Nothing
dd_MS_lamuN = function(ddmodel,pars,N)
{
laM = pars[1]
muM = pars[2]
Kprime = pars[3]
laS = pars[4]
muS = pars[5]
n0 = (ddmodel == 2 | ddmodel == 4)
if(ddmodel == 1 | ddmodel == 1.3)
{
# linear dependence in speciation rate
laMN = max(0,laM * (1 - N/Kprime))
muMN = muM
laSN = max(0,laS * (1 - N/Kprime))
muSN = muS
}
if(ddmodel == 2 | ddmodel == 2.1 | ddmodel == 2.2 | ddmodel == 2.3)
{
# exponential dependence in speciation rate
al = Kprime^(ddmodel != 2.2)
laMN = laM * (N + n0)^(-al)
muMN = muM
laSN = laS * (N + n0)^(-al)
muSN = muM
}
return(c(laMN,muMN,laSN,muSN))
}
#' Function to simulate the macro-evolutionary succession process assuming
#' diversity-dependent diversification
#'
#' Simulating a diversity-dependent diversification process where at a given
#' time a new clade emerges with different inherent speciation rate and
#' extinction rate
#'
#'
#' @param pars Vector of parameters: \cr \cr \code{pars[1]} corresponds to
#' lambda_M (speciation rate of the main clade) \cr \code{pars[2]} corresponds
#' to mu_M (extinction rate of the main clade) \cr \code{pars[3]} corresponds
#' to K' (maximum number of species or a proxy for it in case of exponential
#' decline in speciation rate) \code{pars[4]} corresponds to lambda_S
#' (speciation rate of the novel subclade) \cr \code{pars[5]} corresponds to
#' mu_S (extinction rate) \cr \code{pars[6]} tinn, the time the shift in rates
#' occurs in the lineage leading to the subclade
#' @param age Sets the crown age for the simulation
#' @param ddmodel Sets the model of diversity-dependence: \cr \code{ddmodel ==
#' 1.3} : linear dependence in speciation rate with parameter K' (= diversity
#' where speciation = 0); ddmodel = 1 will be interpreted as this model \cr
#' \code{ddmodel == 2.1} : variant of exponential dependence in speciation rate
#' with offset at infinity; ddmodel = 2 will be interpreted as this model \cr
#' \code{ddmodel == 2.2} : 1/n dependence in speciation rate\cr \code{ddmodel
#' == 2.3} : exponential dependence in speciation rate with parameter x (=
#' exponent)
#' @return \item{ out }{ A list with the following elements: The first element
#' is the tree of extant species in phylo format \cr The second element is the
#' tree of all species, including extinct species, in phylo format \cr The
#' third element is a matrix of all species where \cr - the first column is the
#' time at which a species is born \cr - the second column is the label of the
#' parent of the species; positive and negative values only indicate whether
#' the species belongs to the left or right crown lineage \cr - the third
#' column is the label of the daughter species itself; positive and negative
#' values only indicate whether the species belongs to the left or right crown
#' lineage \cr - the fourth column is the time of extinction of the species \cr
#' If the fourth element equals -1, then the species is still extant.\cr - the
#' fifth column indicates whether the species belong to the main clade (0) or
#' the subclade (1)\cr The fourth element is the subclade tree of extant
#' species (without stem) \cr The fifth element is the subclade tree of all
#' species (without stem) \cr The sixth element is the same as the first,
#' except that it has attributed 0 for the main clade and 1 for the subclade\cr
#' The seventh element is the same as the Second, except that it has attributed
#' 0 for the main clade and 1 for the subclade\cr The sixth and seventh element
#' will be NULL if the subclade does not exist (because it went extinct). }
#' @author Rampal S. Etienne
#' @references - Etienne, R.S. et al. 2012, Proc. Roy. Soc. B 279: 1300-1309,
#' doi: 10.1098/rspb.2011.1439 \cr - Etienne, R.S. & B. Haegeman 2012. Am. Nat.
#' 180: E75-E89, doi: 10.1086/667574
#' @keywords models
#' @examples
#' dd_MS_sim(c(0.2,0.1,20,0.1,0.05,4),10)
#' @export dd_MS_sim
dd_MS_sim = function(pars,age,ddmodel = 1.3)
{
# Simulation of diversity-dependent process
# . start from crown age
# . no additional species at crown node
# . no missing species in present
# pars = [laM muM K laS muS tinn]
# - pars1[1] = laM = (initial) speciation rate of main clade
# - pars1[2] = muM = extinction rate of main clade
# - pars1[3] = K' = maximum number of species
# - pars1[4] = laS = (initial) speciation rate of subclade
# - pars1[5] = muS = extinction rate of subclade
# - pars1[6] = tinn = time of key innovation
# age = crown age
# ddmodel = mode of diversity-dependence
# . ddmodel == 1 : linear dependence in speciation rate with parameter K
# . ddmodel == 1.3: linear dependence in speciation rate with parameter K'
# . ddmodel == 2 : exponential dependence in speciation rate
# . ddmodel == 2.1: variant with offset at infinity
# . ddmodel == 2.2: 1/n dependence in speciation rate
# . ddmodel == 2.3: exponential dependence in speciation rate with parameter x
done = 0
if(pars[6] > age)
{
stop('The key innovation time is before the crown age of the main clade.')
}
if((pars[1] < pars[2]) | (pars[4] < pars[5]))
{
stop('lambda0 is smaller than mu for one or both clades')
}
if(min(pars) < 0)
{
stop('One of the parameters is negative')
}
if(!(ddmodel %in% c(1,1.3,2,2.1,2.2,2.3)))
{
stop('This diversity-dependence model does not exist or is not implemented')
}
while(done == 0)
{
# number of species N at time t
# i = index running through t and N
t = rep(0,1)
L = matrix(0,2,5)
i = 1
t[1] = 0
NM = 2
NS = 0
# L = data structure for lineages,
# . L[,1] = branching times
# . L[,2] = index of parent species
# . L[,3] = index of daughter species
# . L[,4] = time of extinction
# . L[,5] = main clade (0) or subclade (1)
# j = index running through L
L[1,1:5] = c(0,0,-1,-1,0)
L[2,1:5] = c(0,-1,2,-1,0)
linlistM = c(-1,2)
linlistS = NULL
newL = 2
tinn = age - pars[6]
ff = dd_MS_lamuN(ddmodel,pars,NM[i] + NS[i])
laMN = ff[1]
muMN = ff[2]
laSN = ff[3]
muSN = ff[4]
denom = (laMN + muMN) * NM[i] + (laSN + muSN) * NS[i]
t[i + 1] = t[i] + stats::rexp(1,denom)
if(t[i + 1] > tinn & t[i] < tinn)
{
NM[i] = NM[i] - 1
NS[i] = NS[i] + 1
linlistS = sample2(linlistM,1)
L[abs(linlistS),5] = 1
linlistM = linlistM[-which(linlistM == linlistS)]
ff = dd_MS_lamuN(ddmodel,pars,NM[i] + NS[i])
laMN = ff[1]
muMN = ff[2]
laSN = ff[3]
muSN = ff[4]
denom = (laMN + muMN) * NM[i] + (laSN + muSN) * NS[i]
t[i + 1] = tinn + stats::rexp(1,denom)
}
while(t[i + 1] <= age)
{
event = sample2(x = 1:4,size = 1,prob = c(laMN * NM[i], muMN * NM[i], laSN * NS[i], muSN * NS[i]))
i = i + 1
if(event == 1)
{
# speciation event in main clade
ranL = sample2(linlistM,1)
NM[i] = NM[i - 1] + 1
NS[i] = NS[i - 1]
newL = newL + 1
L = rbind(L,c(t[i],ranL,sign(ranL) * newL,-1,0))
linlistM = c(linlistM,sign(ranL) * newL)
} else if(event == 3)
{
# speciation event in subclade
ranL = sample2(linlistS,1)
NM[i] = NM[i - 1]
NS[i] = NS[i - 1] + 1
newL = newL + 1
L = rbind(L,c(t[i],ranL,sign(ranL) * newL,-1,1))
linlistS = c(linlistS,sign(ranL) * newL)
} else if(event == 2)
{
# extinction event in main clade
ranL = sample2(linlistM,1)
NM[i] = NM[i - 1] - 1
NS[i] = NS[i - 1]
L[abs(ranL),4] = t[i]
w = which(linlistM == ranL)
linlistM = linlistM[-w]
linlistM = sort(linlistM)
} else if(event == 4)
{
# extinction event in subclade
ranL = sample2(linlistS,1)
NM[i] = NM[i - 1]
NS[i] = NS[i - 1] - 1
L[abs(ranL),4] = t[i]
w = which(linlistS == ranL)
linlistS = linlistS[-w]
linlistS = sort(linlistS)
}
if(sum(c(linlistM,linlistS) < 0) == 0 | sum(c(linlistM,linlistS) > 0) == 0)
{
t[i + 1] = Inf
} else {
ff = dd_MS_lamuN(ddmodel,pars,NM[i] + NS[i])
laMN = ff[1]
muMN = ff[2]
laSN = ff[3]
muSN = ff[4]
denom = (laMN + muMN) * NM[i] + (laSN + muSN) * NS[i]
t[i + 1] = t[i] + stats::rexp(1,denom)
if(t[i + 1] > tinn & t[i] < tinn)
{
NM[i] = NM[i] - 1
NS[i] = NS[i] + 1
linlistS = sample2(linlistM,1)
L[abs(linlistS),5] = 1
linlistM = linlistM[-which(linlistM == linlistS)]
ff = dd_MS_lamuN(ddmodel,pars,NM[i] + NS[i])
laMN = ff[1]
muMN = ff[2]
laSN = ff[3]
muSN = ff[4]
denom = (laMN + muMN) * NM[i] + (laSN + muSN) * NS[i]
t[i + 1] = tinn + stats::rexp(1,denom)
}
}
}
if(sum(c(linlistM,linlistS) < 0) == 0 | sum(c(linlistM,linlistS) > 0) == 0)
{
done = 0
} else {
done = 1
}
}
L[,1] = age - c(L[,1])
notmin1 = which(L[,4] != -1)
L[notmin1,4] = age - c(L[notmin1,4])
L[which(L[,4] == age + 1),4] = -1
tes = L2phylo(L[,1:4],dropextinct = T)
tas = L2phylo(L[,1:4],dropextinct = F)
tesS = NULL
tes2 = NULL
graphics::par(mfrow = c(2,1))
graphics::plot(tes)
graphics::plot(tas)
cols = c("blue","red")
names(cols) = c(0,1)
if(length(linlistS) > 0)
{
namesS = paste('t',abs(linlistS), sep = "")
if(length(linlistS) == 1)
{
m = which(tes$tip.label == namesS)
b2 = 0
}
else if(length(linlistS) > 1)
{
m = ape::getMRCA(phy = tes,tip = namesS)
tesS = ape::extract.clade(phy = tes,node = m)
b2 = age - ape::node.depth.edgelength(tes)[m]
}
m0 = tes$edge[which(tes$edge[,2] == m),1]
b1 = age - ape::node.depth.edgelength(tes)[m0]
tes2 = phytools::paintSubTree(tes,node = m,state = "1",anc.state = "0",stem = (pars[6] - b2)/(b1 - b2))
phytools::plotSimmap(tes2,cols,lwd = 3,pts = F)
}
tasS = NULL
tas2 = NULL
allS = which(L[,5] == 1)
if(length(allS) > 0)
{
namesS = paste('t',abs(allS), sep = "")
if(length(allS) == 1)
{
m = which(tas$tip.label == namesS)
b2 = 0
}
else if(length(allS) > 1)
{
m = ape::getMRCA(phy = tas,tip = namesS)
tasS = ape::extract.clade(phy = tas,node = m)
b2 = age - ape::node.depth.edgelength(tas)[m]
}
m0 = tas$edge[which(tas$edge[,2] == m),1]
b1 = age - ape::node.depth.edgelength(tas)[m0]
tas2 = phytools::paintSubTree(tas,node = m,state = "1",anc.state = "0", stem = (pars[6] - b2)/(b1 - b2))
phytools::plotSimmap(tas2,cols,lwd = 3,pts = F)
}
out = list(tes = tes,tas = tas,L = L,tesS = tesS,tasS = tasS,tes2 = tes2,tas2 = tas2)
return(out)
}
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