### Phylogenetic tree simulation
sim.tree <- function(ct=15, lambda0=0.8, mu0=0.1, K=40, model="dd", printEv=FALSE, seed=0){
## Set up
if(seed>0){set.seed(seed)}
key=0 # key to go out of the loop
reboot2=0 # reboot in case that the tree is too small
while(key==0){
i = 1
N = 1 # Starting number of species
sigmas = NULL # vector with waiting times rates
Tm = NULL # Waiting times
E = NULL # vector with 0 if extinction and 1 if speciation
n = NULL # vector with number of species at time t_i
S = NULL # vector with species that went extinct/speciation # write this better
sumt = 0 # time in simulation
reboot = 0 # this is in case we want to check how many reboots the simulation had.
newick = paste(sl[1],";",sep="") # Newick tree
identf = data.frame(Spec="aa",Time=0) # Labels of species
L = data.frame(spec='aa', spec_time=0, ext_time=-1, parent = '00') # is this working?
while (sumt < ct){
if(model == "dd"){ # diversity-dependence model
lambda = max(0,lambda0 - (lambda0-mu0)*N/K)
mu = mu0
lambda = rep(lambda,N)
mu = rep(mu,N)
}
if(model == 'cr'){ # constant-rate model
lambda = rep(lambda0,N)
mu = rep(mu0,N)
}
s = sum(lambda)+sum(mu)
sigmas = c(sigmas,s)
if (s == 0){break}
tm = rexp(1,s) # waiting time of iteration i
if(tm+sumt>ct){break}
sumt = tm + sumt
prob = c(lambda,mu)/s # Probability of extinctions and speciations
BD = sample(2*N,1,prob=prob) # speciation/extinction & identification of the species.
n[i] = N
if(BD > N){ # Extinction
E[i] = 0
## for newick output
species = as.character(identf[BD-N,1])
S[i] = species
ind = regexpr(species,newick)[1] + 2
atm = sumt-identf[which(identf[,1]==species),2]
identf = identf[-(BD-N),]
L[L$spec == species,]$ext_time = sumt #?
newick = paste(substr(newick,1,ind),as.character(atm),substring(newick,ind+2),sep="")
N = N-1
if(printEv){print(paste("extinction in time",sumt, sep=" "))} # put it in a log file
}else{ # Speciation
E[i] = 1
## for newick output
species = as.character(identf[BD,1])
S[i] = species
ind = regexpr(species,newick)[1]-1
atm = sumt-identf[which(identf[,1]==species),2]
newick = paste(substr(newick,1,ind),"(",substr(newick,ind+1,ind+4),",",sl[i+1],"):",as.character(atm),substring(newick,ind+5),sep="")
identf = rbind(identf,data.frame(Spec=substr(sl[i+1],1,2),Time=sumt))
identf[identf$Spec == species,2] = sumt
L = rbind(L,data.frame(spec=substr(sl[i+1],1,2), spec_time=sumt, ext_time=-1, parent=species))
N = N+1
if(printEv){print(paste("speciation in time",sumt,sep=" "))} # put it in a log file
}
if (N==0){ # In case all species got extinct: restart
reboot = reboot + 1
N = 1 # Number of species
i = 1
Tm = NULL
sumt = 0
E = NULL # vector with 0 if extinction and 1 if speciation
n = NULL # vector with number of species at time t_i
newick = paste(sl[1],";",sep="") # Newick tree
identf = data.frame(Spec="aa",Time=0)
L = data.frame(spec='aa', spec_time=0, ext_time=-1, parent = '00')
}else { # Otherwise, update values and go to next iteration
Tm[i] = tm
i<-i+1
}
}
####
if(nchar(newick)<7){
reboot2=reboot2+reboot+1
}else{
newick = compphyl(newi=newick,identf=identf,ct=ct) # set extant species to the present
phy = read.tree(text=newick)
dphy = drop.fossil(phy)
if(Ntip(dphy)>2){ #check if the extant species tree is large enough
key=1
}else{
reboot2=reboot2+reboot+1
}
}
}
Tm[i] = ct-sum(Tm)
n[i] = n[i-1] + E[i-1] - (1-E[i-1])
newick.extant = drop.fossil(phy)
newick.extant.p = phylo2vectors(newick.extant) # is it validated?
reboot2 = reboot2 + reboot
return(list(tree=list(wt=Tm, E=E, n=n, S=S, br = cumsum(Tm)), phylo = phy, tree.extant = newick.extant.p, phylo.extant=newick.extant, r=reboot2, L=L,sigmas=sigmas)) #validate reboot 2
}
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