R/gaussianmodified_2006.R

In padpadpadpad/rTPC: Fitting and Analysing Thermal Performance Curves

#' Modified gaussian model for fitting thermal performance curves
#'
#' @param temp temperature in degrees centigrade
#' @param rmax maximum rate at optimum temperature
#' @param topt optimum temperature
#' @param a related to full curve width
#' @param b allows for asymmetry in the curve fit
#' @return a numeric vector of rate values based on the temperatures and parameter values provided to the function
#' @details Equation:
#' \deqn{rate = r_{max} \cdot \exp{\bigg[-0.5 \left(\frac{|temp-t_{opt}|}{a}\right)^b\bigg]}}{%
#' rate = rmax.exp(-0.5.(abs(temp - topt)/a)^b)}
#'
#' Start values in \code{get_start_vals} are derived from the data and \code{gaussian_1987}
#'
#' Limits in \code{get_lower_lims} and \code{get_upper_lims} are based on extreme values that are unlikely to occur in ecological settings.
#'
#' @note Generally we found this model difficult to fit.
#'
#' This function was previously called \code{modifiedgaussian_2006()} however this is now deprecated and will be removed in the future.
#' @concept model
#' @references Angilletta Jr, M. J. (2006). Estimating and comparing thermal performance curves. Journal of Thermal Biology, 31(7), 541-545.
#' @examples
#' # load in ggplot
#' library(ggplot2)
#'
#' # subset for the first TPC curve
#' data('chlorella_tpc')
#' d <- subset(chlorella_tpc, curve_id == 1)
#'
#' # get start values and fit model
#' start_vals <- get_start_vals(d$temp, d$rate, model_name = 'gaussianmodified_2006')
#' # fit model
#' mod <- nls.multstart::nls_multstart(rate~gaussianmodified_2006(temp = temp, rmax, topt, a, b),
#' data = d,
#' iter = c(3,3,3,3),
#' start_lower = start_vals - 10,
#' start_upper = start_vals + 10,
#' lower = get_lower_lims(d$temp, d$rate, model_name = 'gaussianmodified_2006'),
#' upper = get_upper_lims(d$temp, d$rate, model_name = 'gaussianmodified_2006'),
#' supp_errors = 'Y',
#' convergence_count = FALSE)
#'
#' # look at model fit
#' summary(mod)
#'
#' # get predictions
#' preds <- data.frame(temp = seq(min(d$temp), max(d$temp), length.out = 100))
#' preds <- broom::augment(mod, newdata = preds)
#'
#' # plot
#' ggplot(preds) +
#' geom_point(aes(temp, rate), d) +
#' geom_line(aes(temp, .fitted), col = 'blue') +
#' theme_bw()
#'
#' @export gaussianmodified_2006 modifiedgaussian_2006
#' @aliases modifiedgaussian_2006

gaussianmodified_2006 <- function(temp, rmax, topt, a, b){
  est <- rmax * exp(-0.5 * (abs(temp - topt)/a)^b)
  return(est)
}

gaussianmodified_2006.starting_vals <- function(d){
  rmax = max(d$y, na.rm = TRUE)
  topt = mean(d$x[d$y == rmax])
  a = (max(d$x, na.rm = TRUE) - min(d$x, na.rm = TRUE))/2
  b = 2

  return(c(rmax = rmax, topt = topt, a = a, b=b))
}

gaussianmodified_2006.lower_lims <- function(d){
  rmax = min(d$y, na.rm = TRUE)
  topt = min(d$x, na.rm = TRUE)
  a = 0
  b = 0

  return(c(rmax = rmax, topt = topt, a = a, b=b))
}

gaussianmodified_2006.upper_lims <- function(d){
  rmax = max(d$y, na.rm = TRUE) * 10
  topt = max(d$x, na.rm = TRUE)
  a = (max(d$x, na.rm = TRUE) - min(d$x, na.rm = TRUE)) * 10
  b = 100

  return(c(rmax = rmax, topt = topt, a = a, b=b))
}

# FW: Deprecated function, to be removed.

modifiedgaussian_2006 <- function(temp, rmax, topt, a, b){
  return(gaussianmodified_2006(temp=temp, rmax=rmax, topt=topt, a=a, b=b))
}

modifiedgaussian_2006.starting_vals <- function(d){
  # Warn every 8 hours here so it doesn't slow down fitting too much
  cli::cli_warn(c("{.fn modifiedgaussian_2006} has been replaced with {.fn gaussianmodified_2006} and will be removed.", "!"="Please modify your code accordingly"), .frequency="regularly", .frequency_id="modifiedgaussian")
  return(gaussianmodified_2006.starting_vals(d=d))
}

modifiedgaussian_2006.lower_lims <- gaussianmodified_2006.lower_lims

modifiedgaussian_2006.upper_lims <- gaussianmodified_2006.upper_lims