[Vegan-commits] r2969 - in pkg/vegan: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Oct 7 10:22:03 CEST 2015
Author: jarioksa
Date: 2015-10-07 10:22:02 +0200 (Wed, 07 Oct 2015)
New Revision: 2969
Modified:
pkg/vegan/DESCRIPTION
pkg/vegan/R/lines.procrustes.R
pkg/vegan/R/ordiArgAbsorber.R
pkg/vegan/R/points.procrustes.R
pkg/vegan/man/procrustes.Rd
pkg/vegan/man/vegan-internal.Rd
Log:
Merge branch 'cran-2.3' into r-forge-svn-local
Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION 2015-09-24 08:40:35 UTC (rev 2968)
+++ pkg/vegan/DESCRIPTION 2015-10-07 08:22:02 UTC (rev 2969)
@@ -1,7 +1,7 @@
Package: vegan
Title: Community Ecology Package
-Version: 2.3-1
-Date: 2015-09-24
+Version: 2.3-2
+Date: 2015-09-25
Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre,
Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos,
M. Henry H. Stevens, Helene Wagner
Modified: pkg/vegan/R/lines.procrustes.R
===================================================================
--- pkg/vegan/R/lines.procrustes.R 2015-09-24 08:40:35 UTC (rev 2968)
+++ pkg/vegan/R/lines.procrustes.R 2015-10-07 08:22:02 UTC (rev 2969)
@@ -1,12 +1,17 @@
-"lines.procrustes" <-
- function(x, type=c("segments", "arrows"), choices=c(1,2), ...)
+`lines.procrustes` <-
+ function(x, type=c("segments", "arrows"), choices=c(1,2),
+ truemean = FALSE, ...)
{
type <- match.arg(type)
X <- x$X[,choices, drop=FALSE]
Y <- x$Yrot[, choices, drop=FALSE]
+ if (truemean) {
+ X <- sweep(X, 2, x$xmean[choices], "+")
+ Y <- sweep(Y, 2, x$xmean[choices], "+")
+ }
if (type == "segments")
- segments(X[,1], X[,2], Y[,1], Y[,2], ...)
+ ordiArgAbsorber(X[,1], X[,2], Y[,1], Y[,2], FUN = segments, ...)
else
- arrows(X[,1], X[,2], Y[,1], Y[,2], ...)
+ ordiArgAbsorber(X[,1], X[,2], Y[,1], Y[,2], FUN = arrows, ...)
invisible()
}
Modified: pkg/vegan/R/ordiArgAbsorber.R
===================================================================
--- pkg/vegan/R/ordiArgAbsorber.R 2015-09-24 08:40:35 UTC (rev 2968)
+++ pkg/vegan/R/ordiArgAbsorber.R 2015-10-07 08:22:02 UTC (rev 2969)
@@ -1,3 +1,3 @@
`ordiArgAbsorber` <- function(..., shrink, origin, scaling, triangular,
- display, choices, const, FUN)
+ display, choices, const, truemean, FUN)
match.fun(FUN)(...)
Modified: pkg/vegan/R/points.procrustes.R
===================================================================
--- pkg/vegan/R/points.procrustes.R 2015-09-24 08:40:35 UTC (rev 2968)
+++ pkg/vegan/R/points.procrustes.R 2015-10-07 08:22:02 UTC (rev 2969)
@@ -1,19 +1,27 @@
`points.procrustes` <-
- function(x, display = c("target","rotated"), ...)
+ function(x, display = c("target","rotated"), choices = c(1,2),
+ truemean = FALSE, ...)
{
display <- match.arg(display)
- x <- if (display == "target") x$X else x$Yrot
- points(x, ...)
+ X <- if (display == "target") x$X else x$Yrot
+ X <- X[, choices, drop = FALSE]
+ if (truemean)
+ X <- sweep(X, 2, x$xmean[choices], "+")
+ ordiArgAbsorber(X, FUN = points, ...)
invisible()
}
`text.procrustes` <-
- function(x, display = c("target","rotated"), labels, ...)
+ function(x, display = c("target","rotated"), choices = c(1,2),
+ labels, truemean = FALSE, ...)
{
display <- match.arg(display)
- x <- if (display == "target") x$X else x$Yrot
+ X <- if (display == "target") x$X else x$Yrot
+ X <- X[, choices, drop = FALSE]
+ if (truemean)
+ X <- sweep(X, 2, x$xmean[choices], "+")
if (missing(labels))
- labels <- rownames(x)
- text(x, labels = labels, ...)
+ labels <- rownames(X)
+ ordiArgAbsorber(X, labels = labels, FUN = text, ...)
invisible()
}
Modified: pkg/vegan/man/procrustes.Rd
===================================================================
--- pkg/vegan/man/procrustes.Rd 2015-09-24 08:40:35 UTC (rev 2968)
+++ pkg/vegan/man/procrustes.Rd 2015-10-07 08:22:02 UTC (rev 2969)
@@ -22,9 +22,12 @@
\method{plot}{procrustes}(x, kind=1, choices=c(1,2), to.target = TRUE,
type = "p", xlab, ylab, main, ar.col = "blue", len=0.05,
cex = 0.7, ...)
-\method{points}{procrustes}(x, display = c("target", "rotated"), ...)
-\method{text}{procrustes}(x, display = c("target", "rotated"), labels, ...)
-\method{lines}{procrustes}(x, type = c("segments", "arrows"), choices = c(1, 2), ...)
+\method{points}{procrustes}(x, display = c("target", "rotated"),
+ choices = c(1,2), truemean = FALSE, ...)
+\method{text}{procrustes}(x, display = c("target", "rotated"),
+ choices = c(1,2), labels, truemean = FALSE, ...)
+\method{lines}{procrustes}(x, type = c("segments", "arrows"),
+ choices = c(1, 2), truemean = FALSE, ...)
\method{residuals}{procrustes}(object, ...)
\method{fitted}{procrustes}(object, truemean = TRUE, ...)
\method{predict}{procrustes}(object, newdata, truemean = TRUE, ...)
@@ -61,7 +64,8 @@
target and rotated configuration.}
\item{truemean}{Use the original range of target matrix instead of
centring the fitted values. Function \code{plot.procrustes} needs
- \code{truemean = FALSE}.}
+ \code{truemean = FALSE}, and adding graphical items to the plots
+ from the original results may need \code{truemean = TRUE}.}
\item{newdata}{Matrix of coordinates to be rotated and translated to
the target.}
\item{permutations}{a list of control values for the permutations
Modified: pkg/vegan/man/vegan-internal.Rd
===================================================================
--- pkg/vegan/man/vegan-internal.Rd 2015-09-24 08:40:35 UTC (rev 2968)
+++ pkg/vegan/man/vegan-internal.Rd 2015-10-07 08:22:02 UTC (rev 2969)
@@ -27,7 +27,7 @@
ordiNAexclude(x, excluded)
ordiNApredict(omit, x)
ordiArgAbsorber(..., shrink, origin, scaling, triangular,
- display, choices, const, FUN)
+ display, choices, const, truemean, FUN)
centroids.cca(x, mf, wt)
getPermuteMatrix(perm, N, strata = NULL)
howHead(x, ...)
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