moved functions from ape to pegas -> ape 2.4

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@90 6e262413-ae40-0410-9e79-b911bd7a66b7

diff --git a/ChangeLog b/ChangeLog
index b9e9e593c7a87c84907d54373e79ec8d8c867c26..13751957239f34beb73b573549fa7c40ef51e7ba 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,4 +1,4 @@
-               CHANGES IN APE VERSION 2.3-4
+               CHANGES IN APE VERSION 2.4
 
 
 NEW FEATURES
@@ -13,6 +13,18 @@ BUG FIXES
       now ignored.
 
 
+DEPRECATED & DEFUNCT
+
+    o The functions heterozygosity, nuc.div, theta.h, theta.k and
+      theta.s have been moved from ape to pegas.
+
+
+OTHER CHANGES
+
+    o Deprecated functions are now listed in a help page: see
+      help("ape-defunct"), with the quotes!
+
+
                CHANGES IN APE VERSION 2.3-3
 
 

diff --git a/DESCRIPTION b/DESCRIPTION
index 4aa608cbe7624e9a7e0cc3d081a61f908be2a95d..0a4038b281f87bbe7525279186078c70c4d7135e 100644 (file)
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ape
-Version: 2.3-4
-Date: 2009-09-16
+Version: 2.4
+Date: 2009-09-18
 Title: Analyses of Phylogenetics and Evolution
 Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Gangolf Jobb, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Korbinian Strimmer, Damien de Vienne
 Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
@@ -13,11 +13,10 @@ Description: ape provides functions for reading, writing, plotting,
   in a phylogenetic framework, analyses of diversification and
   macroevolution, computing distances from allelic and nucleotide
   data, reading nucleotide sequences, and several tools such as
-  Mantel's test, computation of minimum spanning tree, the population
-  parameter theta based on various approaches, nucleotide diversity,
-  generalized skyline plots, estimation of absolute evolutionary rates
-  and clock-like trees using mean path lengths, non-parametric rate
-  smoothing and penalized likelihood. Phylogeny estimation can be done
-  with the NJ, BIONJ, and ME methods.
+  Mantel's test, computation of minimum spanning tree, generalized
+  skyline plots, estimation of absolute evolutionary rates and
+  clock-like trees using mean path lengths, non-parametric rate
+  smoothing and penalized likelihood. Phylogeny estimation can be
+  done with the NJ, BIONJ, and ME methods.
 License: GPL (>= 2)
 URL: http://ape.mpl.ird.fr/

diff --git a/R/DNA.R b/R/DNA.R
index 919f0ecd88912e69ff85b2ee04181d122936eb7b..72e12582617e0927bdc5d9a2a884d5784b6c46fb 100644 (file)
--- a/R/DNA.R
+++ b/R/DNA.R
@@ -1,4 +1,4 @@
-## DNA.R (2009-09-06)
+## DNA.R (2009-09-18)
 
 ##   Manipulations and Comparisons of DNA Sequences
 
@@ -286,21 +286,6 @@ seg.sites <- function(x)
     which(as.logical(ans[[4]]))
 }
 
-nuc.div <- function(x, variance = FALSE, pairwise.deletion = FALSE)
-{
-    if (pairwise.deletion && variance)
-      warning("cannot compute the variance of nucleotidic diversity\nwith pairwise deletion: try 'pairwise.deletion = FALSE' instead.")
-    if (is.list(x)) x <- as.matrix(x)
-    n <- dim(x)[1]
-    ans <- sum(dist.dna(x, "raw", pairwise.deletion = pairwise.deletion))/
-        (n*(n - 1)/2)
-    if (variance) {
-        var <- (n + 1)*ans/(3*(n + 1)*dim(x)[2]) + 2*(n^2 + n + 3)*ans/(9*n*(n - 1))
-        ans <- c(ans, var)
-    }
-    ans
-}
-
 dist.dna <- function(x, model = "K80", variance = FALSE, gamma = FALSE,
                      pairwise.deletion = FALSE, base.freq = NULL,
                      as.matrix = FALSE)

diff --git a/R/ape-defunct.R b/R/ape-defunct.R
new file mode 100644 (file)
index 0000000..fa885b4
--- /dev/null
+++ b/R/ape-defunct.R
@@ -0,0 +1,26 @@
+klastorin <- function(phy)
+    .Defunct(msg = '\'klastorin\' 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,
+    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,
+    see help("ape-defunct") for details.')
+
+theta.h <- function(x, standard.error = FALSE)
+    .Defunct(msg = '\'theta.h\' has been moved from ape to pegas,
+    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,
+    see help("ape-defunct") for details.')
+
+theta.s <- function(s, n, variance = FALSE)
+    .Defunct(msg = '\'theta.s\' has been moved from ape to pegas,
+    see help("ape-defunct") for details.')

diff --git a/R/klastorin.R b/R/klastorin.R
deleted file mode 100644 (file)
index 3d19128..0000000
--- a/R/klastorin.R
+++ /dev/null
@@ -1,2 +0,0 @@
-klastorin <- function(phy)
-    stop("the function klastorin has been removed from ape")

diff --git a/man/ape-defunct.Rd b/man/ape-defunct.Rd
new file mode 100644 (file)
index 0000000..6549d59
--- /dev/null
+++ b/man/ape-defunct.Rd
@@ -0,0 +1,31 @@
+\name{ape-defunct}
+\alias{klastorin}
+\alias{heterozygosity}
+\alias{H}
+\alias{nuc.div}
+\alias{theta.h}
+\alias{theta.k}
+\alias{theta.s}
+\title{Defunct Ape Functions}
+\description{
+  These functions have been removed from \pkg{ape} or moved to another
+  package.
+}
+\usage{
+klastorin(phy)
+heterozygosity(x, variance = FALSE)
+H(x, variance = FALSE)
+nuc.div(x, variance = FALSE, pairwise.deletion = FALSE)
+theta.h(x, standard.error = FALSE)
+theta.k(x, n = NULL, k = NULL)
+theta.s(s, n, variance = FALSE)
+}
+\details{
+  \code{klastorin} has been removed because it does not seem to be used
+  and this helped to clear some internal C code (this function may be
+  put back with a different coding).
+
+  \code{heterozygosity}, \code{nuc.div}, \code{theta.h}, \code{theta.k}
+  and \code{theta.s} have been moved to \pkg{pegas}.
+}
+\keyword{internal}

diff --git a/man/ape-internal.Rd b/man/ape-internal.Rd
index 0206ccb24a653bb87c2ebc347f3735d28733d4a1..f4e834cf5729270f2b4483442311b237e1a394fe 100644 (file)
--- a/man/ape-internal.Rd
+++ b/man/ape-internal.Rd
@@ -1,5 +1,4 @@
 \name{ape-internal}
-\alias{klastorin}
 \alias{tree.build}
 \alias{f.cherry.yule}
 \alias{f.cherry.uniform}
@@ -44,7 +43,7 @@
 \alias{plotPhyloCoor}
 \title{Internal Ape Functions}
 \description{
-  Internal ape functions.
+  Internal \pkg{ape} functions.
 }
 \note{
   These are not to be called by the user (unless you know what you're doing).