R/get_e.R

In padpadpadpad/rTPC: Fitting and Analysing Thermal Performance Curves

#' Estimate the activation energy of a thermal performance curve
#'
#' @param model nls model object that contains a model of a thermal performance curve
#' @details Fits a modified-Boltzmann equation to all raw data below the optimum temperature (ºC; as estimated by \code{get_topt}).
#' @return Numeric estimate of activation energy (eV)
#' @export get_e

get_e <- function(model){

  # capture environment from model - contains data
  x <- model$m$getEnv()

  # get the name of the temperature column
  formula <- stats::as.formula(model$m$formula())
  param_ind <- all.vars(formula[[3]])[! all.vars(formula[[3]]) %in%
                                        names(model$m$getPars())]

  # get the name of the rate values
  params_dep <- all.vars(formula[[2]])

  # extract the temperature and rate values
  temp <- data.frame(x1 = x[[param_ind]], x2 = x[[params_dep]], stringsAsFactors = FALSE)

  # calculate topt
  topt <- rTPC::get_topt(model)

  # keep just values below topt
  temp <- temp[temp$x1 <= topt,]

  # create K column if needed
  temp$K <- ifelse(temp$x1 < 150, temp$x1 + 273.15, temp$x1)

  # run model
  mod <- stats::nls(x2 ~ lnc*exp(e/8.62e-05*(1/median(K) - 1/K)), temp, start = c(lnc = stats::median(temp$x2), e = 1), na.action = stats::na.omit)
  e = unname(stats::coef(mod)[2])

  return(e)
}