R/Proba_pH.R

In Ghayabh/bacterial-growth: bacterialgrowth Package

#' This function describes the evolution of the single-cell growth probability with pH. For this, we used the model proposed by Jean Christophe Augustin and Aurelia Czarnecka-Kwasiborski in 2012, to describe the increase of the probability from 0 to 1 with increasing values of pH.
#' @details
#' \deqn{\begin{equation}p(\mathrm{pH})=\left\{\begin{array}{ll}
#'0, & \mathrm{pH} \leq \mathrm{pH}_{\mathrm{inf}} \\
#'\frac{\exp (-\mathrm{pH})-\exp \left(-\mathrm{pH}_{\mathrm{inf}}\right)}{\exp \left(-\mathrm{pH}_{\mathrm{sup}}\right)-\exp \left(-\mathrm{pH}_{\mathrm{inf}}\right)}, & \mathrm{pH}_{\mathrm{inf}}<\mathrm{pH}<\mathrm{pH}_{\mathrm{sup}} \\
#'1, & \mathrm{pH} \geq \mathrm{pH}_{\mathrm{sup}}
#'\end{array}\right.\end{equation}}
#'
#' @param pH pH value # a number
#' @param pHinf The cellular minimal pH for growth # a number
#' @param pHsup The cellular maximal pH for growth # a number
#'
#' @return proba_pH_Aug The single-cell growth probability # a number
#' @export
#'
#' @examples
#' Proba_pH(5,pHinf=4.34,pHsup=5.93) the values of phinf & phsup were imported from Augustin's 2012 review
#' Proba_pH(4,pHinf=4.34,pHsup=5.93)
#' Proba_pH(7,pHinf=4.34,pHsup=5.93)
Proba_pH<-function(pH,pHinf,pHsup){
  proba_pH_Aug<-c()
  for (i in 1:length(pH)) {


  if(pH[i]<=pHinf){
    proba_pH_Aug[i]=0
  }

  else
  {if(pH[i]>=pHsup){
    proba_pH_Aug[i]=1
  } else
    proba_pH_Aug[i]<-  (exp(-pH[i])-exp(-pHinf))/(exp(-pHsup)-exp(-pHinf))

  }}
  return(proba_pH_Aug)
}