R/sim_phyl.R

In franciscorichter/dmea: Diversification and Macro-Evolution Analysis

### Phylogenetic tree simulation
sim_phyl <- 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
  reboot2=0
  while(key==0){
  ###
    i = 1
    N = 1 # Starting number of species
    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
    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')
    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)
      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 = identf[BD-N,1]
        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=" "))}
      }else{  # Speciation
        E[i] = 1
        ## for newick output
        species = as.character(identf[BD,1])
        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=" "))}
      }
      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)
      newi = newick
      newick = read.tree(text=newick)
      #####
      phy = newick
      nn <- Ntip(phy)
      x <- dist.nodes(phy)[nn + 1, ][1:nn]
      tol = 1e-08
      dphy = drop.tip(phy, root.edge = T , which(x < max(x) - tol))
      if(Ntip(dphy)>2){
        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(newick)
  newick.extant.p = phylo2p(newick.extant)
  return(list(tree=list(wt=Tm, E=E, n=n, br = cumsum(Tm)), phylo = newick, tree.extant = newick.extant.p, phylo.extant=newick.extant, wt=Tm, E=E, n=n, newick=newick, br = cumsum(Tm), newick.extant = newick.extant, newick.extant.p = newick.extant.p, L=L, r=reboot2,newi=newi))
}