[Vegan-commits] r761 - in branches/1.15: R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Mar 26 10:53:00 CET 2009
Author: jarioksa
Date: 2009-03-26 10:52:59 +0100 (Thu, 26 Mar 2009)
New Revision: 761
Modified:
branches/1.15/R/metaMDSdist.R
branches/1.15/R/points.procrustes.R
branches/1.15/inst/ChangeLog
branches/1.15/man/procrustes.Rd
Log:
merged r689 (add text.procrustes) and r674 (metaMDSdist behavious when set noshare=0)
Modified: branches/1.15/R/metaMDSdist.R
===================================================================
--- branches/1.15/R/metaMDSdist.R 2009-03-26 08:55:54 UTC (rev 760)
+++ branches/1.15/R/metaMDSdist.R 2009-03-26 09:52:59 UTC (rev 761)
@@ -37,7 +37,7 @@
}
}
maxdis <- max(dis)
- if (sum(tmp <- no.shared(comm))/length(dis) > noshare && noshare > 0) {
+ if (noshare > 0 && sum(tmp <- no.shared(comm))/length(dis) > noshare) {
if (trace)
cat("Using step-across dissimilarities:\n")
rn <- range(dis[tmp])
@@ -46,9 +46,9 @@
" stepacross may be meaningless: consider argument 'noshare=0'")
is.na(dis) <- tmp
dis <- stepacross(dis, trace = trace, toolong=0, ...)
+ if (length(unique(distconnected(tmp, trace = trace > 1))) > 1)
+ warning("Data are disconnected, results may be meaningless")
}
- if (length(unique(distconnected(tmp, trace = trace > 1))) > 1)
- warning("Data are disconnected, results may be meaningless")
attr(dis, "maxdis") <- maxdis
attr(dis, "commname") <- commname
attr(dis, "function") <- distname
Modified: branches/1.15/R/points.procrustes.R
===================================================================
--- branches/1.15/R/points.procrustes.R 2009-03-26 08:55:54 UTC (rev 760)
+++ branches/1.15/R/points.procrustes.R 2009-03-26 09:52:59 UTC (rev 761)
@@ -1,4 +1,4 @@
-"points.procrustes" <-
+`points.procrustes` <-
function(x, display = c("target","rotated"), ...)
{
display <- match.arg(display)
@@ -6,3 +6,14 @@
points(x, ...)
invisible()
}
+
+`text.procrustes` <-
+ function(x, display = c("target","rotated"), labels, ...)
+{
+ display <- match.arg(display)
+ x <- if (display == "target") x$X else x$Yrot
+ if (missing(labels))
+ labels <- rownames(x)
+ text(x, labels = labels, ...)
+ invisible()
+}
Modified: branches/1.15/inst/ChangeLog
===================================================================
--- branches/1.15/inst/ChangeLog 2009-03-26 08:55:54 UTC (rev 760)
+++ branches/1.15/inst/ChangeLog 2009-03-26 09:52:59 UTC (rev 761)
@@ -11,6 +11,8 @@
open-ended dissimilarities (Euclidean, Manhattan etc.).
* merged r728: oecosimu.Rd example knows "statistic" argument.
+
+ * merged r689: added text.procrustes.
* merged r683 & r690: anova.cca(..., by = "margin") gained
argument "cutoff = 1", and doc expanded.
@@ -19,6 +21,9 @@
* merged r678: anovacca.bymargin was not setting RNG properly for
the second term.
+
+ * merged r674: metaMDSdist does not evaluate no.shared if set
+ noshared=0.
* merged r673: vegdist doc fixes for Horn-Morisita equation.
Modified: branches/1.15/man/procrustes.Rd
===================================================================
--- branches/1.15/man/procrustes.Rd 2009-03-26 08:55:54 UTC (rev 760)
+++ branches/1.15/man/procrustes.Rd 2009-03-26 09:52:59 UTC (rev 761)
@@ -5,6 +5,7 @@
\alias{print.summary.procrustes}
\alias{plot.procrustes}
\alias{points.procrustes}
+\alias{text.procrustes}
\alias{lines.procrustes}
\alias{residuals.procrustes}
\alias{fitted.procrustes}
@@ -23,6 +24,7 @@
\method{plot}{procrustes}(x, kind=1, choices=c(1,2), xlab, ylab, main,
ar.col = "blue", len=0.05, ...)
\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{residuals}{procrustes}(object, ...)
\method{fitted}{procrustes}(object, truemean = TRUE, ...)
@@ -61,6 +63,8 @@
specified strata.}
\item{ar.col}{Arrow colour.}
\item{len}{Width of the arrow head.}
+ \item{labels}{Character vector of text labels. Rownames of the result
+ object are used as default.}
\item{...}{Other parameters passed to functions. In \code{procrustes}
and \code{protest} parameters are passed to \code{\link{scores}}, in
graphical functions to underlying graphical functions.}
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