R/equ7.R

#' Equation 7
#'
#' @description Equation 7 from Montagnes et al (2008) citing Schoolfield et al. (1981)
#'
#' @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 a data frame of, depending on augment argument, if FALSE, parameters, if TRUE, data with predicted values
#' @export
#'
#' @examples output <- with(Emiliania_huxleyi, equ7(temp=temp, rate=rate))
equ7 <- function(temp,rate, augment=F, return_fit=F){
  #Fit the function
  try_test <- try({
    R<-8.617343e-5
    b <- 1
    c <- 1.05
    d <- 273.15
    a <- max(rate)/max((((temp+273.15)/293.15)*exp(b/R*(1/293.15-1/(temp+273.15))))/(1+exp(c/R*(1/d-1/(temp+273.15)))))

    fit = minpack.lm::nlsLM(rate ~ (a*((temp+273.15)/293.15)*exp(b/R*(1/293.15-1/(temp+273.15))))/(1+exp(c/R*(1/d-1/(temp+273.15)))),
                            control = minpack.lm::nls.lm.control(maxiter = 10^20),start = list(a=a,
                                                                                               b=b,
                                                                                               c=c,
                                                                                               d=d))


      output <- broom::tidy(fit)
      a <- output$estimate[output$term=="a"]
      b <- output$estimate[output$term=="b"]
      c <- output$estimate[output$term=="c"]
      d <- output$estimate[output$term=="d"]
      f_equ= function(t){(a*((t+273.15)/293.15)*exp(b/R*(1/293.15-1/(t+273.15))))/(1+exp(c/R*(1/d-1/(t+273.15))))}  #- for use with optim

  })


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

  output$model <- "equ07"
  print("equ07")
  return(output)
}

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temperatureresponse documentation built on May 2, 2019, 9:43 a.m.