R/calc_t_profile.R

In adsteen/enzalyze: Tools for measuring enzyme activities using fluorogenic/chromogenic substrates

##' Calculates t profile using patented T-RAMP method (note: not actually patented)
##' 
##' @description Calculates t_opt profile based on single-pot heating experiment
##' @param d Data frame containing columns with raw fluorescence, time or elapsed time, and temp
##' @param yvar Column name (as string) for response variable (fl)
##' @param xvar Column name (as string) for time variable (as POSIXct or numeric)
##' @param tvar Column name (as string) for temperature variable
##' @details <<How this works>>
##' @example <<include some examples>>
##' @export
##' 

calc_t_profile <- function(d, yvar="fl", xvar="elapsed", tvar="temp") {
  
  # Sort the data frame by xvar
  d <- d[order(d[ , xvar]), ]
  
  # Pull out separate vectors in order to calculate rise and run
  n <- nrow(d)
  xi <- d[2:n, xvar]
  xo <- d[1:(n-1), xvar]
  
  yi <- d[2:n, yvar]
  yo <- d[1:(n-1), yvar]
  
  Ti <- d[2:n, tvar]
  To <- d[1:(n-1), tvar]
  
  # Calculate slope as rise/run
  rise <- yi-yo
  run <- xi-xo # Should work with POSIXct _or_ numeric
  slope <- rise/run
  
  # Calculate average temp & average time
  temp_av <- To + (Ti-To)/2
  time_av <- xo + (xi+xo)/2
  
  t_profile <- data.frame(temp_av, time_av, slope=slope)
  t_profile
}