From noreply at r-forge.r-project.org  Wed Jan  7 14:01:37 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  7 Jan 2015 14:01:37 +0100 (CET)
Subject: [Vegan-commits] r2924 - in pkg/vegan: . R inst man
Message-ID: <20150107130137.990AB18786B@r-forge.r-project.org>

Author: jarioksa
Date: 2015-01-07 14:01:37 +0100 (Wed, 07 Jan 2015)
New Revision: 2924

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/R/adonis.R
   pkg/vegan/R/anosim.R
   pkg/vegan/R/bioenv.default.R
   pkg/vegan/R/estaccumR.R
   pkg/vegan/R/mantel.R
   pkg/vegan/R/mantel.partial.R
   pkg/vegan/R/metaMDSiter.R
   pkg/vegan/R/mrpp.R
   pkg/vegan/R/oecosimu.R
   pkg/vegan/R/ordiareatest.R
   pkg/vegan/R/orditkplot.R
   pkg/vegan/R/permutest.betadisper.R
   pkg/vegan/R/permutest.cca.R
   pkg/vegan/R/poolaccum.R
   pkg/vegan/R/renyiaccum.R
   pkg/vegan/R/simper.R
   pkg/vegan/R/specaccum.R
   pkg/vegan/R/tsallisaccum.R
   pkg/vegan/R/vegandocs.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/inst/NEWS.Rd
   pkg/vegan/man/isomap.Rd
   pkg/vegan/man/renyi.Rd
   pkg/vegan/man/specaccum.Rd
   pkg/vegan/man/specpool.Rd
   pkg/vegan/man/tsallis.Rd
   pkg/vegan/man/vegandocs.Rd
Log:
Merge branch 'cran-2.2' into r-forge-svn-local

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2014-12-30 15:55:45 UTC (rev 2923)
+++ pkg/vegan/DESCRIPTION	2015-01-07 13:01:37 UTC (rev 2924)
@@ -7,7 +7,7 @@
    M. Henry H. Stevens, Helene Wagner  
 Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>
 Depends: permute (>= 0.7-8), lattice, R (>= 2.15.0)
-Suggests: parallel, tcltk
+Suggests: tcltk
 Imports: MASS, cluster, mgcv
 Description: Ordination methods, diversity analysis and other
   functions for community and vegetation ecologists.

Modified: pkg/vegan/R/adonis.R
===================================================================
--- pkg/vegan/R/adonis.R	2014-12-30 15:55:45 UTC (rev 2923)
+++ pkg/vegan/R/adonis.R	2015-01-07 13:01:37 UTC (rev 2924)
@@ -100,23 +100,23 @@
         if (is.null(parallel))
             parallel <- 1
         hasClus <- inherits(parallel, "cluster")
-        isParal <- (hasClus || parallel > 1) && require(parallel)
+        isParal <- hasClus || parallel > 1
         isMulticore <- .Platform$OS.type == "unix" && !hasClus
         if (isParal && !isMulticore && !hasClus) {
-            parallel <- makeCluster(parallel)
+            parallel <- parallel::makeCluster(parallel)
         }
         if (isParal) {
             if (isMulticore) {
                 f.perms <-
                     sapply(1:nterms, function(i)
-                           unlist(mclapply(1:permutations, function(j)
+                           unlist(parallel::mclapply(1:permutations, function(j)
                                            f.test(tH.s[[i]], G[p[j,], p[j,]],
                                                   df.Exp[i], df.Res, tIH.snterm),
                                            mc.cores = parallel)))
             } else {
                 f.perms <-
                     sapply(1:nterms, function(i)
-                           parSapply(parallel, 1:permutations, function(j)
+                           parallel::parSapply(parallel, 1:permutations, function(j)
                                      f.test(tH.s[[i]], G[p[j,], p[j,]],
                                             df.Exp[i], df.Res, tIH.snterm)))
             }
@@ -129,7 +129,7 @@
         }
         ## Close socket cluster if created here
         if (isParal && !isMulticore && !hasClus)
-            stopCluster(parallel)
+            parallel::stopCluster(parallel)
         ## Round to avoid arbitrary P-values with tied data
         f.perms <- round(f.perms, 12)
         P <- (rowSums(t(f.perms) >= F.Mod)+1)/(permutations+1)

Modified: pkg/vegan/R/anosim.R
===================================================================
--- pkg/vegan/R/anosim.R	2014-12-30 15:55:45 UTC (rev 2923)
+++ pkg/vegan/R/anosim.R	2015-01-07 13:01:37 UTC (rev 2924)
@@ -46,18 +46,19 @@
         if (is.null(parallel))
             parallel <- 1
         hasClus <- inherits(parallel, "cluster")
-        if ((hasClus || parallel > 1)  && require(parallel)) {
+        if (hasClus || parallel > 1) {
             if(.Platform$OS.type == "unix" && !hasClus) {
-                perm <- unlist(mclapply(1:permutations, function(i, ...)
-                                        ptest(permat[i,]),
-                                        mc.cores = parallel))
+                perm <- unlist(parallel::mclapply(1:permutations,
+                                                  function(i, ...)
+                                                  ptest(permat[i,]),
+                                                  mc.cores = parallel))
             } else {
                 if (!hasClus) {
-                    parallel <- makeCluster(parallel)
+                    parallel <- parallel::makeCluster(parallel)
                 }
-                perm <- parRapply(parallel, permat, ptest)
+                perm <- parallel::parRapply(parallel, permat, ptest)
                 if (!hasClus)
-                    stopCluster(parallel)
+                    parallel::stopCluster(parallel)
             }
         } else {
             perm <- sapply(1:permutations, function(i) ptest(permat[i,]))

Modified: pkg/vegan/R/bioenv.default.R
===================================================================
--- pkg/vegan/R/bioenv.default.R	2014-12-30 15:55:45 UTC (rev 2923)
+++ pkg/vegan/R/bioenv.default.R	2015-01-07 13:01:37 UTC (rev 2924)
@@ -72,10 +72,11 @@
     if (is.null(parallel))
         parallel <- 1
     hasClus <- inherits(parallel, "cluster")
-    isParal <- (hasClus || parallel > 1) && require(parallel)
+    isParal <- hasClus || parallel > 1
     isMulticore <- .Platform$OS.type == "unix" && !hasClus
     if (isParal && !isMulticore && !hasClus) {
-        parallel <- makeCluster(parallel)
+        parallel <- parallel::makeCluster(parallel)
+        on.exit(parallel::stopCluster(parallel))
     }
     ## get the number of clusters
     if (inherits(parallel, "cluster"))
@@ -96,13 +97,13 @@
             sets <- as.matrix(t(sets))
         if (isParal && nrow(sets) >= CLUSLIM*nclus) {
             if (isMulticore) {
-                est <- unlist(mclapply(1:nrow(sets), function(j)
+                est <- unlist(parallel::mclapply(1:nrow(sets), function(j)
                                        corfun(comdis,
                                               distfun(x[,sets[j,],drop = FALSE]),
                                               partial, method = method, ...),
                                        mc.cores = parallel))
             } else {
-                est <- parSapply(parallel, 1:nrow(sets), function(j)
+                est <- parallel::parSapply(parallel, 1:nrow(sets), function(j)
                                   corfun(comdis, distfun(x[,sets[j,],drop = FALSE]),
                                          partial, method = method, ...))
             }

Modified: pkg/vegan/R/estaccumR.R
===================================================================
--- pkg/vegan/R/estaccumR.R	2014-12-30 15:55:45 UTC (rev 2923)
+++ pkg/vegan/R/estaccumR.R	2015-01-07 13:01:37 UTC (rev 2924)
@@ -1,21 +1,43 @@
 ##" Individual based accumulation model. Similar to poolaccum but uses
 ##estimateR. Inherits from "poolaccum" class and uses its methods.
 `estaccumR` <-
-    function(x, permutations = 100)
+    function(x, permutations = 100, parallel = getOption("mc.cores"))
 {
     n <- nrow(x)
     N <- seq_len(n)
-    S <- chao <- ace <- matrix(0, nrow = n, ncol = permutations)
-    for (i in 1:permutations) {
-        take <- sample(n)
-        tmp <- estimateR(apply(x[take,], 2, cumsum))
-        S[,i] <- tmp[1,]
-        chao[,i] <- tmp[2,]
-        ace[, i] <- tmp[4,]
+    estFun <- function(idx) {
+        estimateR(apply(x[idx,], 2, cumsum))[c(1,2,4),]
     }
+    permat <- getPermuteMatrix(permutations, n)
+    nperm <- nrow(permat)
+    ## parallel processing
+    if (is.null(parallel))
+        parallel <- 1
+    hasClus <- inherits(parallel, "cluster")
+    if (hasClus || parallel > 1) {
+        if(.Platform$OS.type == "unix" && !hasClus) {
+            tmp <- parallel::mclapply(1:nperm, function(i)
+                            estFun(permat[i,]),
+                            mc.cores = parallel)
+        } else {
+            if (!hasClus) {
+                parallel <- parallel::makeCluster(parallel)
+            }
+            tmp <- parallel::parLapply(parallel, 1:nperm, function(i) estFun(permat[i,]))
+            if (!hasClus)
+                parallel::stopCluster(parallel)
+        }
+    } else {
+        tmp <- lapply(1:permutations, function(i) estFun(permat[i,]))
+    }
+
+    S <- sapply(tmp, function(x) x[1,])
+    chao <- sapply(tmp, function(x) x[2,])
+    ace <- sapply(tmp, function(x) x[3,])
     means <- cbind(N = N, S = rowMeans(S), Chao = rowMeans(chao),
                    ACE = rowMeans(ace))
     out <- list(S = S, chao = chao, ace = ace, N = N, means = means)
+    attr(out, "control") <- attr(permat, "control")
     class(out) <- c("estaccumR", "poolaccum")
     out
 }

Modified: pkg/vegan/R/mantel.R
===================================================================
--- pkg/vegan/R/mantel.R	2014-12-30 15:55:45 UTC (rev 2923)
+++ pkg/vegan/R/mantel.R	2015-01-07 13:01:37 UTC (rev 2924)
@@ -37,19 +37,19 @@
         if (is.null(parallel))
             parallel <- 1
         hasClus <- inherits(parallel, "cluster")
-        if ((hasClus || parallel > 1)  && require(parallel)) {
+        if (hasClus || parallel > 1)  {
             if(.Platform$OS.type == "unix" && !hasClus) {
                 perm <- do.call(rbind,
-                               mclapply(1:permutations,
+                               parallel::mclapply(1:permutations,
                                         function(i, ...) ptest(permat[i,],...),
                                         mc.cores = parallel))
             } else {
                 if (!hasClus) {
-                    parallel <- makeCluster(parallel)
+                    parallel <- parallel::makeCluster(parallel)
                 }
-                perm <- parRapply(parallel, permat, ptest)
+                perm <- parallel::parRapply(parallel, permat, ptest)
                 if (!hasClus)
-                    stopCluster(parallel)
+                    parallel::stopCluster(parallel)
             }
         } else {
             perm <- sapply(1:permutations, function(i, ...) ptest(permat[i,], ...))

Modified: pkg/vegan/R/mantel.partial.R
===================================================================
--- pkg/vegan/R/mantel.partial.R	2014-12-30 15:55:45 UTC (rev 2923)
+++ pkg/vegan/R/mantel.partial.R	2015-01-07 13:01:37 UTC (rev 2924)
@@ -45,19 +45,19 @@
         if (is.null(parallel))
             parallel <- 1
         hasClus <- inherits(parallel, "cluster")
-        if ((hasClus || parallel > 1)  && require(parallel)) {
+        if (hasClus || parallel > 1) {
             if(.Platform$OS.type == "unix" && !hasClus) {
                 perm <- do.call(rbind,
-                               mclapply(1:permutations,
+                               parallel::mclapply(1:permutations,
                                         function(i, ...) ptest(permat[i,],...),
                                         mc.cores = parallel))
             } else {
                 if (!hasClus) {
-                    parallel <- makeCluster(parallel)
+                    parallel <- parallel::makeCluster(parallel)
                 }
-                perm <- parRapply(parallel, permat, ptest)
+                perm <- parallel::parRapply(parallel, permat, ptest)
                 if (!hasClus)
-                    stopCluster(parallel)
+                    parallel::stopCluster(parallel)
             }
         } else {
             perm <- sapply(1:permutations, function(i, ...) ptest(permat[i,], ...))

Modified: pkg/vegan/R/metaMDSiter.R
===================================================================
--- pkg/vegan/R/metaMDSiter.R	2014-12-30 15:55:45 UTC (rev 2923)
+++ pkg/vegan/R/metaMDSiter.R	2015-01-07 13:01:37 UTC (rev 2924)
@@ -74,11 +74,11 @@
     if (is.null(parallel))
         parallel <- 1
     hasClus <- inherits(parallel, "cluster")
-    isParal <- (hasClus || parallel > 1) && require(parallel)
+    isParal <- hasClus || parallel > 1
     isMulticore <- .Platform$OS.type == "unix" && !hasClus
     if (isParal && !isMulticore && !hasClus) {
-        parallel <- makeCluster(parallel)
-        clusterEvalQ(parallel, library(vegan))
+        parallel <-parallel:: makeCluster(parallel)
+        parallel::clusterEvalQ(parallel, library(vegan))
     }
     ## get the number of clusters
     if (inherits(parallel, "cluster"))
@@ -92,7 +92,7 @@
         if (isParal) {
             if (isMulticore) {
                 stry <-
-                    mclapply(1:nclus, function(i)
+                    parallel::mclapply(1:nclus, function(i)
                              switch(engine,
                                     "monoMDS" = monoMDS(dist, init[,,i], k = k,
                                     maxit = maxit, ...),
@@ -102,7 +102,7 @@
                              mc.cores = parallel)
             } else {
                 stry <-
-                    parLapply(parallel, 1:nclus, function(i)
+                    parallel::parLapply(parallel, 1:nclus, function(i)
                               switch(engine,
                                      "monoMDS" = monoMDS(dist, init[,,i], k = k,
                                      maxit = maxit, ...),
@@ -150,7 +150,7 @@
     }
     ## stop socket cluster
     if (isParal && !isMulticore && !hasClus)
-        stopCluster(parallel)
+        parallel::stopCluster(parallel)
     if (!missing(previous.best) && inherits(previous.best, "metaMDS")) {
         tries <- tries + previous.best$tries
     }

Modified: pkg/vegan/R/mrpp.R
===================================================================
--- pkg/vegan/R/mrpp.R	2014-12-30 15:55:45 UTC (rev 2923)
+++ pkg/vegan/R/mrpp.R	2015-01-07 13:01:37 UTC (rev 2924)
@@ -52,19 +52,19 @@
         if (is.null(parallel))
             parallel <- 1
         hasClus <- inherits(parallel, "cluster")
-        if ((hasClus || parallel > 1)  && require(parallel)) {
+        if (hasClus || parallel > 1) {
             if(.Platform$OS.type == "unix" && !hasClus) {
-                m.ds <- unlist(mclapply(1:permutations, function(i, ...)
+                m.ds <- unlist(parallel::mclapply(1:permutations, function(i, ...)
                                         mrpp.perms(perms[,i], dmat, indls, w),
                                         mc.cores = parallel))
             } else {
                 if (!hasClus) {
-                    parallel <- makeCluster(parallel)
+                    parallel <- parallel::makeCluster(parallel)
                 }
-                m.ds <- parCapply(parallel, perms, function(x)
+                m.ds <- parallel::parCapply(parallel, perms, function(x)
                                   mrpp.perms(x, dmat, indls, w))
                 if (!hasClus)
-                    stopCluster(parallel)
+                    parallel::stopCluster(parallel)
             }
         } else {
             m.ds <- apply(perms, 2, function(x) mrpp.perms(x, dmat, indls, w))

Modified: pkg/vegan/R/oecosimu.R
===================================================================
--- pkg/vegan/R/oecosimu.R	2014-12-30 15:55:45 UTC (rev 2923)
+++ pkg/vegan/R/oecosimu.R	2015-01-07 13:01:37 UTC (rev 2924)
@@ -90,13 +90,13 @@
     if (is.null(parallel))
         parallel <- 1
     hasClus <- inherits(parallel, "cluster")
-    if ((hasClus || parallel > 1)  && require(parallel)) {
+    if (hasClus || parallel > 1) {
         if(.Platform$OS.type == "unix" && !hasClus) {
             for (i in seq_len(nbatch)) {
                 ## simulate if no simmat_in
                 if(!simmat_in)
                     x <- simulate(nm, nsim = batches[i], thin = thin)
-                tmp <- mclapply(seq_len(batches[i]),
+                tmp <- parallel::mclapply(seq_len(batches[i]),
                                 function(j)
                                 applynestfun(x[,,j], fun=nestfun,
                                              statistic = statistic, ...),
@@ -106,20 +106,20 @@
         } else {
             ## if hasClus, do not set up and stop a temporary cluster
             if (!hasClus) {
-                parallel <- makeCluster(parallel)
+                parallel <- parallel::makeCluster(parallel)
                 ## make vegan functions available: others may be unavailable
-                clusterEvalQ(parallel, library(vegan))
+                parallel::clusterEvalQ(parallel, library(vegan))
             }
             for(i in seq_len(nbatch)) {
                 if (!simmat_in)
                     x <- simulate(nm, nsim = batches[i], thin = thin)
                 simind <- cbind(simind,
-                                parApply(parallel, x, 3, function(z)
+                                parallel::parApply(parallel, x, 3, function(z)
                                          applynestfun(z, fun = nestfun,
                                                       statistic = statistic, ...)))
             }
             if (!hasClus)
-                stopCluster(parallel)
+                parallel::stopCluster(parallel)
         }
     } else {
         for(i in seq_len(nbatch)) {

Modified: pkg/vegan/R/ordiareatest.R
===================================================================
--- pkg/vegan/R/ordiareatest.R	2014-12-30 15:55:45 UTC (rev 2923)
+++ pkg/vegan/R/ordiareatest.R	2015-01-07 13:01:37 UTC (rev 2924)
@@ -30,19 +30,19 @@
     if (is.null(parallel))
         parallel <- 1
     hasClus <- inherits(parallel, "cluster")
-    if ((hasClus || parallel > 1) && require(parallel)) {
+    if (hasClus || parallel > 1) {
         if(.Platform$OS.type == "unix" && !hasClus) {
             areas <- do.call(cbind,
-                             mclapply(1:permutations,
+                             parallel::mclapply(1:permutations,
                                       function(i, ...) pfun(perm[i,],...),
                                         mc.cores = parallel))
             } else {
                 if (!hasClus) {
-                    parallel <- makeCluster(parallel)
+                    parallel <- parallel::makeCluster(parallel)
                 }
-                areas <- parApply(parallel, perm, MARGIN=1, pfun)
+                areas <- parallel::parApply(parallel, perm, MARGIN=1, pfun)
                 if (!hasClus)
-                    stopCluster(parallel)
+                    parallel::stopCluster(parallel)
             }
     } else {
         areas <- sapply(1:permutations, function(i, ...) pfun(perm[i,], ...))

Modified: pkg/vegan/R/orditkplot.R
===================================================================
--- pkg/vegan/R/orditkplot.R	2014-12-30 15:55:45 UTC (rev 2923)
+++ pkg/vegan/R/orditkplot.R	2015-01-07 13:01:37 UTC (rev 2924)
@@ -8,7 +8,7 @@
 {
     if (!capabilities("tcltk"))
         stop("Your R has no capability for Tcl/Tk")
-    require(tcltk) || stop("requires package tcltk")
+    requireNamespace("tcltk") || stop("requires package tcltk")
 
 ############################
 ### Check and sanitize input

Modified: pkg/vegan/R/permutest.betadisper.R
===================================================================
--- pkg/vegan/R/permutest.betadisper.R	2014-12-30 15:55:45 UTC (rev 2923)
+++ pkg/vegan/R/permutest.betadisper.R	2015-01-07 13:01:37 UTC (rev 2924)
@@ -81,20 +81,21 @@
         parallel <- 1
     }
     hasClus <- inherits(parallel, "cluster")
-    if ((hasClus || parallel > 1L) && requireNamespace("parallel")) {
+    if (hasClus || parallel > 1L) {
         if (.Platform$OS.type == "unix" && !hasClus) {
             Pstats <- do.call("rbind",
-                           mclapply(seq_len(nperm),
+                           parallel::mclapply(seq_len(nperm),
                                     function(x) permFun(permutations[x, , drop = FALSE]),
                                     mc.cores = parallel))
         } else {
             ## if hasClus, don't set up and top a temporary cluster
             if (!hasClus) {
-                parallel <- makeCluster(parallel)
+                parallel <- parallel::makeCluster(parallel)
             }
-            Pstats <- parRapply(parallel, permutations, function(x) permFun(x))
+            Pstats <- parallel::parRapply(parallel, permutations,
+                                          function(x) permFun(x))
             if (!hasClus) {
-                stopCluster(parallel)
+                parallel::stopCluster(parallel)
             }
         }
     } else {

Modified: pkg/vegan/R/permutest.cca.R
===================================================================
--- pkg/vegan/R/permutest.cca.R	2014-12-30 15:55:45 UTC (rev 2923)
+++ pkg/vegan/R/permutest.cca.R	2015-01-07 13:01:37 UTC (rev 2924)
@@ -117,21 +117,21 @@
     if (is.null(parallel))
         parallel <- 1
     hasClus <- inherits(parallel, "cluster")
-    if ((hasClus || parallel > 1)  && require(parallel)) {
+    if (hasClus || parallel > 1) {
         if(.Platform$OS.type == "unix" && !hasClus) {
             tmp <- do.call(rbind,
-                           mclapply(1:nperm,
+                           parallel::mclapply(1:nperm,
                                     function(i) getF(permutations[i,]),
                                     mc.cores = parallel))
         } else {
             ## if hasClus, do not set up and stop a temporary cluster
             if (!hasClus) {
-                parallel <- makeCluster(parallel)
+                parallel <- parallel::makeCluster(parallel)
             }
-            tmp <- parRapply(parallel, permutations, function(i) getF(i))
+            tmp <- parallel::parRapply(parallel, permutations, function(i) getF(i))
             tmp <- matrix(tmp, ncol=3, byrow=TRUE)
             if (!hasClus)
-                stopCluster(parallel)
+                parallel::stopCluster(parallel)
         }
     } else {
         tmp <- getF(permutations)

Modified: pkg/vegan/R/poolaccum.R
===================================================================
--- pkg/vegan/R/poolaccum.R	2014-12-30 15:55:45 UTC (rev 2923)
+++ pkg/vegan/R/poolaccum.R	2015-01-07 13:01:37 UTC (rev 2924)
@@ -5,15 +5,18 @@
     n <- nrow(x)
     m <- ncol(x)
     N <- seq_len(n)
+    ## specpool() is slow, but the vectorized versions below are
+    ## pretty fast. We do not set up parallel processing, but use
+    ## permute API.
+    permat <- getPermuteMatrix(permutations, n)
+    nperm <- nrow(permat)
     S <- chao <- boot <- jack1 <- jack2 <-
-        matrix(0, nrow=n, ncol=permutations)
-    ## specpool() is slow, but the vectorized versions below are
-    ## pretty fast
-    for (i in 1:permutations) {
+        matrix(0, nrow=n, ncol=nperm)
+    for (i in 1:nperm) {
         ## It is a bad practice to replicate specpool equations here:
         ## if we change specpool, this function gets out of sync. You
         ## should be ashamed, Jari Oksanen!
-        take <- sample.int(n, n)
+        take <- permat[i,]
         tmp <- apply(x[take,] > 0, 2, cumsum)
         S[,i] <- rowSums(tmp > 0)
         ## All-zero species are taken as *known* to be missing in
@@ -36,6 +39,7 @@
     out <- list(S = S[take,], chao = chao[take,], jack1 = jack1[take,],
                 jack2 = jack2[take,], boot = boot[take,], N = N[take],
                 means = means[take,])
+    attr(out, "control") <- attr(permat, "control")
     class(out) <- "poolaccum"
     out
 }

Modified: pkg/vegan/R/renyiaccum.R
===================================================================
--- pkg/vegan/R/renyiaccum.R	2014-12-30 15:55:45 UTC (rev 2923)
+++ pkg/vegan/R/renyiaccum.R	2015-01-07 13:01:37 UTC (rev 2924)
@@ -10,14 +10,15 @@
     if (p==1) {
         x <- t(x)
         n <- nrow(x)
-        p <- ncol(x)        
+        p <- ncol(x)
     }
+    pmat <- getPermuteMatrix(permutations, n)
     m <- length(scales)
     result <- array(dim=c(n,m,permutations))
     dimnames(result) <- list(pooled.sites=c(1:n), scale=scales,
                              permutation=c(1:permutations))
     for (k in 1:permutations) {
-        result[,,k] <- as.matrix(renyi((apply(x[sample(n),],2,cumsum)),
+        result[,,k] <- as.matrix(renyi((apply(x[pmat[k,],],2,cumsum)),
                                        scales=scales, ...))
     }
     if (raw)
@@ -47,6 +48,7 @@
                                   scale=scales,
                                   c("mean", "stdev", "min", "max", "Qnt 0.025", "Qnt 0.975", if (collector) "Collector"))
     }
+    attr(result, "control") <- attr(pmat, "control")
     class(result) <- c("renyiaccum", class(result))
     result
 }

Modified: pkg/vegan/R/simper.R
===================================================================
--- pkg/vegan/R/simper.R	2014-12-30 15:55:45 UTC (rev 2923)
+++ pkg/vegan/R/simper.R	2015-01-07 13:01:37 UTC (rev 2924)
@@ -1,12 +1,12 @@
 `simper` <-
-    function(comm, group, permutations = 0, trace = FALSE,  
+    function(comm, group, permutations = 0, trace = FALSE,
              parallel = getOption("mc.cores"), ...)
 {
-    if (any(rowSums(comm, na.rm = TRUE) == 0)) 
+    if (any(rowSums(comm, na.rm = TRUE) == 0))
         warning("you have empty rows: results may be meaningless")
     pfun <- function(x, comm, comp, i, contrp) {
         groupp <- group[perm[x,]]
-        ga <- comm[groupp == comp[i, 1], , drop = FALSE] 
+        ga <- comm[groupp == comp[i, 1], , drop = FALSE]
         gb <- comm[groupp == comp[i, 2], , drop = FALSE]
         n.a <- nrow(ga)
         n.b <- nrow(gb)
@@ -14,7 +14,7 @@
             for(k in seq_len(n.a)) {
                 mdp <- abs(ga[k, , drop = FALSE] - gb[j, , drop = FALSE])
                 mep <- ga[k, , drop = FALSE] + gb[j, , drop = FALSE]
-                contrp[(j-1)*n.a+k, ] <- mdp / sum(mep)  
+                contrp[(j-1)*n.a+k, ] <- mdp / sum(mep)
             }
         }
         colMeans(contrp)
@@ -39,10 +39,10 @@
     if (is.null(parallel))
         parallel <- 1
     hasClus <- inherits(parallel, "cluster")
-    isParal <- (hasClus || parallel > 1) && require(parallel)
+    isParal <- hasClus || parallel > 1
     isMulticore <- .Platform$OS.type == "unix" && !hasClus
     if (isParal && !isMulticore && !hasClus) {
-        parallel <- makeCluster(parallel)
+        parallel <- parallel::makeCluster(parallel)
     }
     for (i in seq_len(nrow(comp))) {
         group.a <- comm[group == comp[i, 1], , drop = FALSE]
@@ -54,11 +54,11 @@
             for (k in seq_len(n.a)) {
                 md <- abs(group.a[k, , drop = FALSE] - group.b[j, , drop = FALSE])
                 me <- group.a[k, , drop = FALSE] + group.b[j, , drop = FALSE]
-                contr[(j-1)*n.a+k, ] <- md / sum(me)	
+                contr[(j-1)*n.a+k, ] <- md / sum(me)
             }
         }
         average <- colMeans(contr)
-        
+
         ## Apply permutations
         if(nperm > 0){
             if (trace)
@@ -67,28 +67,28 @@
 
             if (isParal) {
                 if (isMulticore){
-                    perm.contr <- mclapply(seq_len(nperm), function(d) 
+                    perm.contr <- parallel::mclapply(seq_len(nperm), function(d)
                         pfun(d, comm, comp, i, contrp), mc.cores = parallel)
                     perm.contr <- do.call(cbind, perm.contr)
                 } else {
-                    perm.contr <- parSapply(parallel, seq_len(nperm), function(d) 
+                    perm.contr <- parallel::parSapply(parallel, seq_len(nperm), function(d)
                         pfun(d, comm, comp, i, contrp))
-                }  
+                }
             } else {
-                perm.contr <- sapply(1:nperm, function(d) 
+                perm.contr <- sapply(1:nperm, function(d)
                     pfun(d, comm, comp, i, contrp))
             }
             p <- (rowSums(apply(perm.contr, 2, function(x) x >= average)) + 1) / (nperm + 1)
-        } 
+        }
         else {
           p <- NULL
         }
-        
+
         overall <- sum(average)
         sdi <- apply(contr, 2, sd)
         ratio <- average / sdi
         ava <- colMeans(group.a)
-        avb <- colMeans(group.b) 
+        avb <- colMeans(group.b)
         ord <- order(average, decreasing = TRUE)
         cusum <- cumsum(average[ord] / overall)
         out <- list(species = colnames(comm), average = average,
@@ -98,7 +98,7 @@
     }
     ## Close socket cluster if created here
     if (isParal && !isMulticore && !hasClus)
-        stopCluster(parallel)
+        parallel::stopCluster(parallel)
     attr(outlist, "permutations") <- nperm
     attr(outlist, "control") <- attr(perm, "control")
     class(outlist) <- "simper"
@@ -111,7 +111,7 @@
     cat("cumulative contributions of most influential species:\n\n")
     cusum <- lapply(x, function(z) z$cusum)
     spec <- lapply(x, function(z) z$species[z$ord])
-    for (i in 1:length(cusum)) {
+    for (i in seq_along(cusum)) {
         names(cusum[[i]]) <- spec[[i]]
     }
     ## this probably fails with empty or identical groups that have 0/0 = NaN
@@ -124,20 +124,20 @@
     function(object, ordered = TRUE, digits = max(3, getOption("digits") - 3), ...)
 {
     if (ordered) {
-        out <- lapply(object, function(z) 
-            data.frame(contr = z$average, sd = z$sd, ratio = z$ratio, 
+        out <- lapply(object, function(z)
+            data.frame(contr = z$average, sd = z$sd, ratio = z$ratio,
                        av.a = z$ava, av.b = z$avb)[z$ord, ])
         cusum <- lapply(object, function(z) z$cusum)
-        for(i in 1:length(out)) {
+        for(i in seq_along(out)) {
             out[[i]]$cumsum <- cusum[[i]]
             if(!is.null(object[[i]]$p)) {
                 out[[i]]$p <- object[[i]]$p[object[[i]]$ord]
             }
-        } 
-    } 
+        }
+    }
     else {
-        out <- lapply(object, function(z) 
-            data.frame(cbind(contr = z$average, sd = z$sd, 'contr/sd' = z$ratio, 
+        out <- lapply(object, function(z)
+            data.frame(cbind(contr = z$average, sd = z$sd, 'contr/sd' = z$ratio,
                              ava = z$ava, avb = z$avb, p = z$p)))
     }
     attr(out, "digits") <- digits

Modified: pkg/vegan/R/specaccum.R
===================================================================
--- pkg/vegan/R/specaccum.R	2014-12-30 15:55:45 UTC (rev 2923)
+++ pkg/vegan/R/specaccum.R	2015-01-07 13:01:37 UTC (rev 2924)
@@ -31,14 +31,10 @@
         xout <- weights <- cumsum(w)
         specaccum <- accumulator(x, sites)
     }, random = {
-        perm <- array(dim = c(n, permutations))
+        permat <- getPermuteMatrix(permutations, n)
+        perm <- apply(permat, 1, accumulator, x = x)
         if (!is.null(w))
-            weights <- array(dim = c(n, permutations))
-        for (i in 1:permutations) {
-            perm[, i] <- accumulator(x, ord <- sample(n))
-            if(!is.null(w))
-                weights[,i] <- cumsum(w[ord])
-        }
+            weights <- apply(permat, 1, function(i) cumsum(w[i]))
         sites <- 1:n
         if (is.null(w)) {
             specaccum <- apply(perm, 1, mean)
@@ -113,6 +109,8 @@
     }
     if (method == "rarefaction")
         out$individuals <- ind
+    if (method == "random")
+        attr(out, "control") <- attr(permat, "control")
     class(out) <- "specaccum"
     out
 }

Modified: pkg/vegan/R/tsallisaccum.R
===================================================================
--- pkg/vegan/R/tsallisaccum.R	2014-12-30 15:55:45 UTC (rev 2923)
+++ pkg/vegan/R/tsallisaccum.R	2015-01-07 13:01:37 UTC (rev 2924)
@@ -1,6 +1,6 @@
-tsallisaccum <-
-function (x, scales = seq(0, 2, 0.2), permutations = 100, raw = FALSE,
-          subset, ...)
+`tsallisaccum` <-
+    function (x, scales = seq(0, 2, 0.2), permutations = 100, raw = FALSE,
+              subset, ...)
 {
     if (!missing(subset))
         x <- subset(x, subset)
@@ -12,12 +12,13 @@
         n <- nrow(x)
         p <- ncol(x)
     }
+    pmat <- getPermuteMatrix(permutations, n)
     m <- length(scales)
     result <- array(dim = c(n, m, permutations))
     dimnames(result) <- list(pooled.sites = c(1:n), scale = scales, 
         permutation = c(1:permutations))
     for (k in 1:permutations) {
-        result[, , k] <- as.matrix(tsallis((apply(x[sample(n), 
+        result[, , k] <- as.matrix(tsallis((apply(x[pmat[k,], 
             ], 2, cumsum)), scales = scales, ...))
     }
     if (raw) {
@@ -43,6 +44,7 @@
         dimnames(result) <- list(pooled.sites = c(1:n), scale = scales, 
             c("mean", "stdev", "min", "max", "Qnt 0.025", "Qnt 0.975"))
     }
+    attr(result, "control") <- attr(pmat, "control")
     class(result) <- c("tsallisaccum", "renyiaccum", class(result))
     result
 }

Modified: pkg/vegan/R/vegandocs.R
===================================================================
--- pkg/vegan/R/vegandocs.R	2014-12-30 15:55:45 UTC (rev 2923)
+++ pkg/vegan/R/vegandocs.R	2015-01-07 13:01:37 UTC (rev 2924)
@@ -1,5 +1,5 @@
 `vegandocs` <-
-    function (doc = c("NEWS", "ONEWS", "ChangeLog", "FAQ-vegan.pdf",
+    function (doc = c("NEWS", "ONEWS", "FAQ-vegan.pdf",
               "intro-vegan.pdf", "diversity-vegan.pdf",
               "decision-vegan.pdf", "partitioning.pdf", "permutations.pdf")) 
 {

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2014-12-30 15:55:45 UTC (rev 2923)
+++ pkg/vegan/inst/ChangeLog	2015-01-07 13:01:37 UTC (rev 2924)
@@ -1,5 +1,16 @@
 VEGAN DEVEL VERSIONS at https://github.com/vegandevs/vegan
 
+	ChangeLog provided a detailed development history of vegan, but it
+	is not updated after September 11, 2014. Vegan moved to git source
+	code management and linear ChangeLog is poorly suited for
+	branching git development. Use git log to track the history in
+	your current branch. The main upstream repository of vegan is
+	currently https://github.com/vegandevs/vegan.
+
+	ChangeLog gave technical details and was mainly provided for vegan
+	developers. Most important user-visible changes are listed in the
+	NEWS of the current release and its patched version.
+
 Version 2.1-43 (opened September 11, 2014)
 
 	* cca, rda, capscale: remove u.eig, v.eig and wa.eig items or

Modified: pkg/vegan/inst/NEWS.Rd
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/vegan -r 2924

From noreply at r-forge.r-project.org  Fri Jan  9 08:44:14 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri,  9 Jan 2015 08:44:14 +0100 (CET)
Subject: [Vegan-commits] r2925 - in pkg/vegan: . R inst
Message-ID: <20150109074414.93C211845E3@r-forge.r-project.org>

Author: jarioksa
Date: 2015-01-09 08:44:14 +0100 (Fri, 09 Jan 2015)
New Revision: 2925

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/NAMESPACE
   pkg/vegan/R/adonis.R
   pkg/vegan/R/anosim.R
   pkg/vegan/R/bioenv.default.R
   pkg/vegan/R/estaccumR.R
   pkg/vegan/R/mantel.R
   pkg/vegan/R/mantel.partial.R
   pkg/vegan/R/metaMDSiter.R
   pkg/vegan/R/mrpp.R
   pkg/vegan/R/oecosimu.R
   pkg/vegan/R/ordiareatest.R
   pkg/vegan/R/permutest.betadisper.R
   pkg/vegan/R/permutest.cca.R
   pkg/vegan/R/print.mantel.correlog.R
   pkg/vegan/R/simper.R
   pkg/vegan/inst/NEWS.Rd
Log:
Merge branch 'cran-2.2' into r-forge-svn-local

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2015-01-07 13:01:37 UTC (rev 2924)
+++ pkg/vegan/DESCRIPTION	2015-01-09 07:44:14 UTC (rev 2925)
@@ -1,13 +1,13 @@
 Package: vegan
 Title: Community Ecology Package
 Version: 2.2-1
-Date: 2014-11-18
+Date: 2015-01-12
 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 (>= 0.7-8), lattice, R (>= 2.15.0)
-Suggests: tcltk
+Suggests: parallel, tcltk
 Imports: MASS, cluster, mgcv
 Description: Ordination methods, diversity analysis and other
   functions for community and vegetation ecologists.

Modified: pkg/vegan/NAMESPACE
===================================================================
--- pkg/vegan/NAMESPACE	2015-01-07 13:01:37 UTC (rev 2924)
+++ pkg/vegan/NAMESPACE	2015-01-09 07:44:14 UTC (rev 2925)
@@ -76,11 +76,12 @@
 importFrom(utils, head, tail, str)
 importFrom(tools, Rd2txt, startDynamicHelp)
 import(lattice)
-import(parallel)
+importFrom(parallel, mclapply, makeCluster, stopCluster, clusterEvalQ,
+           parApply, parLapply, parSapply, parRapply, parCapply)
 importFrom(MASS, isoMDS, sammon, Shepard, mvrnorm)
 importFrom(cluster, daisy)
 ## 's' must be imported in mgcv < 1.8-0 (not needed later)
-importFrom(mgcv, gam, s, te)
+importFrom(mgcv, gam, s, te, predict.gam, summary.gam)
 ## Registration of S3 methods defined in vegan
 # adipart: vegan
 S3method(adipart, default)

Modified: pkg/vegan/R/adonis.R
===================================================================
--- pkg/vegan/R/adonis.R	2015-01-07 13:01:37 UTC (rev 2924)
+++ pkg/vegan/R/adonis.R	2015-01-09 07:44:14 UTC (rev 2925)
@@ -103,20 +103,20 @@
         isParal <- hasClus || parallel > 1
         isMulticore <- .Platform$OS.type == "unix" && !hasClus
         if (isParal && !isMulticore && !hasClus) {
-            parallel <- parallel::makeCluster(parallel)
+            parallel <- makeCluster(parallel)
         }
         if (isParal) {
             if (isMulticore) {
                 f.perms <-
                     sapply(1:nterms, function(i)
-                           unlist(parallel::mclapply(1:permutations, function(j)
+                           unlist(mclapply(1:permutations, function(j)
                                            f.test(tH.s[[i]], G[p[j,], p[j,]],
                                                   df.Exp[i], df.Res, tIH.snterm),
                                            mc.cores = parallel)))
             } else {
                 f.perms <-
                     sapply(1:nterms, function(i)
-                           parallel::parSapply(parallel, 1:permutations, function(j)
+                           parSapply(parallel, 1:permutations, function(j)
                                      f.test(tH.s[[i]], G[p[j,], p[j,]],
                                             df.Exp[i], df.Res, tIH.snterm)))
             }
@@ -129,7 +129,7 @@
         }
         ## Close socket cluster if created here
         if (isParal && !isMulticore && !hasClus)
-            parallel::stopCluster(parallel)
+            stopCluster(parallel)
         ## Round to avoid arbitrary P-values with tied data
         f.perms <- round(f.perms, 12)
         P <- (rowSums(t(f.perms) >= F.Mod)+1)/(permutations+1)

Modified: pkg/vegan/R/anosim.R
===================================================================
--- pkg/vegan/R/anosim.R	2015-01-07 13:01:37 UTC (rev 2924)
+++ pkg/vegan/R/anosim.R	2015-01-09 07:44:14 UTC (rev 2925)
@@ -48,17 +48,17 @@
         hasClus <- inherits(parallel, "cluster")
         if (hasClus || parallel > 1) {
             if(.Platform$OS.type == "unix" && !hasClus) {
-                perm <- unlist(parallel::mclapply(1:permutations,
+                perm <- unlist(mclapply(1:permutations,
                                                   function(i, ...)
                                                   ptest(permat[i,]),
                                                   mc.cores = parallel))
             } else {
                 if (!hasClus) {
-                    parallel <- parallel::makeCluster(parallel)
+                    parallel <- makeCluster(parallel)
                 }
-                perm <- parallel::parRapply(parallel, permat, ptest)
+                perm <- parRapply(parallel, permat, ptest)
                 if (!hasClus)
-                    parallel::stopCluster(parallel)
+                    stopCluster(parallel)
             }
         } else {
             perm <- sapply(1:permutations, function(i) ptest(permat[i,]))

Modified: pkg/vegan/R/bioenv.default.R
===================================================================
--- pkg/vegan/R/bioenv.default.R	2015-01-07 13:01:37 UTC (rev 2924)
+++ pkg/vegan/R/bioenv.default.R	2015-01-09 07:44:14 UTC (rev 2925)
@@ -75,8 +75,8 @@
     isParal <- hasClus || parallel > 1
     isMulticore <- .Platform$OS.type == "unix" && !hasClus
     if (isParal && !isMulticore && !hasClus) {
-        parallel <- parallel::makeCluster(parallel)
-        on.exit(parallel::stopCluster(parallel))
+        parallel <- makeCluster(parallel)
+        on.exit(stopCluster(parallel))
     }
     ## get the number of clusters
     if (inherits(parallel, "cluster"))
@@ -97,13 +97,13 @@
             sets <- as.matrix(t(sets))
         if (isParal && nrow(sets) >= CLUSLIM*nclus) {
             if (isMulticore) {
-                est <- unlist(parallel::mclapply(1:nrow(sets), function(j)
+                est <- unlist(mclapply(1:nrow(sets), function(j)
                                        corfun(comdis,
                                               distfun(x[,sets[j,],drop = FALSE]),
                                               partial, method = method, ...),
                                        mc.cores = parallel))
             } else {
-                est <- parallel::parSapply(parallel, 1:nrow(sets), function(j)
+                est <- parSapply(parallel, 1:nrow(sets), function(j)
                                   corfun(comdis, distfun(x[,sets[j,],drop = FALSE]),
                                          partial, method = method, ...))
             }

Modified: pkg/vegan/R/estaccumR.R
===================================================================
--- pkg/vegan/R/estaccumR.R	2015-01-07 13:01:37 UTC (rev 2924)
+++ pkg/vegan/R/estaccumR.R	2015-01-09 07:44:14 UTC (rev 2925)
@@ -16,16 +16,16 @@
     hasClus <- inherits(parallel, "cluster")
     if (hasClus || parallel > 1) {
         if(.Platform$OS.type == "unix" && !hasClus) {
-            tmp <- parallel::mclapply(1:nperm, function(i)
+            tmp <- mclapply(1:nperm, function(i)
                             estFun(permat[i,]),
                             mc.cores = parallel)
         } else {
             if (!hasClus) {
-                parallel <- parallel::makeCluster(parallel)
+                parallel <- makeCluster(parallel)
             }
-            tmp <- parallel::parLapply(parallel, 1:nperm, function(i) estFun(permat[i,]))
+            tmp <- parLapply(parallel, 1:nperm, function(i) estFun(permat[i,]))
             if (!hasClus)
-                parallel::stopCluster(parallel)
+                stopCluster(parallel)
         }
     } else {
         tmp <- lapply(1:permutations, function(i) estFun(permat[i,]))

Modified: pkg/vegan/R/mantel.R
===================================================================
--- pkg/vegan/R/mantel.R	2015-01-07 13:01:37 UTC (rev 2924)
+++ pkg/vegan/R/mantel.R	2015-01-09 07:44:14 UTC (rev 2925)
@@ -40,16 +40,16 @@
         if (hasClus || parallel > 1)  {
             if(.Platform$OS.type == "unix" && !hasClus) {
                 perm <- do.call(rbind,
-                               parallel::mclapply(1:permutations,
+                               mclapply(1:permutations,
                                         function(i, ...) ptest(permat[i,],...),
                                         mc.cores = parallel))
             } else {
                 if (!hasClus) {
-                    parallel <- parallel::makeCluster(parallel)
+                    parallel <- makeCluster(parallel)
                 }
-                perm <- parallel::parRapply(parallel, permat, ptest)
+                perm <- parRapply(parallel, permat, ptest)
                 if (!hasClus)
-                    parallel::stopCluster(parallel)
+                    stopCluster(parallel)
             }
         } else {
             perm <- sapply(1:permutations, function(i, ...) ptest(permat[i,], ...))

Modified: pkg/vegan/R/mantel.partial.R
===================================================================
--- pkg/vegan/R/mantel.partial.R	2015-01-07 13:01:37 UTC (rev 2924)
+++ pkg/vegan/R/mantel.partial.R	2015-01-09 07:44:14 UTC (rev 2925)
@@ -48,16 +48,16 @@
         if (hasClus || parallel > 1) {
             if(.Platform$OS.type == "unix" && !hasClus) {
                 perm <- do.call(rbind,
-                               parallel::mclapply(1:permutations,
+                               mclapply(1:permutations,
                                         function(i, ...) ptest(permat[i,],...),
                                         mc.cores = parallel))
             } else {
                 if (!hasClus) {
-                    parallel <- parallel::makeCluster(parallel)
+                    parallel <- makeCluster(parallel)
                 }
-                perm <- parallel::parRapply(parallel, permat, ptest)
+                perm <- parRapply(parallel, permat, ptest)
                 if (!hasClus)
-                    parallel::stopCluster(parallel)
+                    stopCluster(parallel)
             }
         } else {
             perm <- sapply(1:permutations, function(i, ...) ptest(permat[i,], ...))

Modified: pkg/vegan/R/metaMDSiter.R
===================================================================
--- pkg/vegan/R/metaMDSiter.R	2015-01-07 13:01:37 UTC (rev 2924)
+++ pkg/vegan/R/metaMDSiter.R	2015-01-09 07:44:14 UTC (rev 2925)
@@ -77,8 +77,8 @@
     isParal <- hasClus || parallel > 1
     isMulticore <- .Platform$OS.type == "unix" && !hasClus
     if (isParal && !isMulticore && !hasClus) {
-        parallel <-parallel:: makeCluster(parallel)
-        parallel::clusterEvalQ(parallel, library(vegan))
+        parallel <- makeCluster(parallel)
+        clusterEvalQ(parallel, library(vegan))
     }
     ## get the number of clusters
     if (inherits(parallel, "cluster"))
@@ -92,7 +92,7 @@
         if (isParal) {
             if (isMulticore) {
                 stry <-
-                    parallel::mclapply(1:nclus, function(i)
+                    mclapply(1:nclus, function(i)
                              switch(engine,
                                     "monoMDS" = monoMDS(dist, init[,,i], k = k,
                                     maxit = maxit, ...),
@@ -102,7 +102,7 @@
                              mc.cores = parallel)
             } else {
                 stry <-
-                    parallel::parLapply(parallel, 1:nclus, function(i)
+                    parLapply(parallel, 1:nclus, function(i)
                               switch(engine,
                                      "monoMDS" = monoMDS(dist, init[,,i], k = k,
                                      maxit = maxit, ...),
@@ -150,7 +150,7 @@
     }
     ## stop socket cluster
     if (isParal && !isMulticore && !hasClus)
-        parallel::stopCluster(parallel)
+        stopCluster(parallel)
     if (!missing(previous.best) && inherits(previous.best, "metaMDS")) {
         tries <- tries + previous.best$tries
     }

Modified: pkg/vegan/R/mrpp.R
===================================================================
--- pkg/vegan/R/mrpp.R	2015-01-07 13:01:37 UTC (rev 2924)
+++ pkg/vegan/R/mrpp.R	2015-01-09 07:44:14 UTC (rev 2925)
@@ -54,17 +54,17 @@
         hasClus <- inherits(parallel, "cluster")
         if (hasClus || parallel > 1) {
             if(.Platform$OS.type == "unix" && !hasClus) {
-                m.ds <- unlist(parallel::mclapply(1:permutations, function(i, ...)
+                m.ds <- unlist(mclapply(1:permutations, function(i, ...)
                                         mrpp.perms(perms[,i], dmat, indls, w),
                                         mc.cores = parallel))
             } else {
                 if (!hasClus) {
-                    parallel <- parallel::makeCluster(parallel)
+                    parallel <- makeCluster(parallel)
                 }
-                m.ds <- parallel::parCapply(parallel, perms, function(x)
+                m.ds <- parCapply(parallel, perms, function(x)
                                   mrpp.perms(x, dmat, indls, w))
                 if (!hasClus)
-                    parallel::stopCluster(parallel)
+                    stopCluster(parallel)
             }
         } else {
             m.ds <- apply(perms, 2, function(x) mrpp.perms(x, dmat, indls, w))

Modified: pkg/vegan/R/oecosimu.R
===================================================================
--- pkg/vegan/R/oecosimu.R	2015-01-07 13:01:37 UTC (rev 2924)
+++ pkg/vegan/R/oecosimu.R	2015-01-09 07:44:14 UTC (rev 2925)
@@ -96,7 +96,7 @@
                 ## simulate if no simmat_in
                 if(!simmat_in)
                     x <- simulate(nm, nsim = batches[i], thin = thin)
-                tmp <- parallel::mclapply(seq_len(batches[i]),
+                tmp <- mclapply(seq_len(batches[i]),
                                 function(j)
                                 applynestfun(x[,,j], fun=nestfun,
                                              statistic = statistic, ...),
@@ -106,20 +106,20 @@
         } else {
             ## if hasClus, do not set up and stop a temporary cluster
             if (!hasClus) {
-                parallel <- parallel::makeCluster(parallel)
+                parallel <- makeCluster(parallel)
                 ## make vegan functions available: others may be unavailable
-                parallel::clusterEvalQ(parallel, library(vegan))
+                clusterEvalQ(parallel, library(vegan))
             }
             for(i in seq_len(nbatch)) {
                 if (!simmat_in)
                     x <- simulate(nm, nsim = batches[i], thin = thin)
                 simind <- cbind(simind,
-                                parallel::parApply(parallel, x, 3, function(z)
+                                parApply(parallel, x, 3, function(z)
                                          applynestfun(z, fun = nestfun,
                                                       statistic = statistic, ...)))
             }
             if (!hasClus)
-                parallel::stopCluster(parallel)
+                stopCluster(parallel)
         }
     } else {
         for(i in seq_len(nbatch)) {

Modified: pkg/vegan/R/ordiareatest.R
===================================================================
--- pkg/vegan/R/ordiareatest.R	2015-01-07 13:01:37 UTC (rev 2924)
+++ pkg/vegan/R/ordiareatest.R	2015-01-09 07:44:14 UTC (rev 2925)
@@ -33,16 +33,16 @@
     if (hasClus || parallel > 1) {
         if(.Platform$OS.type == "unix" && !hasClus) {
             areas <- do.call(cbind,
-                             parallel::mclapply(1:permutations,
+                             mclapply(1:permutations,
                                       function(i, ...) pfun(perm[i,],...),
                                         mc.cores = parallel))
             } else {
                 if (!hasClus) {
-                    parallel <- parallel::makeCluster(parallel)
+                    parallel <- makeCluster(parallel)
                 }
-                areas <- parallel::parApply(parallel, perm, MARGIN=1, pfun)
+                areas <- parApply(parallel, perm, MARGIN=1, pfun)
                 if (!hasClus)
-                    parallel::stopCluster(parallel)
+                    stopCluster(parallel)
             }
     } else {
         areas <- sapply(1:permutations, function(i, ...) pfun(perm[i,], ...))

Modified: pkg/vegan/R/permutest.betadisper.R
===================================================================
--- pkg/vegan/R/permutest.betadisper.R	2015-01-07 13:01:37 UTC (rev 2924)
+++ pkg/vegan/R/permutest.betadisper.R	2015-01-09 07:44:14 UTC (rev 2925)
@@ -84,18 +84,18 @@
     if (hasClus || parallel > 1L) {
         if (.Platform$OS.type == "unix" && !hasClus) {
             Pstats <- do.call("rbind",
-                           parallel::mclapply(seq_len(nperm),
+                           mclapply(seq_len(nperm),
                                     function(x) permFun(permutations[x, , drop = FALSE]),
                                     mc.cores = parallel))
         } else {
             ## if hasClus, don't set up and top a temporary cluster
             if (!hasClus) {
-                parallel <- parallel::makeCluster(parallel)
+                parallel <- makeCluster(parallel)
             }
-            Pstats <- parallel::parRapply(parallel, permutations,
+            Pstats <- parRapply(parallel, permutations,
                                           function(x) permFun(x))
             if (!hasClus) {
-                parallel::stopCluster(parallel)
+                stopCluster(parallel)
             }
         }
     } else {

Modified: pkg/vegan/R/permutest.cca.R
===================================================================
--- pkg/vegan/R/permutest.cca.R	2015-01-07 13:01:37 UTC (rev 2924)
+++ pkg/vegan/R/permutest.cca.R	2015-01-09 07:44:14 UTC (rev 2925)
@@ -120,18 +120,18 @@
     if (hasClus || parallel > 1) {
         if(.Platform$OS.type == "unix" && !hasClus) {
             tmp <- do.call(rbind,
-                           parallel::mclapply(1:nperm,
+                           mclapply(1:nperm,
                                     function(i) getF(permutations[i,]),
                                     mc.cores = parallel))
         } else {
             ## if hasClus, do not set up and stop a temporary cluster
             if (!hasClus) {
-                parallel <- parallel::makeCluster(parallel)
+                parallel <- makeCluster(parallel)
             }
-            tmp <- parallel::parRapply(parallel, permutations, function(i) getF(i))
+            tmp <- parRapply(parallel, permutations, function(i) getF(i))
             tmp <- matrix(tmp, ncol=3, byrow=TRUE)
             if (!hasClus)
-                parallel::stopCluster(parallel)
+                stopCluster(parallel)
         }
     } else {
         tmp <- getF(permutations)

Modified: pkg/vegan/R/print.mantel.correlog.R
===================================================================
--- pkg/vegan/R/print.mantel.correlog.R	2015-01-07 13:01:37 UTC (rev 2924)
+++ pkg/vegan/R/print.mantel.correlog.R	2015-01-09 07:44:14 UTC (rev 2925)
@@ -6,4 +6,4 @@
     cat('\n')
 	printCoefmat(x$mantel.res, P.values=TRUE, signif.stars=TRUE, Pvalues = TRUE)
     invisible(x) 
-}
\ No newline at end of file
+}

Modified: pkg/vegan/R/simper.R
===================================================================
--- pkg/vegan/R/simper.R	2015-01-07 13:01:37 UTC (rev 2924)
+++ pkg/vegan/R/simper.R	2015-01-09 07:44:14 UTC (rev 2925)
@@ -42,7 +42,7 @@
     isParal <- hasClus || parallel > 1
     isMulticore <- .Platform$OS.type == "unix" && !hasClus
     if (isParal && !isMulticore && !hasClus) {
-        parallel <- parallel::makeCluster(parallel)
+        parallel <- makeCluster(parallel)
     }
     for (i in seq_len(nrow(comp))) {
         group.a <- comm[group == comp[i, 1], , drop = FALSE]
@@ -67,11 +67,11 @@
 
             if (isParal) {
                 if (isMulticore){
-                    perm.contr <- parallel::mclapply(seq_len(nperm), function(d)
+                    perm.contr <- mclapply(seq_len(nperm), function(d)
                         pfun(d, comm, comp, i, contrp), mc.cores = parallel)
                     perm.contr <- do.call(cbind, perm.contr)
                 } else {
-                    perm.contr <- parallel::parSapply(parallel, seq_len(nperm), function(d)
+                    perm.contr <- parSapply(parallel, seq_len(nperm), function(d)
                         pfun(d, comm, comp, i, contrp))
                 }
             } else {
@@ -98,7 +98,7 @@
     }
     ## Close socket cluster if created here
     if (isParal && !isMulticore && !hasClus)
-        parallel::stopCluster(parallel)
+        stopCluster(parallel)
     attr(outlist, "permutations") <- nperm
     attr(outlist, "control") <- attr(perm, "control")
     class(outlist) <- "simper"

Modified: pkg/vegan/inst/NEWS.Rd
===================================================================
--- pkg/vegan/inst/NEWS.Rd	2015-01-07 13:01:37 UTC (rev 2924)
+++ pkg/vegan/inst/NEWS.Rd	2015-01-09 07:44:14 UTC (rev 2925)
@@ -8,8 +8,10 @@
     \itemize{
 
       \item This is a maintenance release to avoid warning messages
-      caused by changes in CRAN repository.
-    
+      caused by changes in CRAN repository. The namespace usage is also
+      more stringent to avoid warnings and notes in development versions
+      of \R.
+
     }
   }% end general
 
@@ -26,6 +28,10 @@
   \subsection{BUG FIXES}{
     \itemize{
 
+      \item \code{ordisurf} failed if \pkg{gam} package was loaded due
+      to namespace issues: some support functions of \pkg{gam} were used
+      instead of \pkg{mgcv} functions.
+
       \item \code{tolerance} function failed for unconstrained
       correspondence analysis.
 


From noreply at r-forge.r-project.org  Fri Jan  9 08:53:53 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri,  9 Jan 2015 08:53:53 +0100 (CET)
Subject: [Vegan-commits] r2926 - www
Message-ID: <20150109075353.B3FF7185F7A@r-forge.r-project.org>

Author: jarioksa
Date: 2015-01-09 08:53:53 +0100 (Fri, 09 Jan 2015)
New Revision: 2926

Modified:
   www/NEWS.html
Log:
update news


Modified: www/NEWS.html
===================================================================
--- www/NEWS.html	2015-01-09 07:44:14 UTC (rev 2925)
+++ www/NEWS.html	2015-01-09 07:53:53 UTC (rev 2926)
@@ -17,7 +17,9 @@
 
 <ul>
 <li><p> This is a maintenance release to avoid warning messages
-caused by changes in CRAN repository.
+caused by changes in CRAN repository. The namespace usage is also
+more stringent to avoid warnings and notes in development versions
+of <font face="Courier New,Courier" color="#666666"><b>R</b></font>.
 </p>
 </li></ul>
 
@@ -41,6 +43,11 @@
 
 
 <ul>
+<li> <p><code>ordisurf</code> failed if <span class="pkg">gam</span> package was loaded due
+to namespace issues: some support functions of <span class="pkg">gam</span> were used
+instead of <span class="pkg">mgcv</span> functions.
+</p>
+</li>
 <li> <p><code>tolerance</code> function failed for unconstrained
 correspondence analysis.
 </p>


From noreply at r-forge.r-project.org  Thu Jan 22 12:31:36 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 22 Jan 2015 12:31:36 +0100 (CET)
Subject: [Vegan-commits] r2927 - in pkg/vegan: . R man
Message-ID: <20150122113136.D25F11877C7@r-forge.r-project.org>

Author: jarioksa
Date: 2015-01-22 12:31:36 +0100 (Thu, 22 Jan 2015)
New Revision: 2927

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/R/showvarparts.R
   pkg/vegan/man/varpart.Rd
Log:
Merge branch 'cran-2.2' into r-forge-svn-local

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2015-01-09 07:53:53 UTC (rev 2926)
+++ pkg/vegan/DESCRIPTION	2015-01-22 11:31:36 UTC (rev 2927)
@@ -1,6 +1,6 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 2.2-1
+Version: 2.2-2
 Date: 2015-01-12
 Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, 
    Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, 

Modified: pkg/vegan/R/showvarparts.R
===================================================================
--- pkg/vegan/R/showvarparts.R	2015-01-09 07:53:53 UTC (rev 2926)
+++ pkg/vegan/R/showvarparts.R	2015-01-22 11:31:36 UTC (rev 2927)
@@ -1,24 +1,74 @@
-"showvarparts" <-
-function(parts = 2, labels, ...)
+`showvarparts` <-
+    function(parts, labels, bg = NULL, alpha=63, Xnames, id.size=1.2, ...)
 {
     rad <- 0.725
+    ## Default names
+    if (missing(Xnames))
+        Xnames <- paste("X", seq_len(parts), sep="")
+    ## transparent fill colours
+    if (!is.null(bg)) {
+        bg <- rgb(t(col2rgb(bg)), alpha = alpha, maxColorValue = 255)
+        if (length(bg) < parts)
+            bg <- rep(bg, length.out = parts)
+    }
+    ## centroids of circles (parts < 4) or individual fractions (parts
+    ## == 4)
     cp <- switch(parts,
-                 c(0,0),
-                 c(0,0, 1,0),
-                 c(0,0, 1,0, 0.5, -sqrt(3/4)),
-                 c(-0.5,0.3, 0.5, 0.3, 0, -sqrt(3/4)+0.3)
+                 matrix(c(0,0), ncol=2, byrow=TRUE),
+                 matrix(c(0,0, 1,0), ncol=2, byrow=TRUE),
+                 matrix(c(0,0, 1,0, 0.5, -sqrt(3/4)), ncol=2, byrow=TRUE),
+                 structure(
+                     c(-1.2, -0.6, 0.6, 1.2, -0.7, 0, -0.7, 0, 0.7, 0.7,
+                       0.3, -0.4, 0.4, -0.3, 0, 0, 0.7, 0.7, 0, 0.3, 0.4,
+                       -0.6,-1.2, -0.6, 0.3, -0.7, 0, 0, -0.7, -0.4),
+                     .Dim = c(15L, 2L))
                  )
-    cp <- matrix(cp, ncol=2, byrow=TRUE)
+    ## plot limits
+    if (parts < 4) {
+        xlim <- range(cp[,1]) + c(-rad, rad)
+        ylim <- range(cp[,2]) + c(-rad, rad)
+    } else {
+        xlim <- c(-1.7, 1.7)
+        ylim <- c(-1.7, 1.1)
+    }
+    ## plot
     plot(cp, axes=FALSE, xlab="", ylab="", asp=1, type="n", 
-         xlim = (range(cp[,1]) + c(-rad, rad)),
-         ylim = (range(cp[,2]) + c(-rad, rad)))
+         xlim = xlim, ylim = ylim)
     box()
-    symbols(cp, circles = rep(rad, min(parts,3)), inches = FALSE, add=TRUE, ...)
-    if (parts == 4) {
-        symbols(0, 0.2, rectangles=cbind(1, 0.5), inches=FALSE, add=TRUE, ...)
-        symbols(sqrt(1/2), -sqrt(3/4)+0.2, rectangles=cbind(0.5,0.3),
-                inches=FALSE, add=TRUE, ...)
+    if (parts < 4) {
+        symbols(cp, circles = rep(rad, min(parts,3)), inches = FALSE,
+                add=TRUE, bg = bg, ...)
+        ## Explanatory data set names added by PL
+        if(parts==2) {
+            pos.names = matrix(c(-0.65,1.65,0.65,0.65),2,2)
+        } else if(parts==3) {
+            pos.names = matrix(c(-0.65,1.65,-0.16,0.65,0.65,-1.5),3,2)
+        }
+        text(pos.names,labels=Xnames[1:parts], cex=id.size)
+    } else {
+        ## Draw ellipses with veganCovEllipse. Supply 2x2
+        ## matrix(c(d,a,a,d), 2, 2) which defines an ellipse of
+        ## semi-major axis length sqrt(d+a) semi-minor axis sqrt(d-a).
+        d <- 1
+        a <- 1/sqrt(2)
+        ## Small ellipses X2, X3 at the centroid
+        e2 <- veganCovEllipse(matrix(c(d,-a,-a,d), 2, 2))
+        e3 <- veganCovEllipse(matrix(c(d, a, a,d), 2, 2))
+        ## wider ellipses X1, X4 at sides going through the centroid
+        L <- d+a
+        W <- (sqrt(L) - sqrt(d-a))^2
+        d <- (L+W)/2
+        a <- (L-W)/2
+        cnt <- sqrt(W/2)
+        e1 <- veganCovEllipse(matrix(c(d,-a,-a,d), 2, 2), c(-cnt, -cnt))
+        e4 <- veganCovEllipse(matrix(c(d, a, a,d), 2, 2), c( cnt, -cnt))
+        polygon(rbind(e1,NA,e2,NA,e3,NA,e4), col = bg, ...)
+        ## Explanatory data set names added by PL
+        pos.names = matrix(c(-1.62,-1.10,1.10,1.62,0.54,1.00,1.00,0.54),4,2)
+        text(pos.names,labels=Xnames[1:4], cex=id.size)
     }
+    
+    ## label fractions
     nlabs <- switch(parts, 2, 4, 8, 16)
     if (missing(labels))
         labels <- paste("[", letters[1:nlabs], "]", sep="")
@@ -29,19 +79,10 @@
            text(rbind(cp[1,], colMeans(cp), cp[2,]), labels[-nlabs], ...),
            text(rbind(cp, colMeans(cp[1:2,]), colMeans(cp[2:3,]),
                       colMeans(cp[c(1,3),]), colMeans(cp)), labels[-nlabs], ...),
-           text(rbind(1.4*cp, c(0.8, -sqrt(3/4)+0.2),
-                      colMeans(cp[1:2,]) + c(0,0.25),
-                      colMeans(cp[2:3,]), colMeans(cp[c(1,3),]),
-                      cp[1,] + c(0.1,0), cp[2,] -c(0.1,0),
-                      c(0.6, -sqrt(3/4)+0.2), colMeans(cp[1:2,]),
-                      colMeans(cp)-c(0,0.12), colMeans(cp[2:3,]) + c(0,0.14),
-                      colMeans(cp[c(1,3),]) + c(0, 0.14),
-                      colMeans(cp) + c(0,0.08)),
-                labels[-nlabs], ...)
+           text(cp, labels[-nlabs], ...)
            )
     xy <- par("usr")
     text(xy[2] - 0.05*diff(xy[1:2]), xy[3] + 0.05*diff(xy[3:4]),
          paste("Residuals =", labels[nlabs]), pos = 2, ...)
     invisible()
 }
-

Modified: pkg/vegan/man/varpart.Rd
===================================================================
--- pkg/vegan/man/varpart.Rd	2015-01-09 07:53:53 UTC (rev 2926)
+++ pkg/vegan/man/varpart.Rd	2015-01-22 11:31:36 UTC (rev 2927)
@@ -21,7 +21,8 @@
 
 \usage{
 varpart(Y, X, ..., data, transfo, scale = FALSE)
-showvarparts(parts, labels, ...)
+showvarparts(parts, labels, bg = NULL, alpha = 63, Xnames,
+    id.size = 1.2,  ...)
 \method{plot}{varpart234}(x, cutoff = 0, digits = 1, ...)
 }
 
@@ -53,6 +54,21 @@
 \item{parts}{Number of explanatory tables (circles) displayed.}
 \item{labels}{Labels used for displayed fractions. Default is to use
   the same letters as in the printed output.}
+\item{bg}{Fill colours of circles or ellipses.}
+\item{alpha}{Transparency of the fill colour.  The argument takes
+    precedence over possible transparency definitions of the
+    colour. The value must be in range \eqn{0...255}, and low values
+    are more transparent.  Transparency is not available in all
+    graphics devices or file formats.}
+  
+\item{Xnames}{Names for sources of variation. Default names are \code{X1},
+  \code{X2}, \code{X3} and \code{X4}. \code{Xnames=NA},
+  \code{Xnames=NULL} and \code{Xnames=""} produce no names. The names
+  can be changed to other names. Use short names. }
+
+\item{id.size}{A numerical value giving the character expansion factor
+  for the names of circles or ellipses. }
+
 \item{x}{The \code{varpart} result.}
 \item{cutoff}{The values below \code{cutoff} will not be displayed.}
 \item{digits}{The number of significant digits; the number of decimal
@@ -113,10 +129,17 @@
   \code{[n]}, and the joint fraction between all four tables is
   \code{[o]}.
 
-  There is a \code{plot} function that displays the Venn
-  diagram and labels each intersection (individual fraction) with the
-  adjusted R squared if this is higher than \code{cutoff}.  A helper
-  function \code{showvarpart} displays the fraction labels.
+  There is a \code{plot} function that displays the Venn diagram and
+  labels each intersection (individual fraction) with the adjusted R
+  squared if this is higher than \code{cutoff}.  A helper function
+  \code{showvarpart} displays the fraction labels. The circles and
+  ellipses are labelled by short default names or by names defined by
+  the user in argument \code{Xnames}. Longer explanatory file names can
+  be written on the varpart output plot as follows: use option
+  \code{Xnames=NA}, then add new names using the \code{text} function. A
+  bit of fiddling with coordinates (see \code{\link{locator}}) and
+  character size should allow users to place names of reasonably short
+  lengths on the \code{varpart} plot.
   
 }
 
@@ -239,11 +262,9 @@
 mod <- varpart(mite, ~ ., mite.pcnm, data=mite.env, transfo="hel")
 mod
 
-## argument 'bg' is passed to circle drawing, and the following
-## defines semitransparent colours
-col2 <- rgb(c(1,1),c(1,0), c(0,1), 0.3)
-showvarparts(2, bg = col2)
-plot(mod, bg = col2)
+## Use fill colours
+showvarparts(2, bg = c("hotpink","skyblue"))
+plot(mod, bg = c("hotpink","skyblue"))
 # Alternative way of to conduct this partitioning
 # Change the data frame with factors into numeric model matrix
 mm <- model.matrix(~ SubsDens + WatrCont + Substrate + Shrub + Topo, mite.env)[,-1]
@@ -258,8 +279,8 @@
 mod <- varpart(mite, ~ SubsDens + WatrCont, ~ Substrate + Shrub + Topo,
    mite.pcnm, data=mite.env, transfo="hel")
 mod
-showvarparts(3)
-plot(mod)
+showvarparts(3, bg=2:4)
+plot(mod, bg=2:4)
 # An alternative formulation of the previous model using
 # matrices mm1 amd mm2 and Hellinger transformed species data
 mm1 <- model.matrix(~ SubsDens + WatrCont, mite.env)[,-1]
@@ -276,9 +297,9 @@
 mod <- varpart(mite, ~ SubsDens + WatrCont, ~Substrate + Shrub + Topo,
   mite.pcnm[,1:11], mite.pcnm[,12:22], data=mite.env, transfo="hel")
 mod
-plot(mod)
+plot(mod, bg=2:5)
 # Show values for all partitions by putting 'cutoff' low enough:
-plot(mod, cutoff = -Inf, cex = 0.7)
+plot(mod, cutoff = -Inf, cex = 0.7, bg=2:5)
 }
 
 \keyword{ multivariate }


From noreply at r-forge.r-project.org  Thu Jan 22 13:08:42 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 22 Jan 2015 13:08:42 +0100 (CET)
Subject: [Vegan-commits] r2928 - pkg/vegan/inst
Message-ID: <20150122120842.44EF8184B54@r-forge.r-project.org>

Author: jarioksa
Date: 2015-01-22 13:08:42 +0100 (Thu, 22 Jan 2015)
New Revision: 2928

Modified:
   pkg/vegan/inst/NEWS.Rd
Log:
Merge branch 'cran-2.2' into r-forge-svn-local

Modified: pkg/vegan/inst/NEWS.Rd
===================================================================
--- pkg/vegan/inst/NEWS.Rd	2015-01-22 11:31:36 UTC (rev 2927)
+++ pkg/vegan/inst/NEWS.Rd	2015-01-22 12:08:42 UTC (rev 2928)
@@ -2,6 +2,22 @@
 \title{vegan News}
 \encoding{UTF-8}
 
+\section{Changes in version 2.2-2}{
+
+  \subsection{NEW FEATURES}{
+    \itemize{
+
+      \item The \code{varpart} plots of four-component models were
+      redesigned following Legendre, Borcard & Roberts \emph{Ecology}
+      93, 1234--1240 (2012), and they use now four ellipses instead of
+      three circles and two rectangles. The components are now labelled
+      in plots, and the circles and ellipses can be easily filled with
+      transparent background colour.
+
+    }
+  } % new features
+} % v2.2-2
+
 \section{Changes in version 2.2-1}{
 
   \subsection{GENERAL}{


From noreply at r-forge.r-project.org  Thu Jan 22 13:10:05 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 22 Jan 2015 13:10:05 +0100 (CET)
Subject: [Vegan-commits] r2929 - www
Message-ID: <20150122121005.DE11D187700@r-forge.r-project.org>

Author: jarioksa
Date: 2015-01-22 13:10:05 +0100 (Thu, 22 Jan 2015)
New Revision: 2929

Modified:
   www/NEWS.html
Log:
NEWS about varpart update


Modified: www/NEWS.html
===================================================================
--- www/NEWS.html	2015-01-22 12:08:42 UTC (rev 2928)
+++ www/NEWS.html	2015-01-22 12:10:05 UTC (rev 2929)
@@ -8,6 +8,26 @@
 
 <h2>vegan News</h2>
 
+<h3>Changes in version 2.2-2</h3>
+
+
+
+<h4>NEW FEATURES</h4>
+
+
+<ul>
+<li><p> The <code>varpart</code> plots of four-component models were
+redesigned following Legendre, Borcard &amp; Roberts <EM>Ecology</EM>
+93, 1234&ndash;1240 (2012), and they use now four ellipses instead of
+three circles and two rectangles. The components are now labelled
+in plots, and the circles and ellipses can be easily filled with
+transparent background colour.
+</p>
+</li></ul>
+
+ 
+
+
 <h3>Changes in version 2.2-1</h3>
 
 


From noreply at r-forge.r-project.org  Tue Jan 27 13:26:15 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 27 Jan 2015 13:26:15 +0100 (CET)
Subject: [Vegan-commits] r2930 - in pkg/vegan: R man
Message-ID: <20150127122615.41D60187844@r-forge.r-project.org>

Author: jarioksa
Date: 2015-01-27 13:26:14 +0100 (Tue, 27 Jan 2015)
New Revision: 2930

Modified:
   pkg/vegan/R/cascadeKM.R
   pkg/vegan/man/cascadeKM.Rd
   pkg/vegan/man/cca.Rd
   pkg/vegan/man/sipoo.Rd
Log:
Merge branch 'cran-2.2' into r-forge-svn-local

Modified: pkg/vegan/R/cascadeKM.R
===================================================================
--- pkg/vegan/R/cascadeKM.R	2015-01-22 12:10:05 UTC (rev 2929)
+++ pkg/vegan/R/cascadeKM.R	2015-01-27 12:26:14 UTC (rev 2930)
@@ -47,9 +47,6 @@
     h <- 1
     for(ii in inf.gr:sup.gr)
     {
-        ## Initialization
-        ## set.seed(ii)  
-        ## Set.seed ? ?t? enlev? car il rend instable la fonction kmeans
         j <- ii - inf.gr + 1
         tmp <- kmeans(data, ii, iter.max = 50, nstart=iter)
         size[1:ii,h] <- tmp$size

Modified: pkg/vegan/man/cascadeKM.Rd
===================================================================
--- pkg/vegan/man/cascadeKM.Rd	2015-01-22 12:10:05 UTC (rev 2929)
+++ pkg/vegan/man/cascadeKM.Rd	2015-01-27 12:26:14 UTC (rev 2930)
@@ -145,7 +145,7 @@
 \references{
 
   Calinski, T. and J. Harabasz. 1974. A dendrite method for cluster
-  analysis. \emph{Commun. Stat.} \strong{3}: 1-27.
+  analysis. \emph{Commun. Stat.} \strong{3}: 1--27.
 
   Dolnicar, S., K. Grabler and J. A. Mazanec. 1999.  A tale of three
   cities: perceptual charting for analyzing destination images. Pp.
@@ -155,18 +155,18 @@
   
   Gower, J. C. 1966. Some distance properties of latent root and vector
   methods used in multivariate analysis. \emph{Biometrika} \strong{53}:
-  325-338.
+  325--338.
   
   Legendre, P. & L. Legendre. 2012. \emph{Numerical ecology}, 3rd
   English edition. Elsevier Science BV, Amsterdam.
   
   Milligan, G. W. & M. C. Cooper. 1985. An examination of procedures for
   determining the number of clusters in a data set. \emph{Psychometrika}
-  \strong{50}: 159-179.
+  \strong{50}: 159--179.
 
-  Weingessel, A., Dimitriadou, A. and Dolnicar, S. \emph{An Examination
-  Of Indexes For Determining The Number Of Clusters In Binary Data
-  Sets}, \url{http://www.wu-wien.ac.at/am/wp99.htm#29}
+  Weingessel, A., Dimitriadou, A. and Dolnicar, S. 2002. An examination
+  of indexes for determining the number of clusters in binary data
+  sets. \emph{Psychometrika} \strong{67}: 137--160.
 }
 
 \author{ Marie-Helene Ouellette

Modified: pkg/vegan/man/cca.Rd
===================================================================
--- pkg/vegan/man/cca.Rd	2015-01-22 12:10:05 UTC (rev 2929)
+++ pkg/vegan/man/cca.Rd	2015-01-27 12:26:14 UTC (rev 2930)
@@ -190,7 +190,7 @@
 }
 \author{
   The responsible author was Jari Oksanen, but the code borrows heavily
-  from Dave Roberts (\url{http://labdsv.nr.usu.edu/}).
+  from Dave Roberts (Montana State University, USA).
 }
 
 \seealso{

Modified: pkg/vegan/man/sipoo.Rd
===================================================================
--- pkg/vegan/man/sipoo.Rd	2015-01-22 12:10:05 UTC (rev 2929)
+++ pkg/vegan/man/sipoo.Rd	2015-01-27 12:26:14 UTC (rev 2930)
@@ -15,10 +15,8 @@
   these unique). The example gives the areas of the studies islands in
   hectares. 
 }
+
 \source{
-\url{http://www.aics-research.com/nested/}
-}
-\references{
 Simberloff, D. & Martin, J.-L.  (1991). 
 Nestedness of insular avifaunas:
 simple summary statistics masking


From noreply at r-forge.r-project.org  Tue Jan 27 13:30:19 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 27 Jan 2015 13:30:19 +0100 (CET)
Subject: [Vegan-commits] r2931 - pkg/vegan/R
Message-ID: <20150127123019.DC139187844@r-forge.r-project.org>

Author: jarioksa
Date: 2015-01-27 13:30:19 +0100 (Tue, 27 Jan 2015)
New Revision: 2931

Modified:
   pkg/vegan/R/orditkplot.R
Log:
Merge branch 'cran-2.2' into r-forge-svn-local

Modified: pkg/vegan/R/orditkplot.R
===================================================================
--- pkg/vegan/R/orditkplot.R	2015-01-27 12:26:14 UTC (rev 2930)
+++ pkg/vegan/R/orditkplot.R	2015-01-27 12:30:19 UTC (rev 2931)
@@ -164,7 +164,8 @@
                        command=function() tcltk::tkpostscript(can, x=0, y=0,
                        height=height, width=width,
                        file=tcltk::tkgetSaveFile(
-                         filetypes="{{EPS file} {.eps}}")))
+                         filetypes="{{EPS file} {.eps}}",
+                         defaultextension=".eps")))
     dismiss <- tcltk::tkbutton(buts, text="Dismiss",
                                command=function() tcltk::tkdestroy(w))
     ## Dump current plot to an "orditkplot" object (internally)
@@ -244,7 +245,18 @@
         if (!isTRUE(unname(capabilities("tiff"))))
             falt["tiff"] <- FALSE
         ftypes <- ftypes[falt]
-        fname <- tcltk::tkgetSaveFile(filetypes=ftypes)
+        ## External Tcl/Tk in Windows seems to buggy with type
+        ## extensions of the file name: the extension is not
+        ## automatically appended, but defaultextension is interpreted
+        ## wrongly so that its value is not used as extension but
+        ## correct appending is done if defaultextension has any
+        ## value. The following kluge is against Tcl/Tk documentation,
+        ## and should be corrected if Tcl/Tk is fixed.
+        if (.Platform$OS.type == "windows")
+            fname <- tcltk::tkgetSaveFile(filetypes=ftypes,
+                                          defaultextension = TRUE)
+        else
+            fname <- tcltk::tkgetSaveFile(filetypes=ftypes)
         if(tcltk::tclvalue(fname) == "")
             return(NULL)
         fname <- tcltk::tclvalue(fname)