R/DAISIE_ExpEIN.R

In xieshu95/Test-Trasie: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

#' The expected number of endemics and non-endemics under the DAISIE model
#' 
#' This function calculates the expected number of endemics, non-endemics and
#' the sum of these for a given set of parameter values, a given mainland
#' species pool size and a given time
#' 
#' 
#' @param t The time at which the expectations need to be computed
#' @param pars Vector of parameters: \cr \cr \code{pars[1]} corresponds to
#' lambda^c (cladogenesis rate) \cr \code{pars[2]} corresponds to mu
#' (extinction rate) \cr \code{pars[3]} corresponds to K (clade-level carrying
#' capacity) \cr \code{pars[4]} corresponds to gamma (immigration rate) \cr
#' \code{pars[5]} corresponds to lambda^a (anagenesis rate)
#' @param M The size of the mainland pool, i.e the number of species that can
#' potentially colonize the island
#' @param initEI The initial values of the number of endemics and non-endemics
#' @return \item{out}{The output is a list with three elements: \cr \cr
#' \code{ExpE} The number of endemic species \cr \code{ExpI} The number of
#' non-endemic species \cr \code{ExpN} The sum of the number of endemics and
#' non-endemics }
#' @author Rampal S. Etienne
#' @references Valente, L.M., A.B. Phillimore and R.S. Etienne (2015).
#' Equilibrium and non-equilibrium dynamics simultaneously operate in the
#' Galapagos islands. Ecology Letters 18: 844-852.
#' @keywords models
#' @examples
#' 
#' ### Compute the expected values at t = 4, for a mainland pool size of 1000 potential
#' # colonists and a vector of 5 parameters (cladogenesis, extinction, clade-level carrying
#' # capacity, immigration, anagenesis)
#'  
#' DAISIE_ExpEIN(
#'    t = 4,
#'    pars = c(0.5,0.1,Inf,0.01,0.4),
#'    M = 1000
#'    )
#' 
#' @export DAISIE_ExpEIN
DAISIE_ExpEIN = function(t,pars,M,initEI = c(0,0))
{
   pars1 = pars
   lac = pars1[1]
   mu = pars1[2]
   ga = pars1[4]
   laa = pars1[5]
   if(!is.na(pars1[11]))
   {
       M2 = M - DDD::roundn(pars1[11] * M)
   } else {
       M2 = M
   }
   A = mu - lac
   B = lac + mu + ga + laa
   C = laa + 2 * lac + ga
   DD = laa + 2 * lac
   E0 = initEI[1]
   I0 = initEI[2] 
   if(t == Inf)
   {
      Imm = ga * M2 / B
      End = DD/A * Imm
   } else {
      #Imm = M2 * ga / B * (1 - exp(-B * t))
      #End = M2 * ga * (laa + 2 * lac) * (1/(A * B) - exp(-A*t) / (A * C) + exp(-B*t)/(B * C))
      Imm = M2 * ga / B - (M2 * ga / B - I0) * exp(-B * t)
      End = DD/C * (M2 * ga / A - M2 * ga/ B + (C / DD * E0 - M2 * ga / A + I0) * exp(-A * t) + (M2 * ga / B - I0) * exp(-B * t))
   }
   All = End + Imm
   expEIN = list(End,Imm,All)
   names(expEIN) = c("ExpE","ExpI","ExpN")
   return(expEIN)
}