R/equ11.R

In low-decarie/temperatureresponse: Temperature Response

#' Equation 11
#'
#' @description Equation in Montagnes et al. 2008
#'
#' @param temp temperature (in Celsius)
#' @param rate rate measurement
#' @param augment logical wether the dataset with fits should be returned instead of the parameter values
#' @param return_fit logical wether the model fit object should be returned
#'
#' @return depends on augment: if false, fitting parameters or fitted data
#' @export
#'
#' @examples output <- with(Emiliania_huxleyi, equ11(temp=temp, rate=rate))

equ11 <- function(temp,rate,augment=F,return_fit=F){
  #Fit the function
  try_test <- try({

    c=-0.005
    b=(-2*c*temp[rate==max(rate)])[1]
    a=max(rate)-max(b*temp +c*(temp^2))


    fit = minpack.lm::nlsLM(rate ~ a + b*temp +c*(temp^2),start = list(a=a, b=b,c=-2))


    output <- broom::tidy(fit)
    a <- output$estimate[output$term=="a"]
    b <- output$estimate[output$term=="b"]
    c <- output$estimate[output$term=="c"]
    f_equ= function(t){a + b*t + c *t^2}

  })

  output <- temperatureresponse::amend_output(output,
                                              fit,
                                              f_equ,
                                              temp,
                                              rate,
                                              try_test,
                                              augment,
                                              return_fit)

  output$model <- "equ11"

  print("equ11")
  return(output)
}