R/fecalHormoneCalc.R

In mwhalen18/krspfecals: KRSP Auxilary Fecal Database

#' Calculate hormone concentration levels
#' @description
#' fecalHormoneCalc takes a joined table with extract and assay data and caclualtes final hormone concentration in ng/g
#' This is a clunky function that will \bold{only work with unaltered hormone tables}
#' \cr
#' The steroid hormone concentration calculation is done following De Palma (???):
#' \deqn{
#' ((pg/well) x ExtractVolume(uL) x Dilution Factor) / (FecalWeight(g) x SampleVolume(uL) x 1000)
#' }
#'
#' @param .data a dataframe that contains both extract and hormone data
#' @examples
#' \dontrun{
#' con = fecalConnect(RMySQL::MySQL(), group = "krspfecals-aws")
#' extracts = tbl(con, "extracts")
#' cort = tbl(con, "cort")
#' joined = left_join(extracts, cort)
#' joined$cort_ng_g = fecalHormoneCalc(joined, "cort")
#' }
#' @export

fecalHormoneCalc = function(.data){
  if(!is.data.frame(.data)){
    stop("data must be a data frame")
  }
  hormone = (.data$final_concentration * (500 + (.data$mass_extracted_g*1000)) * .data$dilution) /
    (.data$mass_extracted_g * .data$volume_used * 1000)
  return(hormone)
}