[Vegan-commits] r881 - in pkg/vegan: R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Jun 28 15:23:20 CEST 2009
Author: jarioksa
Date: 2009-06-28 15:23:20 +0200 (Sun, 28 Jun 2009)
New Revision: 881
Modified:
pkg/vegan/R/biplot.rda.R
pkg/vegan/R/ordilabel.R
pkg/vegan/R/ordilattice.getEnvfit.R
pkg/vegan/R/ordiplot3d.R
pkg/vegan/R/ordixyplot.R
pkg/vegan/R/plot.spantree.R
pkg/vegan/R/points.cca.R
pkg/vegan/R/summary.cca.R
pkg/vegan/R/text.cca.R
pkg/vegan/inst/ChangeLog
pkg/vegan/man/biplot.rda.Rd
Log:
pass args of scores (like 'const' in scores.rda) to other functions, and clean output in summary.cca
Modified: pkg/vegan/R/biplot.rda.R
===================================================================
--- pkg/vegan/R/biplot.rda.R 2009-06-28 09:52:11 UTC (rev 880)
+++ pkg/vegan/R/biplot.rda.R 2009-06-28 13:23:20 UTC (rev 881)
@@ -5,7 +5,7 @@
biplot.rda <- function(x, choices = c(1, 2), scaling = 2,
display = c("sites", "species"),
- type, xlim, ylim, col = c(1,2), ...) {
+ type, xlim, ylim, col = c(1,2), const, ...) {
if(!inherits(x, "rda"))
stop("'biplot.rda' is only for objects of class 'rda'")
if(!is.null(x$CCA))
@@ -15,7 +15,7 @@
if (length(col) == 1)
col <- c(col,col)
g <- scores(x, choices = choices, display = display,
- scaling = scaling)
+ scaling = scaling, const)
if (!is.list(g)) {
g <- list(default = g)
names(g) <- display
Modified: pkg/vegan/R/ordilabel.R
===================================================================
--- pkg/vegan/R/ordilabel.R 2009-06-28 09:52:11 UTC (rev 880)
+++ pkg/vegan/R/ordilabel.R 2009-06-28 13:23:20 UTC (rev 881)
@@ -2,7 +2,9 @@
function(x, display, labels, choices = c(1,2), priority,
cex = 0.8, fill = "white", border = NULL, ...)
{
- x <- scores(x, display = display, choices = choices, ...)
+ if (missing(display))
+ display <- "sites"
+ x <- scores(x, choices = choices, display = display, ...)
if (missing(labels))
labels <- rownames(x)
if (!missing(priority)) {
Modified: pkg/vegan/R/ordilattice.getEnvfit.R
===================================================================
--- pkg/vegan/R/ordilattice.getEnvfit.R 2009-06-28 09:52:11 UTC (rev 880)
+++ pkg/vegan/R/ordilattice.getEnvfit.R 2009-06-28 13:23:20 UTC (rev 881)
@@ -3,8 +3,8 @@
{
if (!missing(envfit) && !is.null(envfit))
object <- envfit
- bp <- scores(object, display = "bp", choices = choices)
- cn <- scores(object, display = "cn", choices = choices)
+ bp <- scores(object, display = "bp", choices = choices, ...)
+ cn <- scores(object, display = "cn", choices = choices, ...)
bp <- bp[!(rownames(bp) %in% rownames(cn)),, drop=FALSE]
left <- as.character(formula[[2]])
right <- formula[[3]]
Modified: pkg/vegan/R/ordiplot3d.R
===================================================================
--- pkg/vegan/R/ordiplot3d.R 2009-06-28 09:52:11 UTC (rev 880)
+++ pkg/vegan/R/ordiplot3d.R 2009-06-28 13:23:20 UTC (rev 881)
@@ -3,12 +3,14 @@
arr.len = 0.1, arr.col = 4, envfit, xlab, ylab, zlab, ...)
{
require(scatterplot3d) || stop("Requires package 'scatterplot3d'")
- x <- scores(object, display = display, choices = choices)
+ local
+ x <- scores(object, display = display, choices = choices, ...)
if (missing(xlab)) xlab <- colnames(x)[1]
if (missing(ylab)) ylab <- colnames(x)[2]
if (missing(zlab)) zlab <- colnames(x)[3]
- pl <- scatterplot3d(x[, 1], x[, 2], x[, 3],
- xlab = xlab, ylab = ylab, zlab = zlab, ...)
+ pl <- ordiArgAbsorber(x[, 1], x[, 2], x[, 3],
+ xlab = xlab, ylab = ylab, zlab = zlab,
+ FUN = "scatterplot3d", ...)
pl$points3d(range(x[, 1]), c(0, 0), c(0, 0), type = "l",
col = ax.col)
pl$points3d(c(0, 0), range(x[, 2]), c(0, 0), type = "l",
@@ -18,8 +20,8 @@
if (!missing(envfit) || !is.null(object$CCA)) {
if (!missing(envfit))
object <- envfit
- bp <- scores(object, dis = "bp", choices = choices)
- cn <- scores(object, dis = "cn", choices = choices)
+ bp <- scores(object, dis = "bp", choices = choices, ...)
+ cn <- scores(object, dis = "cn", choices = choices, ...)
if (!is.null(cn) && !any(is.na(cn))) {
bp <- bp[!(rownames(bp) %in% rownames(cn)), , drop = FALSE]
cn.xyz <- pl$xyz.convert(cn)
Modified: pkg/vegan/R/ordixyplot.R
===================================================================
--- pkg/vegan/R/ordixyplot.R 2009-06-28 09:52:11 UTC (rev 880)
+++ pkg/vegan/R/ordixyplot.R 2009-06-28 13:23:20 UTC (rev 881)
@@ -4,8 +4,6 @@
type = c("p", "biplot"), ...)
{
localXyplot <- function(..., shrink, origin, scaling) xyplot(...)
- localOrdilattice.getEnvfit <-
- function(..., shrink, origin, scaling) ordilattice.getEnvfit(...)
require(lattice) || stop("requires package 'lattice'")
p <- as.data.frame(scores(x, display = display, choices = choices, ...))
if (!is.null(data))
@@ -17,7 +15,7 @@
if ("biplot" %in% type && (!is.null(x$CCA) || !missing(envfit))) {
if (missing(envfit))
envfit <- NULL
- env <- localOrdilattice.getEnvfit(formula, x, envfit, choices, ...)
+ env <- ordilattice.getEnvfit(formula, x, envfit, choices, ...)
if (!is.null(env$arrows)) {
mul <- apply(p[,colnames(env$arrows)], 2, range)/apply(env$arrows, 2, range)
mul <- min(mul[is.finite(mul) & mul > 0])
Modified: pkg/vegan/R/plot.spantree.R
===================================================================
--- pkg/vegan/R/plot.spantree.R 2009-06-28 09:52:11 UTC (rev 880)
+++ pkg/vegan/R/plot.spantree.R 2009-06-28 13:23:20 UTC (rev 881)
@@ -19,15 +19,16 @@
y[dup, ] <- y[dup,] + runif(2*sum(dup), -0.01, 0.01)
ord <- FUN(d, y)
}
- ord <- scores(ord, display = "sites")
- plot(ord, asp = 1, type = "n", ...)
+ ord <- scores(ord, display = "sites", ...)
+ ordiArgAbsorber(ord, asp = 1, type = "n", FUN = "plot", ...)
lines(x, ord)
if (type == "p" || type == "b")
- points(ord, cex = cex, ...)
+ ordiArgAbsorber(ord, cex = cex, FUN = "points", ...)
else if (type == "t") {
if (missing(labels))
labels <- x$labels
- ordilabel(ord, display = "sites", labels = labels, cex = cex, ...)
+ x <- scores(ord, display = "sites", ...)
+ ordiArgAbsorber(x, labels = labels, cex = cex, FUN = "ordilabel", ...)
}
ord <- list(sites = ord)
class(ord) <- "ordiplot"
Modified: pkg/vegan/R/points.cca.R
===================================================================
--- pkg/vegan/R/points.cca.R 2009-06-28 09:52:11 UTC (rev 880)
+++ pkg/vegan/R/points.cca.R 2009-06-28 13:23:20 UTC (rev 881)
@@ -1,17 +1,19 @@
`points.cca` <-
function (x, display = "sites", choices = c(1, 2), scaling = 2,
- arrow.mul, head.arrow = 0.05, select, ...)
+ arrow.mul, head.arrow = 0.05, select, const, ...)
{
formals(arrows) <- c(formals(arrows), alist(... = ))
if (length(display) > 1)
stop("Only one `display' item can be added in one command.")
- pts <- scores(x, choices = choices, display = display, scaling = scaling)
+ pts <- scores(x, choices = choices, display = display, scaling = scaling,
+ const)
if (!missing(select))
pts <- pts[select, , drop = FALSE]
if (display == "cn") {
cnam <- rownames(pts)
points(pts, ...)
- pts <- scores(x, choices = choices, display = "bp", scaling = scaling)
+ pts <- scores(x, choices = choices, display = "bp", scaling = scaling,
+ const)
bnam <- rownames(pts)
pts <- pts[!(bnam %in% cnam), , drop = FALSE]
if (nrow(pts) == 0)
Modified: pkg/vegan/R/summary.cca.R
===================================================================
--- pkg/vegan/R/summary.cca.R 2009-06-28 09:52:11 UTC (rev 880)
+++ pkg/vegan/R/summary.cca.R 2009-06-28 13:23:20 UTC (rev 881)
@@ -18,13 +18,20 @@
summ <- list(summ)
names(summ) <- nms[display]
}
+ if (length(display) > 0) {
+ for (i in 1:length(summ)) {
+ rownames(summ[[i]]) <- rownames(summ[[i]], do.NULL = FALSE,
+ prefix = substr(names(summ)[i], 1, 3))
+ }
+ }
summ$call <- object$call
summ$tot.chi <- object$tot.chi
summ$partial.chi <- object$pCCA$tot.chi
summ$constr.chi <- object$CCA$tot.chi
summ$unconst.chi <- object$CA$tot.chi
summ$cont <- summary(eigenvals(object))
- summ$concont <- summary(eigenvals(object, constrained = TRUE))
+ if (!is.null(object$CCA))
+ summ$concont <- summary(eigenvals(object, constrained = TRUE))
summ$ev.head <- c(summ$ev.con, summ$ev.uncon)[1:axes]
summ$scaling <- scaling
summ$digits <- digits
Modified: pkg/vegan/R/text.cca.R
===================================================================
--- pkg/vegan/R/text.cca.R 2009-06-28 09:52:11 UTC (rev 880)
+++ pkg/vegan/R/text.cca.R 2009-06-28 13:23:20 UTC (rev 881)
@@ -1,11 +1,12 @@
`text.cca` <-
function (x, display = "sites", labels, choices = c(1, 2), scaling = 2,
- arrow.mul, head.arrow = 0.05, select, ...)
+ arrow.mul, head.arrow = 0.05, select, const, ...)
{
formals(arrows) <- c(formals(arrows), alist(... = ))
if (length(display) > 1)
stop("Only one `display' item can be added in one command.")
- pts <- scores(x, choices = choices, display = display, scaling = scaling)
+ pts <- scores(x, choices = choices, display = display, scaling = scaling,
+ const)
if (!missing(labels))
rownames(pts) <- labels
if (!missing(select))
@@ -13,7 +14,8 @@
if (display == "cn") {
cnam <- rownames(pts)
text(pts, labels = cnam, ...)
- pts <- scores(x, choices = choices, display = "bp", scaling = scaling)
+ pts <- scores(x, choices = choices, display = "bp", scaling = scaling,
+ const)
bnam <- rownames(pts)
pts <- pts[!(bnam %in% cnam), , drop = FALSE]
if (nrow(pts) == 0)
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2009-06-28 09:52:11 UTC (rev 880)
+++ pkg/vegan/inst/ChangeLog 2009-06-28 13:23:20 UTC (rev 881)
@@ -11,6 +11,24 @@
communities.
* betadisper: fix bug in removal of (effectively) zero Eigenvalues.
+
+ * summary.cca: takes care that all scores have rownames --
+ head/tail fail without names. No ugly printing for constrained
+ eigenvalues when these do not exist in unconstrained models.
+
+ * biplot.rda: honour args to scores ('scaling', 'const').
+
+ * points/text for cca: accept 'const' argument for rda scores.
+
+ * ordilabel: no superfluous warnigns when args ('scaling',
+ 'const') are given to scores.
+
+ * ordiplot3d: honour args to scores ('scaling', 'const') and
+ without warnings.
+
+ * ordixyplot: honour ags to scores ('scaling', 'const').
+
+ * spantree: plot honours args to scores ('scaling', 'const').
Version 1.16-19 (closed June 17, 2009)
Modified: pkg/vegan/man/biplot.rda.Rd
===================================================================
--- pkg/vegan/man/biplot.rda.Rd 2009-06-28 09:52:11 UTC (rev 880)
+++ pkg/vegan/man/biplot.rda.Rd 2009-06-28 13:23:20 UTC (rev 881)
@@ -7,7 +7,8 @@
}
\usage{
\method{biplot}{rda}(x, choices = c(1, 2), scaling = 2,
- display = c("sites", "species"), type, xlim, ylim, col = c(1,2), ...)
+ display = c("sites", "species"), type, xlim, ylim, col = c(1,2),
+ const, ...)
}
\arguments{
@@ -34,6 +35,7 @@
\item{xlim, ylim}{the x and y limits (min, max) of the plot.}
\item{col}{Colours used for sites and species (in this order). If only
one colour is given, it is used for both.}
+ \item{dots}{General scaling constant for \code{\link{scores.rda}}.}
\item{\dots}{Other parameters for plotting functions.}
}
\details{
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