X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=R%2Fklastorin.R;h=3d19128e3d5b97bb30b683ed3d26a71a5ff47ab0;hb=7e78dcfcf1bca3d6aaca7ae92ab0f4fb3d9cc711;hp=27ba6eff4a64933ef10851ad0a989376088f2d5e;hpb=0f717ab8186382152b581c9dd67bf85779112e7f;p=ape.git

diff --git a/R/klastorin.R b/R/klastorin.R
index 27ba6ef..3d19128 100644
--- a/R/klastorin.R
+++ b/R/klastorin.R
@@ -1,59 +1,2 @@
-## klastorin.R (2003-05-26)
-
-##   Klastorin's (1982) classifification method, applied to
-##   phylogenetic trees as suggested by Misawa and Tajima (2000)
-
-## Copyright 2003 Gangolf Jobb
-
-## This file is part of the R-package `ape'.
-## See the file ../COPYING for licensing issues.
-
-########### PRIVATE ##############
-
-getMisawaTajima <- function()
-  .C("getMisawaTajima", result = integer(klastorin_nTips()),
-     PACKAGE = "ape")$result
-
-### functions to set and extract phylo tree ###
-
-buildTreeFromPhylo <- function(tree) {
-    lowerNodes <- tree$edge[,1]
-    upperNodes <- tree$edge[,2]
-    edgeLengths <- tree$edge.length
-    tipLabels <- tree$tip.label
-    .C("buildTreeFromPhylo", as.integer(lowerNodes),
-       as.integer(upperNodes), as.double(edgeLengths),
-       as.integer(length(edgeLengths)),
-       as.character(tipLabels),
-       as.integer(length(tipLabels)),
-       result = integer(1), PACKAGE = "ape"
-       )$result
-}
-
-destroyTree <- function()
-  .C("destroyTree", result = integer(1),
-     PACKAGE = "ape")$result
-
-getError <- function()
-  .C("getError", result = integer(1),
-     PACKAGE = "ape")$result
-
-klastorin_nTips <- function()
-  .C("nTips", result = integer(1),
-     PACKAGE = "ape")$result
-
-########### PUBLIC ##############
-
 klastorin <- function(phy)
-{
-    if (!inherits(phy, "phylo"))
-      stop("object \"phy\" is not of class \"phylo\"")
-    ## added by EP for the new coding of "phylo" (2006-10-04):
-    phy <- new2old.phylo(phy)
-    ## End
-    buildTreeFromPhylo(phy)
-    if (getError() !=0) stop("Could not load \"phylo\" object")
-    tmp <- getMisawaTajima()
-    destroyTree()
-    tmp
-}
+    stop("the function klastorin has been removed from ape")