for the sample. If `measurement_type == "Ref"`, this is the name of a standard.
#'   Only values existing in [elco::irms_standards()] are allowed}.
#'   \item{sample_mass}{A units vector representing the mass of the sample \[g\].}
#'   \item{time}{A POSIXct vector with the date and time when the sample was measured.}
#'   \item{file_name}{A character vector with the full path to the .RUN file containing the raw
#'   data for the corresponding measurement.}
#'   \item{d15N_area}{A numeric vector with the area of the chromatogram peak for the N content and
#'   \eqn{\delta^{15}\text{N\textperthousand}} value.}
#'   \item{d15N}{A numeric vector with the \eqn{\delta^{15}\text{N\textperthousand}} value.}
#'   \item{d13C_area}{A numeric vector with the area of the chromatogram peak for the C content and
#'   \eqn{\delta^{13}\text{C\textperthousand}} value.}
#'   \item{d13C}{A numeric vector with the \eqn{\delta^{13}\text{C\textperthousand}} value.}
#'   \item{d18O}{A numeric vector with the \eqn{\delta^{18}\text{O\textperthousand}} value.}
#'   \item{C_m}{A numeric vector with the relative mass fraction of C.}
#'   \item{N_m}{A numeric vector with the relative mass fraction of N.}
#' }
#' @return An object of class `irms_std`. This is identical to `x`, but has
#' an additional class attribute.
elco_new_irms_std <- function(x) {

  # checks
  elco_check_irms(x)
  elco_irms_check_standards(x)

  structure(x, class = c("irms_std", class(x)))

}

#' Checks if an object is of class `irms_std`.
#'
#' `elco_check_irms_std` checks if an object is of class [`irms_std()`][elco::elco_new_irms_std].
#'
#' @param x An object.
#' @return An object of class [`irms_std()`][elco::elco_new_irms_std].
#' @keywords internal
elco_check_irms_std <- function(x) {
  x_sym <- as.character(rlang::get_expr(rlang::enquo(x)))
  if(!inherits(x, "irms_std"))
    rlang::abort(paste0("`", x_sym, "` must be of class `irms_std`, not ", class(x)[[1]], "."))
  x
}