[Vegan-commits] r1554 - in branches/1.17: R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Mar 26 16:52:37 CET 2011
Author: jarioksa
Date: 2011-03-26 16:52:36 +0100 (Sat, 26 Mar 2011)
New Revision: 1554
Modified:
branches/1.17/R/anova.ccabyaxis.R
branches/1.17/R/ordilabel.R
branches/1.17/inst/ChangeLog
branches/1.17/inst/NEWS
branches/1.17/man/ordilabel.Rd
Log:
merge r 1550:1552: ordilabel gained 'xpd' and anova.cca(..., by = 'axis') fix
Modified: branches/1.17/R/anova.ccabyaxis.R
===================================================================
--- branches/1.17/R/anova.ccabyaxis.R 2011-03-23 17:51:28 UTC (rev 1553)
+++ branches/1.17/R/anova.ccabyaxis.R 2011-03-26 15:52:36 UTC (rev 1554)
@@ -14,11 +14,26 @@
} else {
u <- object$CCA$u
}
+ ## Get conditions
+ if (!is.null(object$pCCA)) {
+ CondMat <- qr.X(object$pCCA$QR)
+ ## deweight if CCA
+ if (!inherits(object, "rda"))
+ CondMat <- sweep(CondMat, 1, sqrt(object$rowsum), "/")
+ }
+ else
+ CondMat <- NULL
## pad with NA rows if there is a subset
if (!is.null(object$subset)) {
lc <- matrix(NA, nrow=length(object$subset),
- ncol = ncol(u))
+ ncol = NCOL(u))
lc[object$subset,] <- u
+ if (!is.null(CondMat)) {
+ tmp <- matrix(NA, nrow=length(object$subset),
+ ncol = NCOL(CondMat))
+ tmp[object$subset,] <- CondMat
+ CondMat <- tmp
+ }
object$call$subset <- object$subset
} else {
lc <- u
@@ -34,6 +49,8 @@
environment(object$terms) <- environment()
fla <- paste(". ~ ", axnam[1], "+ Condition(",
paste(axnam[-1], collapse="+"),")")
+ if (!is.null(CondMat))
+ fla <- paste(fla, " + Condition(CondMat)")
fla <- update(formula(object), fla)
sol <- anova(update(object, fla, data=lc), ...)
out[c(1, rnk + 1), ] <- sol
@@ -48,11 +65,12 @@
for (.ITRM in 2:rnk) {
fla <- paste(".~", axnam[.ITRM], "+Condition(",
paste(axnam[-(.ITRM)], collapse="+"),")")
+ if (!is.null(CondMat))
+ fla <- paste(fla, "+ Condition(CondMat)")
fla <- update(formula(object), fla)
sol <- update(object, fla, data = lc)
assign(".Random.seed", seed, envir = .GlobalEnv)
- out[.ITRM, ] <- as.matrix(anova(sol, ...))[1,
- ]
+ out[.ITRM, ] <- as.matrix(anova(sol, ...))[1,]
if (out[.ITRM, "N.Perm"] > bigperm) {
bigperm <- out[.ITRM, "N.Perm"]
bigseed <- get(".Random.seed", envir = .GlobalEnv,
Modified: branches/1.17/R/ordilabel.R
===================================================================
--- branches/1.17/R/ordilabel.R 2011-03-23 17:51:28 UTC (rev 1553)
+++ branches/1.17/R/ordilabel.R 2011-03-26 15:52:36 UTC (rev 1554)
@@ -1,7 +1,7 @@
`ordilabel` <-
function(x, display, labels, choices = c(1,2), priority,
cex = 0.8, fill = "white", border = NULL, col = NULL,
- ...)
+ xpd = TRUE, ...)
{
if (missing(display))
display <- "sites"
@@ -24,8 +24,9 @@
col <- par("fg")
for (i in 1:nrow(x)) {
polygon(x[i,1] + c(-1,1,1,-1)*w[i], x[i,2] + c(-1,-1,1,1)*h[i],
- col = fill, border = border)
- text(x[i,1], x[i,2], labels = labels[i], cex = cex, col = col, ...)
+ col = fill, border = border, xpd = xpd)
+ text(x[i,1], x[i,2], labels = labels[i], cex = cex, col = col,
+ xpd = xpd, ...)
}
invisible(x)
}
Modified: branches/1.17/inst/ChangeLog
===================================================================
--- branches/1.17/inst/ChangeLog 2011-03-23 17:51:28 UTC (rev 1553)
+++ branches/1.17/inst/ChangeLog 2011-03-26 15:52:36 UTC (rev 1554)
@@ -4,13 +4,18 @@
Version 1.17-9 (opened March 9, 2011)
- * merged 1534: typo in vegdist.Rd.
-
+ * merged 1551,2: anova.cca(..., by = "axis") failed in partial
+ models.
+
+ * merged 1550: ordilabel gained arg 'xpd'.
+
* merged 1541,8: metaMDSiter got more flexible 'previous.tries.
* merged 1538,9, 1542,5: ordisurf gaine new arguments and got a
new plot method.
+ * merged 1534: typo in vegdist.Rd.
+
* merged r1533,7, 1544,7: metaMDSrotate works with > 2 dim.
* merged r1532: fix gettextf in d/r/rarefy.
Modified: branches/1.17/inst/NEWS
===================================================================
--- branches/1.17/inst/NEWS 2011-03-23 17:51:28 UTC (rev 1553)
+++ branches/1.17/inst/NEWS 2011-03-26 15:52:36 UTC (rev 1554)
@@ -5,8 +5,11 @@
CHANGES IN VEGAN 1.17-9
+ - anova of cca/rda/capscale results gave wrong results in partial
+ models. The bug was introduced in vegan 1.17-7.
+
- diversity and related functions rarefy, rrarefy and specnumber
- accept now a vector input. Earlier a single site had to be
+ accept now vector input. Earlier a single site had to be
analysed either as a one-row matrix or using non-default setting
MARGIN = 2.
@@ -26,6 +29,9 @@
of dimensions so that the first axis is parallel to a fitted
environmental vector. Earlier only two dimensions worked.
+ - ordilabel: gained argument 'xpd' that allows labels outside the
+ plot area. This allows labels above axes, for instance.
+
- ordisurf: gained several new arguments to control the gam
fitting. Also gained an argument to suppress plotting, and a new
plot method. The fitted model can be specified with a formula.
Modified: branches/1.17/man/ordilabel.Rd
===================================================================
--- branches/1.17/man/ordilabel.Rd 2011-03-23 17:51:28 UTC (rev 1553)
+++ branches/1.17/man/ordilabel.Rd 2011-03-26 15:52:36 UTC (rev 1554)
@@ -11,7 +11,7 @@
\usage{
ordilabel(x, display, labels, choices = c(1, 2), priority, cex = 0.8,
- fill = "white", border = NULL, col = NULL, ...)
+ fill = "white", border = NULL, col = NULL, xpd = TRUE, ...)
}
\arguments{
@@ -31,7 +31,9 @@
\item{border}{The colour and visibility of the border of the label as
defined in \code{\link{polygon}}).}
\item{col}{Text colour. Default \code{NULL} will give the value of
- \code{border} or \code{par("fg")} if \code{border} is \code{NULL}.}
+ \code{border} or \code{par("fg")} if \code{border} is \code{NULL}.}
+ \item{xpd}{Draw labels also outside the plot region (see
+ \code{\link{par}}).}
\item{\dots}{Other arguments (passed to \code{\link{text}}). }
}
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