[Vegan-commits] r2586 - in pkg/vegan: . R inst inst/doc man

Mon Aug 19 10:50:29 CEST 2013

Author: jarioksa
Date: 2013-08-19 10:50:29 +0200 (Mon, 19 Aug 2013)
New Revision: 2586

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/R/density.anosim.R
   pkg/vegan/R/densityplot.oecosimu.R
   pkg/vegan/R/ordicloud.R
   pkg/vegan/R/ordiresids.R
   pkg/vegan/R/ordisplom.R
   pkg/vegan/R/ordixyplot.R
   pkg/vegan/R/plot.poolaccum.R
   pkg/vegan/R/plot.radfit.frame.R
   pkg/vegan/R/plot.renyi.R
   pkg/vegan/R/plot.renyiaccum.R
   pkg/vegan/R/radlattice.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/inst/doc/diversity-vegan.Rnw
   pkg/vegan/man/adonis.Rd
   pkg/vegan/man/density.adonis.Rd
   pkg/vegan/man/oecosimu.Rd
Log:
vegan depends on lattice and version up to 2.1-33

Modified: pkg/vegan/DESCRIPTION
===================================================================

--- pkg/vegan/DESCRIPTION	2013-08-19 07:45:39 UTC (rev 2585)
+++ pkg/vegan/DESCRIPTION	2013-08-19 08:50:29 UTC (rev 2586)
@@ -1,13 +1,12 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 2.1-32
-Date: July 10, 2013
+Version: 2.1-33
+Date: August 19, 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 (>= 0.7-4), R (>= 2.12.0)
-Imports: lattice
+Depends: permute (>= 0.7-4), lattice, R (>= 2.12.0)
 Suggests: MASS, mgcv, cluster, parallel, scatterplot3d, rgl, tcltk
 Description: Ordination methods, diversity analysis and other
   functions for community and vegetation ecologists.

Modified: pkg/vegan/R/density.anosim.R
===================================================================
--- pkg/vegan/R/density.anosim.R	2013-08-19 07:45:39 UTC (rev 2585)
+++ pkg/vegan/R/density.anosim.R	2013-08-19 08:50:29 UTC (rev 2586)
@@ -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: pkg/vegan/R/densityplot.oecosimu.R
===================================================================
--- pkg/vegan/R/densityplot.oecosimu.R	2013-08-19 07:45:39 UTC (rev 2585)
+++ pkg/vegan/R/densityplot.oecosimu.R	2013-08-19 08:50:29 UTC (rev 2586)
@@ -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: pkg/vegan/R/ordicloud.R
===================================================================
--- pkg/vegan/R/ordicloud.R	2013-08-19 07:45:39 UTC (rev 2585)
+++ pkg/vegan/R/ordicloud.R	2013-08-19 08:50:29 UTC (rev 2586)
@@ -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: pkg/vegan/R/ordiresids.R
===================================================================
--- pkg/vegan/R/ordiresids.R	2013-08-19 07:45:39 UTC (rev 2585)
+++ pkg/vegan/R/ordiresids.R	2013-08-19 08:50:29 UTC (rev 2586)
@@ -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: pkg/vegan/R/ordisplom.R
===================================================================
--- pkg/vegan/R/ordisplom.R	2013-08-19 07:45:39 UTC (rev 2585)
+++ pkg/vegan/R/ordisplom.R	2013-08-19 08:50:29 UTC (rev 2586)
@@ -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: pkg/vegan/R/ordixyplot.R
===================================================================
--- pkg/vegan/R/ordixyplot.R	2013-08-19 07:45:39 UTC (rev 2585)
+++ pkg/vegan/R/ordixyplot.R	2013-08-19 08:50:29 UTC (rev 2586)
@@ -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: pkg/vegan/R/plot.poolaccum.R
===================================================================
--- pkg/vegan/R/plot.poolaccum.R	2013-08-19 07:45:39 UTC (rev 2585)
+++ pkg/vegan/R/plot.poolaccum.R	2013-08-19 08:50:29 UTC (rev 2586)
@@ -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: pkg/vegan/R/plot.radfit.frame.R
===================================================================
--- pkg/vegan/R/plot.radfit.frame.R	2013-08-19 07:45:39 UTC (rev 2585)
+++ pkg/vegan/R/plot.radfit.frame.R	2013-08-19 08:50:29 UTC (rev 2586)
@@ -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: pkg/vegan/R/plot.renyi.R
===================================================================
--- pkg/vegan/R/plot.renyi.R	2013-08-19 07:45:39 UTC (rev 2585)
+++ pkg/vegan/R/plot.renyi.R	2013-08-19 08:50:29 UTC (rev 2586)
@@ -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: pkg/vegan/R/plot.renyiaccum.R
===================================================================
--- pkg/vegan/R/plot.renyiaccum.R	2013-08-19 07:45:39 UTC (rev 2585)
+++ pkg/vegan/R/plot.renyiaccum.R	2013-08-19 08:50:29 UTC (rev 2586)
@@ -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: pkg/vegan/R/radlattice.R
===================================================================
--- pkg/vegan/R/radlattice.R	2013-08-19 07:45:39 UTC (rev 2585)
+++ pkg/vegan/R/radlattice.R	2013-08-19 08:50:29 UTC (rev 2586)
@@ -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: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2013-08-19 07:45:39 UTC (rev 2585)
+++ pkg/vegan/inst/ChangeLog	2013-08-19 08:50:29 UTC (rev 2586)
@@ -2,8 +2,13 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 2.1-32 (opened July 10, 2013)
+Version 2.1-33 (opened August 23, 2013)
 
+	* DESCRIPTION: new dependence on lattice. Passes new strict R
+	checks with NOTE on unavoidable ':::' calls.
+	
+Version 2.1-32 (closed August 19, 2013)
+
 	* opened a new version with the CRAN release of vegan 2.0-8.
 
 	* merged Eduard Szöcs's code on dispersion weighting of

Modified: pkg/vegan/inst/doc/diversity-vegan.Rnw
===================================================================
--- pkg/vegan/inst/doc/diversity-vegan.Rnw	2013-08-19 07:45:39 UTC (rev 2585)
+++ pkg/vegan/inst/doc/diversity-vegan.Rnw	2013-08-19 08:50:29 UTC (rev 2586)
@@ -118,9 +118,6 @@
 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{figure}
 <<fig=true,echo=false>>=
 print(plot(R))

Modified: pkg/vegan/man/adonis.Rd
===================================================================
--- pkg/vegan/man/adonis.Rd	2013-08-19 07:45:39 UTC (rev 2585)
+++ pkg/vegan/man/adonis.Rd	2013-08-19 08:50:29 UTC (rev 2586)
@@ -204,7 +204,6 @@
 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: pkg/vegan/man/density.adonis.Rd
===================================================================
--- pkg/vegan/man/density.adonis.Rd	2013-08-19 07:45:39 UTC (rev 2585)
+++ pkg/vegan/man/density.adonis.Rd	2013-08-19 08:50:29 UTC (rev 2586)
@@ -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: pkg/vegan/man/oecosimu.Rd
===================================================================
--- pkg/vegan/man/oecosimu.Rd	2013-08-19 07:45:39 UTC (rev 2585)
+++ pkg/vegan/man/oecosimu.Rd	2013-08-19 08:50:29 UTC (rev 2586)
@@ -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

