various bug fixes

[ape.git] / R / ape-defunct.R

diff --git a/R/ape-defunct.R b/R/ape-defunct.R
index 58049ae721a255d3999bd3ac338e1d8b10412979..c89dc06738df17dd295a6f644659d7918d5d5837 100644 (file)
--- a/R/ape-defunct.R
+++ b/R/ape-defunct.R
@@ -2,41 +2,34 @@ klastorin <- function(phy)
     .Defunct(msg = '\'klastorin\' has been removed from ape,
     see help("ape-defunct") for details.')
 
-mlphylo <-
-    function(x, phy, model = DNAmodel(), search.tree = FALSE,
-             quiet = FALSE, value = NULL, fixed = FALSE)
+mlphylo <- function(...)
     .Defunct(msg = '\'mlphylo\' has been removed from ape,
     see help("ape-defunct") for details.')
 
-DNAmodel <- function(model = "K80", partition = 1,
-         ncat.isv = 1, invar = FALSE,
-         equal.isv = TRUE, equal.invar = 1)
+DNAmodel <- function(...)
     .Defunct(msg = '\'DNAmodel\' has been removed from ape,
     see help("ape-defunct") for details.')
 
-sh.test <- function(..., x, model = DNAmodel(), B = 100)
+sh.test <- function(...)
     .Defunct(msg = '\'sh.test\' has been removed from ape,
     see help("ape-defunct") for details.')
 
-heterozygosity <- function (x, variance = FALSE)
-    .Defunct(msg = '\'heterozygosity\' has been moved from ape to pegas,
+evolve.phylo <- function(phy, value, var)
+    .Defunct(msg = '\'evolve.phylo\' has been removed from ape,
     see help("ape-defunct") for details.')
 
-H <- function(x, variance = FALSE)
-    heterozygosity (x, variance = FALSE)
-
-nuc.div <- function(x, variance = FALSE, pairwise.deletion = FALSE)
-    .Defunct(msg = '\'nuc.div\' has been moved from ape to pegas,
+plot.ancestral <- function(...)
+    .Defunct(msg = '\'plot.ancestral\' has been removed from ape,
     see help("ape-defunct") for details.')
 
-theta.h <- function(x, standard.error = FALSE)
-    .Defunct(msg = '\'theta.h\' has been moved from ape to pegas,
+chronogram <- function(...)
+    .Defunct(msg = '\'chronogram\' has been removed from ape,
     see help("ape-defunct") for details.')
 
-theta.k <- function(x, n = NULL, k = NULL)
-    .Defunct(msg = '\'theta.k\' has been moved from ape to pegas,
+ratogram <- function(...)
+    .Defunct(msg = '\'ratogram\' has been removed from ape,
     see help("ape-defunct") for details.')
 
-theta.s <- function(s, n, variance = FALSE)
-    .Defunct(msg = '\'theta.s\' has been moved from ape to pegas,
+NPRS.criterion <- function(...)
+    .Defunct(msg = '\'NPRS.criterion\' has been removed from ape,
     see help("ape-defunct") for details.')