R/get_rmax.R

In padpadpadpad/rTPC: Fitting and Analysing Thermal Performance Curves

#' Estimate maximum rate of a thermal performance curve
#'
#' @param model nls model object that contains a model of a thermal performance curve
#' @details Maximum rate is calculated by predicting over the temperature range using the previously estimated parameters and picking the maximum rate value. Predictions are done every 0.001 ºC.
#' @return Numeric estimate of maximum rate
#' @export get_rmax

get_rmax <- 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())]

  # extract the temperature values
  vals <- x[[param_ind]]
  newdata <- data.frame(x = seq(min(vals), max(vals), by = 0.001), stringsAsFactors = FALSE)
  # rename to be the correct column name
  names(newdata) <- param_ind

  # predict over a whole wide range of data
  newdata$preds <- stats::predict(model, newdata = newdata)
  rmax = newdata[newdata$preds == max(newdata$preds),'preds']
  return(mean(rmax))
}