From noreply at r-forge.r-project.org Tue Jun 9 11:45:33 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 9 Jun 2015 11:45:33 +0200 (CEST) Subject: [Vegan-commits] r2951 - in pkg/vegan: . R man Message-ID: <20150609094533.D775B186734@r-forge.r-project.org> Author: jarioksa Date: 2015-06-09 11:45:33 +0200 (Tue, 09 Jun 2015) New Revision: 2951 Modified: pkg/vegan/DESCRIPTION pkg/vegan/R/centroids.cca.R pkg/vegan/R/ordiR2step.R pkg/vegan/man/monoMDS.Rd pkg/vegan/man/vegan-package.Rd Log: Merge branch 'cran-2.3' into r-forge-svn-local Modified: pkg/vegan/DESCRIPTION =================================================================== --- pkg/vegan/DESCRIPTION 2015-05-25 06:52:06 UTC (rev 2950) +++ pkg/vegan/DESCRIPTION 2015-06-09 09:45:33 UTC (rev 2951) @@ -1,12 +1,12 @@ Package: vegan Title: Community Ecology Package -Version: 2.3-0 -Date: 2015-05-21 +Version: 2.3-1 +Date: 2015-05-28 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 -Depends: permute (>= 0.7-8), lattice, R (>= 2.15.0) +Depends: permute (>= 0.8-0), lattice, R (>= 2.15.0) Suggests: parallel, tcltk Imports: MASS, cluster, mgcv Description: Ordination methods, diversity analysis and other Modified: pkg/vegan/R/centroids.cca.R =================================================================== --- pkg/vegan/R/centroids.cca.R 2015-05-25 06:52:06 UTC (rev 2950) +++ pkg/vegan/R/centroids.cca.R 2015-06-09 09:45:33 UTC (rev 2951) @@ -1,7 +1,7 @@ `centroids.cca` <- function(x, mf, wt) { - facts <- sapply(mf, is.factor) + facts <- sapply(mf, is.factor) | sapply(mf, is.character) if (!any(facts)) return(NULL) mf <- mf[, facts, drop = FALSE] Modified: pkg/vegan/R/ordiR2step.R =================================================================== --- pkg/vegan/R/ordiR2step.R 2015-05-25 06:52:06 UTC (rev 2950) +++ pkg/vegan/R/ordiR2step.R 2015-06-09 09:45:33 UTC (rev 2951) @@ -21,6 +21,11 @@ R2.0 <- 0 else R2.0 <- RsquareAdj(object)$adj.r.squared + ## only accepts upper scope + if (is.list(scope) && length(scope) <= 2L) + scope <- scope$upper + if (is.null(scope) || !length(add.scope(object, scope))) + stop("needs upper 'scope': no terms can be added") ## Get R2 of the scope if (inherits(scope, "rda")) scope <- delete.response(formula(scope)) Modified: pkg/vegan/man/monoMDS.Rd =================================================================== --- pkg/vegan/man/monoMDS.Rd 2015-05-25 06:52:06 UTC (rev 2950) +++ pkg/vegan/man/monoMDS.Rd 2015-06-09 09:45:33 UTC (rev 2951) @@ -138,7 +138,7 @@ components so that the first dimension shows the major variation. It is possible to rotate the solution so that the first axis is parallel to a given environmental variable using function - \code{\link{metaMDSrotate}}. + \code{\link{MDSrotate}}. } Modified: pkg/vegan/man/vegan-package.Rd =================================================================== --- pkg/vegan/man/vegan-package.Rd 2015-05-25 06:52:06 UTC (rev 2950) +++ pkg/vegan/man/vegan-package.Rd 2015-06-09 09:45:33 UTC (rev 2951) @@ -23,11 +23,9 @@ fields. Package \pkg{BiodiversityR} provides a GUI for a large subset of \pkg{vegan} functionality. -The \pkg{vegan} package is developed at R-Forge -(\url{http://vegan.r-forge.r-project.org}). The R-Forge provides -up-to-date information and mailing lists for help queries and bug -reports. Bug reports can also be emailed to the function authors or to -the package maintainers. +The \pkg{vegan} package is developed at GitHub +(\url{https://github.com/vegandevs/vegan/}). GitHub provides up-to-date +information and forums for bug reports. The \pkg{vegan} documents can be read with \code{\link{vegandocs}} function. In addition to \code{\link{vignette}}s of basic usage, you @@ -49,9 +47,6 @@ R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Helene Wagner. Many other people have contributed to individual functions: see credits in function help pages. - -The maintainers at the R-Forge are Jari Oksanen -and Gavin Simpson . } \examples{ ### Example 1: Unconstrained ordination From noreply at r-forge.r-project.org Tue Jun 16 13:43:03 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 16 Jun 2015 13:43:03 +0200 (CEST) Subject: [Vegan-commits] r2952 - pkg/vegan/R Message-ID: <20150616114303.38A011833AE@r-forge.r-project.org> Author: jarioksa Date: 2015-06-16 13:43:02 +0200 (Tue, 16 Jun 2015) New Revision: 2952 Modified: pkg/vegan/R/adonis.R pkg/vegan/R/rarecurve.R Log: Merge branch 'cran-2.3' into r-forge-svn-local Modified: pkg/vegan/R/adonis.R =================================================================== --- pkg/vegan/R/adonis.R 2015-06-09 09:45:33 UTC (rev 2951) +++ pkg/vegan/R/adonis.R 2015-06-16 11:43:02 UTC (rev 2952) @@ -134,11 +134,11 @@ stopCluster(parallel) ## Round to avoid arbitrary P-values with tied data f.perms <- round(f.perms, 12) + F.Mod <- round(F.Mod, 12) P <- (rowSums(t(f.perms) >= F.Mod)+1)/(permutations+1) } else { # no permutations f.perms <- P <- rep(NA, nterms) } - F.Mod <- round(F.Mod, 12) SumsOfSqs = c(SS.Exp.each, SS.Res, sum(SS.Exp.each) + SS.Res) tab <- data.frame(Df = c(df.Exp, df.Res, n-1), SumsOfSqs = SumsOfSqs, Modified: pkg/vegan/R/rarecurve.R =================================================================== --- pkg/vegan/R/rarecurve.R 2015-06-09 09:45:33 UTC (rev 2951) +++ pkg/vegan/R/rarecurve.R 2015-06-16 11:43:02 UTC (rev 2952) @@ -2,6 +2,9 @@ function(x, step = 1, sample, xlab = "Sample Size", ylab = "Species", label = TRUE, col, lty, ...) { + ## check input data: must be counts + if (!identical(all.equal(x, round(x)), TRUE)) + stop("function accepts only integers (counts)") ## sort out col and lty if (missing(col)) col <- par("col")