final changes for ape 2.4 including removing mlphylo!

[ape.git] / man / ape-defunct.Rd

diff --git a/man/ape-defunct.Rd b/man/ape-defunct.Rd
index 6549d5925477e6196799f621b084a23dcb7bf95f..cb31e0256508fdad5ce5f723e01082a154e8b505 100644 (file)
--- a/man/ape-defunct.Rd
+++ b/man/ape-defunct.Rd
@@ -1,5 +1,8 @@
 \name{ape-defunct}
 \alias{klastorin}
+\alias{mlphylo}
+\alias{DNAmodel}
+\alias{sh.test}
 \alias{heterozygosity}
 \alias{H}
 \alias{nuc.div}
@@ -13,6 +16,12 @@
 }
 \usage{
 klastorin(phy)
+mlphylo(x, phy, model = DNAmodel(), search.tree = FALSE,
+        quiet = FALSE, value = NULL, fixed = FALSE)
+DNAmodel(model = "K80", partition = 1,
+         ncat.isv = 1, invar = FALSE,
+         equal.isv = TRUE, equal.invar = 1)
+sh.test(..., x, model = DNAmodel(), B = 100)
 heterozygosity(x, variance = FALSE)
 H(x, variance = FALSE)
 nuc.div(x, variance = FALSE, pairwise.deletion = FALSE)
@@ -25,6 +34,10 @@ theta.s(s, n, variance = FALSE)
   and this helped to clear some internal C code (this function may be
   put back with a different coding).
 
+  \code{mlphylo}, \code{DNAmodel} and \code{sh.test} have been removed:
+  see the package \pkg{phangorn} for a much better implementation of
+  these methods (and others).
+
   \code{heterozygosity}, \code{nuc.div}, \code{theta.h}, \code{theta.k}
   and \code{theta.s} have been moved to \pkg{pegas}.
 }