clean up

R/ancestral.R

@@ -390,7 +390,7 @@ ptree <- function(tree, data, acctran=TRUE, return = "prob", tips=FALSE, ...) {
   f$traverse(edge)
   tmp <- reorder(tree)$edge
   tmp <- tmp[tmp[,2]>Ntip(tree),]
-  if(length(tmp)>0 && acctran==TRUE)f$acctran_traverse(tmp)
+  if(length(tmp)>0 && acctran)f$acctran_traverse(tmp)
   res <- res_state <- vector("list", nNode)
   res <- vector("list", m)
   att$names <- c(tree$tip.label, tree$node.label) #makeAncNodeLabel(tree, ...)

R/phylo.R

@@ -636,47 +636,6 @@ guess_model <- function(x){
 }
 
 
-# needs to go in phangorn extra
-optEdgeMulti <- function(object, control = pml.control(epsilon = 1e-8,
-                           maxit = 10, trace = 1, tau = 1e-8), ...) {
-  tree <- object$tree
-  theta <- object$tree$edge.length
-  weight <- attr(object$data, "weight")
-  ll0 <- object$logLik
-  eps <- 1
-  iter <- 0
-  iter2 <- 0
-  scale <- 1
-  # l <- length(theta)
-  while (abs(eps) > control$eps && iter < control$maxit) {
-    dl <- score(object)
-    thetaNew <- log(theta) + scale * solve(dl[[2]], dl[[1]]) # + diag(l) * 1e-10
-    newtheta <- exp(thetaNew)
-    tree$edge.length <- as.numeric(newtheta)
-    object <- update(object, tree = tree)
-    ll1 <- object$logLik
-    eps <- (ll0 - ll1) / ll1
-    if (eps < 0) {
-      newtheta <- theta
-      scale <- scale / 2
-      tree$edge.length <- as.numeric(theta)
-      ll1 <- ll0
-      iter2 <- iter2 + 1
-    }
-    else {
-      scale <- 1
-      iter2 <- 0
-    }
-    theta <- newtheta
-    if (iter2 == 0 && control$trace > 0) cat("loglik: ", ll1, "\n")
-    ll0 <- ll1
-    if (iter2 == 10) iter2 <- 0
-    if (iter2 == 0) iter <- iter + 1
-  }
-  object <- update(object, tree = tree)
-  object
-}
-
 
 # add data for internal use parent.frame(n) for higher nestings
 # update.pmlNew <- function(object, ..., evaluate = TRUE) {