removing evolve.phylo + bug fix in as.phylo.hclust

[ape.git] / R / evolve.phylo.R

diff --git a/R/evolve.phylo.R b/R/evolve.phylo.R
deleted file mode 100644 (file)
index e3fcee8..0000000
--- a/R/evolve.phylo.R
+++ /dev/null
@@ -1,66 +0,0 @@
-## evolve.tree.R (2005-12-04)
-
-##   Character Simulation under a Brownian Model
-
-## Copyright 2005 Julien Dutheil
-
-## This file is part of the R-package `ape'.
-## See the file ../COPYING for licensing issues.
-
-evolve.phylo <- function(phy, value, var) {
-  if (!("phylo" %in% class(phy)))
-      stop("object \"phy\" is not of class \"phylo\"")
-  if (is.null(phy$edge.length))
-      stop("tree \" phy\" must have branch lengths.")
-  nchar <- max(length(value), length(var))
-  value <- rep(value, length=nchar)
-  var   <- rep(var,   length=nchar)
-  char.names <- names(value);
-
-  ## added by EP for the new coding of "phylo" (2006-10-04):
-  phy <- new2old.phylo(phy)
-  ## End
-  edges <- phy$edge
-  nodes <- unique(as.vector(edges))
-  n <- length(nodes) # Number of nodes
-  root <- match("-1", nodes)
-  states<-list();
-  states[["-1"]] <- value
-  for(node in nodes[-root]) {
-    edge.index <- match(node, edges[,2])
-    edge.length <- phy$edge.length[edge.index]
-    ancestor <- edges[edge.index, 1]
-    ancestor.node.index <- match(ancestor, nodes)
-    ancestor.states <- states[[ancestor.node.index]]
-    index <- match(node, nodes)
-    x <- numeric(nchar)
-    for(i in 1:nchar) {
-      x[i] <- rnorm(1, mean=ancestor.states[i], sd=sqrt(var[i]*edge.length))
-    }
-    states[[index]] <- x;
-  }
-  nodes.states <- as.data.frame(matrix(ncol=nchar, nrow=0))
-  if(!is.null(char.names)) names(nodes.states) <- char.names
-  count <- 1
-  for(i in unique(edges[,1])) {
-    nodes.states[i,] <- states[[match(i, nodes)]]
-    count <- count + 1
-  }
-
-  nl <- length(phy$tip.label) #Number of leaves
-  leaves.states <- as.data.frame(matrix(ncol=nchar, nrow=0))
-  if(!is.null(char.names)) names(leaves.states) <- char.names
-  count <- 1
-  for(i in 1:nl) {
-    leaves.states[as.character(count),] <- states[[match(as.character(i), nodes)]]
-    count <- count + 1
-  }
-
-  phy[["node.character"]] <- nodes.states;
-  phy[["tip.character"]]  <- leaves.states;
-  if(! "ancestral" %in% class(phy)) class(phy) <- c("ancestral", class(phy));
-  ## added by EP for the new coding of "phylo" (2006-10-04):
-  phy <- old2new.phylo(phy)
-  ## End
-  return(phy)
-}