R/load_direct_quant.R

In bentrueman/fffprocessr: Process FFF-UV-MALS-ICP-MS Data

#' Read and clean ICP-MS data files generated by the iCAP-RQ
#'
#' @param path Relative path to the ICP-MS (.xlsx) input files.
#' @param int_stds A character vector of internal standards to be removed from the output.
#'
#' @return A tibble with columns `date`, `sample`, `value`, and `param`.
#' @importFrom readxl read_excel
#' @importFrom rlang set_names .data
#' @importFrom tidyr pivot_longer
#' @importFrom tidyselect matches
#' @importFrom dplyr filter transmute
#' @importFrom stringr str_extract str_remove str_detect
#' @importFrom purrr map_dfr
#' @export
#'
#' @examples
#' path <- system.file("extdata", package = "fffprocessr")
#' load_direct_quant(path = paste0(path, "/direct_quantification"))
load_direct_quant <- function(path, int_stds = c("45Sc", "115In", "159Tb")) {
  path %>%
    list.files(pattern = "\\.xlsx$", full.names = TRUE) %>%
    set_names() %>%
    map_dfr(read_excel, .id = "file") %>%
    filter(.data$`Sample Type` == "UNKNOWN") %>%
    pivot_longer(matches("^\\d"), names_to = "param") %>%
    filter(!str_detect(.data$param, paste(int_stds, collapse = "|"))) %>%
    transmute(
      date = str_extract(.data$file, "\\d{4}-\\d{2}-\\d{2}") %>%
        as.Date(),
      sample = .data$Label,
      value = str_remove(.data$value, ",") %>% as.numeric(),
      param = str_extract(.data$param, "\\d+[A-Z][a-z]?")
    )
}