[Vegan-commits] r2595 - in branches/2.0: . R inst inst/doc man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Aug 26 09:29:17 CEST 2013
Author: jarioksa
Date: 2013-08-26 09:29:16 +0200 (Mon, 26 Aug 2013)
New Revision: 2595
Modified:
branches/2.0/DESCRIPTION
branches/2.0/NAMESPACE
branches/2.0/R/density.anosim.R
branches/2.0/R/densityplot.oecosimu.R
branches/2.0/R/ordicloud.R
branches/2.0/R/ordiresids.R
branches/2.0/R/ordisplom.R
branches/2.0/R/ordixyplot.R
branches/2.0/R/plot.poolaccum.R
branches/2.0/R/plot.radfit.frame.R
branches/2.0/R/plot.renyi.R
branches/2.0/R/plot.renyiaccum.R
branches/2.0/R/prepanel.ordi3d.R
branches/2.0/R/radlattice.R
branches/2.0/inst/ChangeLog
branches/2.0/inst/doc/diversity-vegan.Rnw
branches/2.0/man/adonis.Rd
branches/2.0/man/density.adonis.Rd
branches/2.0/man/oecosimu.Rd
Log:
vegan 2.0-9 depends on lattice (merge 2584,6 + edit NAMESPACE)
Modified: branches/2.0/DESCRIPTION
===================================================================
--- branches/2.0/DESCRIPTION 2013-08-26 07:11:27 UTC (rev 2594)
+++ branches/2.0/DESCRIPTION 2013-08-26 07:29:16 UTC (rev 2595)
@@ -1,14 +1,13 @@
Package: vegan
Title: Community Ecology Package
Version: 2.0-9
-Date: July 10, 2013
+Date: August 26, 2013
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
Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>
-Depends: permute
-Imports: lattice
-Suggests: MASS, mgcv, lattice, cluster, scatterplot3d, rgl, tcltk
+Depends: lattice, permute
+Suggests: MASS, mgcv, cluster, scatterplot3d, rgl, tcltk
Description: Ordination methods, diversity analysis and other
functions for community and vegetation ecologists.
License: GPL-2
Modified: branches/2.0/NAMESPACE
===================================================================
--- branches/2.0/NAMESPACE 2013-08-26 07:11:27 UTC (rev 2594)
+++ branches/2.0/NAMESPACE 2013-08-26 07:29:16 UTC (rev 2595)
@@ -62,8 +62,9 @@
## Registration of S3 methods
import(stats)
import(graphics)
+import(lattice)
+import(permute)
importFrom(utils, head, tail)
-importFrom(lattice, densityplot)
importFrom(tools, Rd2txt, startDynamicHelp)
## nobs only exists in R 2.13.0 -- import from permute with older R
if (getRversion() < "2.13.0") {
Modified: branches/2.0/R/density.anosim.R
===================================================================
--- branches/2.0/R/density.anosim.R 2013-08-26 07:11:27 UTC (rev 2594)
+++ branches/2.0/R/density.anosim.R 2013-08-26 07:29:16 UTC (rev 2595)
@@ -39,7 +39,6 @@
`densityplot.adonis` <-
function(x, data, xlab = "Null", ...)
{
- require(lattice) || stop("requires package 'lattice'")
obs <- x$aov.tab$F.Model
obs <- obs[!is.na(obs)]
sim <- rbind(obs, x$f.perms)
Modified: branches/2.0/R/densityplot.oecosimu.R
===================================================================
--- branches/2.0/R/densityplot.oecosimu.R 2013-08-26 07:11:27 UTC (rev 2594)
+++ branches/2.0/R/densityplot.oecosimu.R 2013-08-26 07:29:16 UTC (rev 2595)
@@ -1,7 +1,6 @@
`densityplot.oecosimu` <-
function(x, data, xlab = "Simulated", ...)
{
- require(lattice) || stop("requires package 'lattice'")
obs <- x$oecosimu$statistic
sim <- rbind(obs, t(x$oecosimu$simulated))
nm <- names(obs)[col(sim)]
Modified: branches/2.0/R/ordicloud.R
===================================================================
--- branches/2.0/R/ordicloud.R 2013-08-26 07:11:27 UTC (rev 2594)
+++ branches/2.0/R/ordicloud.R 2013-08-26 07:29:16 UTC (rev 2595)
@@ -4,7 +4,6 @@
prepanel = "prepanel.ordi3d", ...)
{
localCloud <- function(..., shrink, origin, scaling) cloud(...)
- require(lattice) || stop("requires package 'lattice'")
x <- as.data.frame(scores(x, display = display, choices = choices, ...))
if (!is.null(data))
x <- cbind(x, data)
Modified: branches/2.0/R/ordiresids.R
===================================================================
--- branches/2.0/R/ordiresids.R 2013-08-26 07:11:27 UTC (rev 2594)
+++ branches/2.0/R/ordiresids.R 2013-08-26 07:29:16 UTC (rev 2595)
@@ -2,7 +2,6 @@
function(x, kind = c("residuals", "scale", "qqmath"), residuals = "working",
type = c("p", "smooth", "g"), formula, ...)
{
- require(lattice) || stop("requires package lattice")
kind <- match.arg(kind)
if (!inherits(x, "cca") || is.null(x$CCA) || x$CCA$rank == 0)
stop("function is only available for constrained ordination")
Modified: branches/2.0/R/ordisplom.R
===================================================================
--- branches/2.0/R/ordisplom.R 2013-08-26 07:11:27 UTC (rev 2594)
+++ branches/2.0/R/ordisplom.R 2013-08-26 07:29:16 UTC (rev 2595)
@@ -3,7 +3,6 @@
panel = "panel.ordi", type = "p", ...)
{
localSplom <- function(..., shrink, origin, scaling) splom(...)
- require(lattice) || stop("requires package 'lattice'")
x <- as.data.frame(scores(x, display = display, choices = choices, ...))
if (is.null(data))
data <- x
Modified: branches/2.0/R/ordixyplot.R
===================================================================
--- branches/2.0/R/ordixyplot.R 2013-08-26 07:11:27 UTC (rev 2594)
+++ branches/2.0/R/ordixyplot.R 2013-08-26 07:29:16 UTC (rev 2595)
@@ -4,7 +4,6 @@
type = c("p", "biplot"), ...)
{
localXyplot <- function(..., shrink, origin, scaling) xyplot(...)
- require(lattice) || stop("requires package 'lattice'")
p <- as.data.frame(scores(x, display = display, choices = choices, ...))
if (!is.null(data))
p <- cbind(p, data)
Modified: branches/2.0/R/plot.poolaccum.R
===================================================================
--- branches/2.0/R/plot.poolaccum.R 2013-08-26 07:11:27 UTC (rev 2594)
+++ branches/2.0/R/plot.poolaccum.R 2013-08-26 07:29:16 UTC (rev 2595)
@@ -1,7 +1,6 @@
`plot.poolaccum` <-
function(x, alpha = 0.05, type = c("l","g"), ...)
{
- require(lattice) || stop("Needs package 'lattice'")
m <- summary(x, alpha = alpha, ...)
n <- nrow(m[[1]])
Size <- as.vector(sapply(m, function(x) c(x[,1], x[,1], rev(x[,1]))))
Modified: branches/2.0/R/plot.radfit.frame.R
===================================================================
--- branches/2.0/R/plot.radfit.frame.R 2013-08-26 07:11:27 UTC (rev 2594)
+++ branches/2.0/R/plot.radfit.frame.R 2013-08-26 07:29:16 UTC (rev 2595)
@@ -2,7 +2,6 @@
function (x, order.by, BIC = FALSE, model, legend = TRUE, as.table = TRUE,
...)
{
- require(lattice)
modnam <- names(x[[1]]$models)
if (!missing(model))
pick <- pmatch(model, modnam, nomatch = FALSE)
Modified: branches/2.0/R/plot.renyi.R
===================================================================
--- branches/2.0/R/plot.renyi.R 2013-08-26 07:11:27 UTC (rev 2594)
+++ branches/2.0/R/plot.renyi.R 2013-08-26 07:29:16 UTC (rev 2595)
@@ -1,7 +1,6 @@
`plot.renyi` <-
function(x, ...)
{
- require(lattice) || stop("requires lattice")
if (inherits(x, "data.frame")) {
plt <- factor(rep(rownames(x), ncol(x)), levels=rownames(x))
alp <- factor(rep(colnames(x), each=nrow(x)), levels=colnames(x))
Modified: branches/2.0/R/plot.renyiaccum.R
===================================================================
--- branches/2.0/R/plot.renyiaccum.R 2013-08-26 07:11:27 UTC (rev 2594)
+++ branches/2.0/R/plot.renyiaccum.R 2013-08-26 07:29:16 UTC (rev 2595)
@@ -1,7 +1,6 @@
`plot.renyiaccum` <-
function (x, what=c("mean", "Qnt 0.025", "Qnt 0.975"), type = "l", ...)
{
- require(lattice) || stop("requires package lattice")
if (any(what %in% colnames(x[,1,])))
x <- x[,,what]
dm <- dim(x)
Modified: branches/2.0/R/prepanel.ordi3d.R
===================================================================
--- branches/2.0/R/prepanel.ordi3d.R 2013-08-26 07:11:27 UTC (rev 2594)
+++ branches/2.0/R/prepanel.ordi3d.R 2013-08-26 07:29:16 UTC (rev 2595)
@@ -2,5 +2,5 @@
function(xlim = xlim, ylim = ylim, zlim = zlim, aspect = c(1,1), ...)
{
aspect = c(diff(ylim)/diff(xlim), diff(zlim)/diff(xlim))
- lattice:::prepanel.default.cloud(xlim = xlim, ylim = ylim, zlim = zlim, aspect = aspect, ...)
+ prepanel.default.cloud(xlim = xlim, ylim = ylim, zlim = zlim, aspect = aspect, ...)
}
Modified: branches/2.0/R/radlattice.R
===================================================================
--- branches/2.0/R/radlattice.R 2013-08-26 07:11:27 UTC (rev 2594)
+++ branches/2.0/R/radlattice.R 2013-08-26 07:29:16 UTC (rev 2595)
@@ -3,7 +3,6 @@
{
if (!inherits(x, "radfit"))
stop("function only works with 'radfit' results for single site")
- require(lattice) || stop("requires package 'lattice'")
y <- x$y
fv <- unlist(fitted(x))
mods <- names(x$models)
Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog 2013-08-26 07:11:27 UTC (rev 2594)
+++ branches/2.0/inst/ChangeLog 2013-08-26 07:29:16 UTC (rev 2595)
@@ -6,6 +6,7 @@
* merge 2590: typos.
* merge r2588: remove unneeded utils::: in vegandocs (some remain).
+ * merge 2584,6: vegan Depends on lattice, avoid lattice:::
* merge r2583,7: remove cross-references to disappear in R-3.0-2.
* merge r2580,1: literature refs in specaccum.Rd and
betadisper.Rd.
Modified: branches/2.0/inst/doc/diversity-vegan.Rnw
===================================================================
--- branches/2.0/inst/doc/diversity-vegan.Rnw 2013-08-26 07:11:27 UTC (rev 2594)
+++ branches/2.0/inst/doc/diversity-vegan.Rnw 2013-08-26 07:29:16 UTC (rev 2595)
@@ -127,9 +127,6 @@
diversities are higher than in another site. We can inspect this
graphically using the standard \code{plot} function for the
\code{renyi} result (Fig. \ref{fig:renyi}).
-<<echo=false,results=hide>>=
-require(lattice, quietly=TRUE)
-@
\begin{SCfigure}
<<fig=true,echo=false>>=
print(plot(R))
Modified: branches/2.0/man/adonis.Rd
===================================================================
--- branches/2.0/man/adonis.Rd 2013-08-26 07:11:27 UTC (rev 2594)
+++ branches/2.0/man/adonis.Rd 2013-08-26 07:29:16 UTC (rev 2595)
@@ -199,7 +199,6 @@
Agropyron <- with(dat, as.numeric(field) + as.numeric(NO3)+2) +rnorm(12)/2
Schizachyrium <- with(dat, as.numeric(field) - as.numeric(NO3)+2) +rnorm(12)/2
total <- Agropyron + Schizachyrium
-library(lattice)
dotplot(total ~ NO3, dat, jitter.x=TRUE, groups=field,
type=c('p','a'), xlab="NO3", auto.key=list(columns=3, lines=TRUE) )
Modified: branches/2.0/man/density.adonis.Rd
===================================================================
--- branches/2.0/man/density.adonis.Rd 2013-08-26 07:11:27 UTC (rev 2594)
+++ branches/2.0/man/density.adonis.Rd 2013-08-26 07:29:16 UTC (rev 2595)
@@ -106,7 +106,6 @@
data(dune.env)
mod <- adonis(dune ~ Management, data = dune.env)
plot(density(mod))
-library(lattice)
mod <- adonis(dune ~ Management * Moisture, dune.env)
densityplot(mod)
}
Modified: branches/2.0/man/oecosimu.Rd
===================================================================
--- branches/2.0/man/oecosimu.Rd 2013-08-26 07:11:27 UTC (rev 2594)
+++ branches/2.0/man/oecosimu.Rd 2013-08-26 07:29:16 UTC (rev 2595)
@@ -261,8 +261,7 @@
plot(as.ts(out))
lag.plot(as.ts(out))
acf(as.ts(out))
-## Density plot: needs lattice
-require(lattice)
+## Density plot
densityplot(out, as.table = TRUE)
## Use quantitative null models to compare
## mean Bray-Curtis dissimilarities
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