[Vegan-commits] r365 - in pkg: . R inst
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu May 22 10:21:30 CEST 2008
Author: jarioksa
Date: 2008-05-22 10:21:30 +0200 (Thu, 22 May 2008)
New Revision: 365
Modified:
pkg/DESCRIPTION
pkg/R/factorfit.R
pkg/R/inertcomp.R
pkg/R/intersetcor.R
pkg/R/ordicluster.R
pkg/R/ordiellipse.R
pkg/R/ordispider.R
pkg/R/ordisurf.R
pkg/R/orglspider.R
pkg/R/vectorfit.R
pkg/inst/ChangeLog
Log:
workaround to R 2.7.0 where weights() give an error if object has no weights: weights.default defined internally. Some functions worked only with 'cca' objects, but did not check their input
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2008-05-21 08:53:29 UTC (rev 364)
+++ pkg/DESCRIPTION 2008-05-22 08:21:30 UTC (rev 365)
@@ -1,7 +1,7 @@
Package: vegan
Title: Community Ecology Package
-Version: 1.14-0
-Date: May 15, 2008
+Version: 1.14-1
+Date: May 22, 2008
Author: Jari Oksanen, Roeland Kindt, Pierre Legendre, Bob O'Hara, Gavin L. Simpson,
M. Henry H. Stevens
Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>
Modified: pkg/R/factorfit.R
===================================================================
--- pkg/R/factorfit.R 2008-05-21 08:53:29 UTC (rev 364)
+++ pkg/R/factorfit.R 2008-05-22 08:21:30 UTC (rev 365)
@@ -2,6 +2,7 @@
function (X, P, permutations = 0, strata, choices = c(1, 2),
display = c("sites","lc"), w = weights(X), ...)
{
+ weights.default <- function(object, ...) NULL
display <- match.arg(display)
w <- eval(w)
P <- as.data.frame(P)
Modified: pkg/R/inertcomp.R
===================================================================
--- pkg/R/inertcomp.R 2008-05-21 08:53:29 UTC (rev 364)
+++ pkg/R/inertcomp.R 2008-05-22 08:21:30 UTC (rev 365)
@@ -4,6 +4,8 @@
{
display <- match.arg(display)
statistic <- match.arg(statistic)
+ if (!inherits(object, "cca"))
+ stop("can be used only with objects inheriting from 'cca'")
if (inherits(object, "capscale") && display == "species")
stop("cannot analyse species with 'capscale'")
pCCA <- object$pCCA$Fit
Modified: pkg/R/intersetcor.R
===================================================================
--- pkg/R/intersetcor.R 2008-05-21 08:53:29 UTC (rev 364)
+++ pkg/R/intersetcor.R 2008-05-22 08:21:30 UTC (rev 365)
@@ -1,5 +1,7 @@
intersetcor <- function(object)
{
+ if (!inherits(object, "cca"))
+ stop("can be used only with objects inheriting from 'cca'")
w <- weights(object)
wa <- sweep(object$CCA$wa, 1, sqrt(w), "*")
cor(qr.X(object$CCA$QR), wa)
Modified: pkg/R/ordicluster.R
===================================================================
--- pkg/R/ordicluster.R 2008-05-21 08:53:29 UTC (rev 364)
+++ pkg/R/ordicluster.R 2008-05-22 08:21:30 UTC (rev 365)
@@ -2,6 +2,7 @@
function (ord, cluster, prune=0, display="sites", w = weights(ord, display),
...)
{
+ weights.default <- function(object, ...) NULL
w <- eval(w)
mrg <- cluster$merge
ord <- scores(ord, display = display, ...)
Modified: pkg/R/ordiellipse.R
===================================================================
--- pkg/R/ordiellipse.R 2008-05-21 08:53:29 UTC (rev 364)
+++ pkg/R/ordiellipse.R 2008-05-22 08:21:30 UTC (rev 365)
@@ -5,6 +5,7 @@
{
if (!require(ellipse))
stop("Requires package `ellipse' (from CRAN)")
+ weights.default <- function(object, ...) NULL
kind <- match.arg(kind)
draw <- match.arg(draw)
pts <- scores(ord, display = display, ...)
Modified: pkg/R/ordispider.R
===================================================================
--- pkg/R/ordispider.R 2008-05-21 08:53:29 UTC (rev 364)
+++ pkg/R/ordispider.R 2008-05-22 08:21:30 UTC (rev 365)
@@ -2,6 +2,7 @@
function (ord, groups, display = "sites", w = weights(ord, display),
show.groups, ...)
{
+ weights.default <- function(object, ...) NULL
if (inherits(ord, "cca") && missing(groups)) {
lc <- scores(ord, display = "lc", ...)
wa <- scores(ord, display = "wa", ...)
Modified: pkg/R/ordisurf.R
===================================================================
--- pkg/R/ordisurf.R 2008-05-21 08:53:29 UTC (rev 364)
+++ pkg/R/ordisurf.R 2008-05-22 08:21:30 UTC (rev 365)
@@ -3,6 +3,7 @@
col = "red", thinplate = TRUE, add = FALSE, display = "sites",
w = weights(x), main, nlevels = 10, levels, labcex = 0.6, ...)
{
+ weights.default <- function(object, ...) NULL
GRID = 25
w <- eval(w)
if (!is.null(w) && length(w) == 1)
Modified: pkg/R/orglspider.R
===================================================================
--- pkg/R/orglspider.R 2008-05-21 08:53:29 UTC (rev 364)
+++ pkg/R/orglspider.R 2008-05-22 08:21:30 UTC (rev 365)
@@ -2,6 +2,7 @@
function (object, groups, display = "sites",
w = weights(object, display), choices = 1:3, ...)
{
+ weights.default <- function(object, ...) NULL
if (inherits(object, "cca") && missing(groups)) {
lc <- scores(object, display = "lc", choices = choices, ...)
wa <- scores(object, display = "wa", choices = choices, ...)
Modified: pkg/R/vectorfit.R
===================================================================
--- pkg/R/vectorfit.R 2008-05-21 08:53:29 UTC (rev 364)
+++ pkg/R/vectorfit.R 2008-05-22 08:21:30 UTC (rev 365)
@@ -2,6 +2,7 @@
function (X, P, permutations = 0, strata, choices = c(1, 2),
display = c("sites", "lc"), w = weights(X), ...)
{
+ weights.default <- function(object, ...) NULL
display <- match.arg(display)
w <- eval(w)
X <- scores(X, display = display, choices, ...)
Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog 2008-05-21 08:53:29 UTC (rev 364)
+++ pkg/inst/ChangeLog 2008-05-22 08:21:30 UTC (rev 365)
@@ -2,8 +2,26 @@
VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
-Version 1.14-0 (opened May 14, 2008)
+Version 1.14-1 (opened May 22, 2008)
+ * weights failed in several ordination utilities, because
+ weights.default in R 2.7.0 (stats) could not cope with objects
+ that do not have weights. R 2.6.2 still returned NULL for those
+ objects, but now weights.default gives an error. As a workaround
+ several vegan functions define internally
+ weights.default <- function(object, ...) NULL
+ to get back the old behaviour. Concerns orglspider, ordicluster,
+ ordispider, ordiellipse, ordisurf, factorfit, vectorfit.
+
+ * inertcomp and intersetcor only work with objects inheriting from
+ "cca", but they did not check that the object was of the correct
+ type and so could end up with calling weights.default or give
+ obscure error messages.
+
+Version 1.14-0 (closed May 21, 2008)
+
+ * The base of the release version 1.13-0.
+
Version 1.12-15 (closed May 14, 2008)
* closed the revision and made it as the base of release branch
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