R/rezende_2019.R

In padpadpadpad/rTPC: Fitting and Analysing Thermal Performance Curves

#' Rezende model for fitting thermal performance curves
#'
#' @param temp temperature in degrees centigrade
#' @param q10 defines the fold change in performance as a result of increasing the temperature by 10 ºC
#' @param a parameter describing shifts in rate
#' @param b parameter threshold temperature (ºC) beyond which the downward curve starts
#' @param c parameter controlling the rate of decline beyond the threshold temperature, b
#' @references Rezende, Enrico L., and Francisco Bozinovic. Thermal performance across levels of biological organization. Philosophical Transactions of the Royal Society B 374.1778 (2019): 20180549.
#' @return a numeric vector of rate values based on the temperatures and parameter values provided to the function
#' @details Equation:
#' \deqn{\textrm{if} \quad temp < b: rate = a \cdot 10 ^{\frac{\log_{10} (q_{10})}{(\frac{10}{temp})}}}{%
#' rate = (a.10^(log10(q10)/(10/temp)))}
#' \deqn{\textrm{if} \quad temp > b: rate = a \cdot 10 ^{\frac{\log_{10} (q_{10})}{(\frac{10}{temp})}} \cdot \bigg(1-c \cdot (b-temp)^2 \bigg)}{%
#' rate = (a.10^(log10(q10)/(10/temp))).(1-c.(b - temp)^2))}
#'
#' Start values in \code{get_start_vals} are derived from the data and previous values in the literature.
#'
#' 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 easy to fit.
#' @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 = 'rezende_2019')
#' # fit model
#' mod <- nls.multstart::nls_multstart(rate~rezende_2019(temp = temp, q10, a, b, c),
#' data = d,
#' iter = c(4,4,4,4),
#' start_lower = start_vals - 10,
#' start_upper = start_vals + 10,
#' lower = get_lower_lims(d$temp, d$rate, model_name = 'rezende_2019'),
#' upper = get_upper_lims(d$temp, d$rate, model_name = 'rezende_2019'),
#' 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 rezende_2019

rezende_2019 <- function(temp, q10, a, b, c){

  est <-{ifelse(temp < b, (a*10^(log10(q10)/(10/temp))), (a*10^(log10(q10)/(10/temp)))*(1-c*(b - temp)^2))}
  return(est)
}