R/fit_bd_backbone_c.R

In RPANDA: Phylogenetic ANalyses of DiversificAtion

fit_bd_backbone_c <- function (phylo, tot_time, f.lamb, f.mu, lamb_par, mu_par, f = 1, 
                               backbone, spec_times, branch_times, # options for backbone analysis
                               meth = "Nelder-Mead", cst.lamb = FALSE, cst.mu = FALSE, 
                               expo.lamb = FALSE, expo.mu = FALSE, fix.mu = FALSE, dt = 1e-3, 
                               cond = "crown", model, rate.max, n.max) 
{
  if (!inherits(phylo, "phylo"))
    stop("object \"phylo\" is not of class \"phylo\"")
  
  div <- function(par, phylo, branch_times, model, backbone){
    
    if(backbone == "crown.shift"){
      if(max(unlist(branch_times)) > max(branching.times(phylo))){
        tmrca <- max(unlist(branch_times))
      } else{
        tmrca <- max(branching.times(phylo))
      }
      
    } else {
      tmrca <- max(branching.times(phylo))
    }
    
    time_seq <- c(tmrca, seq(floor(tmrca),0,by=-1))
    if(model == "BCST"){
      lambda <- par[1]
      res <- Ntip(phylo)/f[[1]]*exp(-abs(lambda)*time_seq)
    }
    
    if(model == "BCST_DCST"){
      lambda <- par[1]
      mu <- par[2]
      res <- Ntip(phylo)/f[[1]]*exp(-abs(lambda)*time_seq+abs(mu)*time_seq)
    }
    
    if(model == "BVAR"){
      lambda <- par[1]
      alpha <- par[2]
      res <- Ntip(phylo)/f[[1]]*exp(abs(lambda)/alpha*(1-exp(alpha*time_seq)))
    }
    
    if(model == "BVAR_DCST"){
      lambda <- par[1]
      alpha <- par[2]
      mu <- par[3]
      res <- Ntip(phylo)/f[[1]]*exp(abs(lambda)/alpha*(1-exp(alpha*time_seq))+abs(mu)*time_seq)
    }
    
    if(model == "BCST_DVAR"){
      lambda <- par[1]
      mu <- par[2]
      beta <- par[3]
      res <- Ntip(phylo)/f[[1]]*exp(-abs(lambda)*time_seq-abs(mu)/beta*(1-exp(beta*time_seq)))
    }
    
    if(model == "BVAR_DVAR"){
      lambda <- par[1]
      alpha <- par[2]
      mu <- par[3]
      beta <- par[4]
      res <- Ntip(phylo)/f[[1]]*exp(abs(lambda)/alpha*(1-exp(alpha*time_seq))-abs(mu)/beta*(1-exp(beta*time_seq)))
    }
    return(res)
  }
  
  rate <- function(par, tot_time, model){
    
    agei <- tot_time[[1]]
    
    if (grepl("BCST", model)){
      rate_data <- data.frame(Lambda = par)
      rate_spec <- rep(rate_data$Lambda[1], length(c(seq(agei,0,by=-1),0)))
      rate_ext <- rep(NA, length(c(seq(agei,0,by=-1),0)))
    }
    
    if (grepl("BCST_DCST", model)){
      rate_data <- data.frame(Lambda = par[1], Mu = par[2])
      rate_spec <- rep(rate_data$Lambda[1], length(c(seq(agei,0,by=-1),0)))
      rate_ext <- rep(rate_data$Mu[1], length(c(seq(agei,0,by=-1),0)))
    }
    
    if (grepl("BVAR", model)){
      rate_data <- data.frame(Lambda = par[1], Alpha = par[2])
      rate_spec <- rate_data$Lambda[1] *exp(rate_data$Alpha[1] * c(seq(agei,0,by=-1),0))
      rate_ext <- rep(NA, length(c(seq(agei,0,by=-1),0)))
    }
    
    if (grepl("BVAR_DCST", model)){
      rate_data <- data.frame(Lambda = par[1], Alpha = par[2], Mu = par[3])
      rate_spec <- rate_data$Lambda[1] *exp(rate_data$Alpha[1] * c(seq(agei,0,by=-1),0))
      rate_ext <- rep(rate_data$Mu[1], length(c(seq(agei,0,by=-1),0)))
    }
    
    if (grepl("BCST_DVAR", model)){
      rate_data <- data.frame(Lambda = par[1], Mu = par[2], Beta = par[3])
      rate_spec <- rep(rate_data$Lambda[1], length(c(seq(agei,0,by=-1),0)))
      rate_ext <- rate_data$Mu[1] *exp(rate_data$Beta[1] * c(seq(agei,0,by=-1),0))
    }
    
    if (grepl("BVAR_DVAR", model)){
      rate_data <- data.frame(Lambda = par[1], Alpha = par[2], Mu = par[3], Beta = par[4])
      rate_spec <- rate_data$Lambda[1] *exp(rate_data$Alpha[1] * c(seq(agei,0,by=-1),0))
      rate_ext <- rate_data$Mu[1] *exp(rate_data$Beta[1] * c(seq(agei,0,by=-1),0))
    }
    rate_df2 <- rbind(rate_spec, rate_ext)
    
    return(rate_df2)
  }
  
  
  if (!inherits(phylo, "phylo")) 
    stop("object \"phylo\" is not of class \"phylo\"")
  nobs <- Ntip(phylo)
  if (fix.mu == FALSE) {
    init <- c(lamb_par, mu_par)
    p <- length(init)
    optimLH1 <- function(init, phylo. = phylo, backbone. = backbone, branch_times. = branch_times, tot_time. = tot_time, model. = model, n.max. = n.max, rate.max. = rate.max) {
      lamb_par <- init[1:length(lamb_par)]
      mu_par <- init[(1 + length(lamb_par)):length(init)]
      f.lamb.par <- function(t) {
        abs(f.lamb(t, lamb_par))
      }
      f.mu.par <- function(t) {
        abs(f.mu(t, mu_par))
      }
      
      rate.test <- rate(init, tot_time, model) 
      
      check1 <- length(lamb_par) == 1 & length(mu_par) == 1 & lamb_par[1] <= mu_par[1]
      check2 <- min(rate.test, na.rm = T) < 0
      if(all(is.na(rate.test[2,]))){
        check3 <- F
      } else {
        check3 <- ifelse(apply(rate.test, 2, function(x) x[1] - x[2])[1] < 0, T, F)
      }
      
      if(!is.null(n.max)){ # constraint on maximum diversity
        div.test <- div(init, phylo = phylo, backbone = backbone, branch_times = branch_times, model = model)
        if(max(div.test, na.rm = T) > n.max | any(c(check1, check2, check3) == T)){
          LH <- Inf
        } else {
          LH <- likelihood_bd_backbone(phylo, tot_time, f, f.lamb.par, f.mu.par,
                                       backbone, spec_times, branch_times,
                                       cst.lamb = cst.lamb, cst.mu = cst.mu, 
                                       expo.lamb = expo.lamb, expo.mu = expo.mu, dt = dt, 
                                       cond = cond)
        }
      }
      
      if(!is.null(rate.max)){ # constraint on maximum rate
        if(max(rate.test, na.rm = T) > rate.max | min(rate.test, na.rm = T) < 0 | any(c(check1, check2, check3) == T)){
          LH <- Inf
        } else {
          LH <- likelihood_bd_backbone(phylo, tot_time, f, f.lamb.par, f.mu.par,
                                       backbone, spec_times, branch_times,
                                       cst.lamb = cst.lamb, cst.mu = cst.mu, 
                                       expo.lamb = expo.lamb, expo.mu = expo.mu, dt = dt, 
                                       cond = cond)
        }
      }
      
      return(-LH)
    }
    temp <- suppressWarnings(optim(init, optimLH1, method = meth))
    lamb.par <- temp$par[1:length(lamb_par)]
    mu.par <- temp$par[(1 + length(lamb_par)):length(init)]
    f.lamb.par <- function(t) {
      abs(f.lamb(t, lamb.par))
    }
    f.mu.par <- function(t) {
      abs(f.mu(t, mu.par))
    }
    res <- list(model = "birth death", LH = -temp$value, 
                aicc = 2 * temp$value + 2 * p + (2 * p * (p + 1))/(nobs - 
                                                                     p - 1), lamb_par = lamb.par, mu_par = mu.par, 
                f.lamb = Vectorize(f.lamb.par), f.mu = Vectorize(f.mu.par))
  }
  else {
    init <- c(lamb_par)
    p <- length(init)
    optimLH2 <- function(init, phylo. = phylo, backbone. = backbone, tot_time. = tot_time, branch_times. = branch_times, model. = model) {
      lamb_par <- init[1:length(lamb_par)]
      f.lamb.par <- function(t) {
        abs(f.lamb(t, lamb_par))
      }
      f.mu.par <- function(t) {
        abs(f.mu(t, mu_par))
      }
      
      rate.test <- rate(init, tot_time = tot_time, model = model) 
      check2 <- min(rate.test, na.rm = T) < 0
      
      if(!is.null(n.max)){
        div.test <- div(init, phylo = phylo, backbone = backbone, branch_times = branch_times, model = model) 
        if(max(div.test, na.rm = T) > n.max){
          LH <- Inf
        } else {
          LH <- likelihood_bd_backbone(phylo, tot_time, f, f.lamb.par, f.mu.par, 
                                       backbone, spec_times, branch_times,
                                       cst.lamb = cst.lamb, cst.mu = TRUE, 
                                       expo.lamb = expo.lamb, dt = dt, cond = cond)
        }
      }
      
      if(!is.null(rate.max)){
        rate.test <- rate(init, tot_time, model) 
        if(max(rate.test, na.rm = T) > rate.max | check2){
          LH <- Inf
        } else {
          LH <- likelihood_bd_backbone(phylo, tot_time, f, f.lamb.par, f.mu.par, 
                                       backbone, spec_times, branch_times,
                                       cst.lamb = cst.lamb, cst.mu = TRUE, 
                                       expo.lamb = expo.lamb, dt = dt, cond = cond)
        }
      }
      
      return(-LH)
    }
    temp <- suppressWarnings(optim(init, optimLH2, method = meth))
    lamb.par <- temp$par[1:length(lamb_par)]
    f.lamb.par <- function(t) {
      abs(f.lamb(t, lamb.par))
    }
    f.mu.par <- function(t) {
      abs(f.mu(t, mu_par))
    }
    res <- list(model = "birth.death", LH = -temp$value, 
                aicc = 2 * temp$value + 2 * p + (2 * p * (p + 1))/(nobs - 
                                                                     p - 1), lamb_par = lamb.par, f.lamb = Vectorize(f.lamb.par))
  }
  class(res) <- "fit.bd"
  return(res)
}