From noreply at r-forge.r-project.org Thu Aug 1 15:43:24 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 1 Aug 2013 15:43:24 +0200 (CEST) Subject: [Vegan-commits] r2578 - in pkg/vegan: R inst tests Message-ID: <20130801134324.3E5CD1812ED@r-forge.r-project.org> Author: jarioksa Date: 2013-08-01 15:43:23 +0200 (Thu, 01 Aug 2013) New Revision: 2578 Modified: pkg/vegan/R/make.commsim.R pkg/vegan/inst/ChangeLog pkg/vegan/tests/oecosimu-tests.Rout.save Log: replace indshuffle with much faster stats::rmultinom in make.commsim Modified: pkg/vegan/R/make.commsim.R =================================================================== --- pkg/vegan/R/make.commsim.R 2013-07-28 05:04:40 UTC (rev 2577) +++ pkg/vegan/R/make.commsim.R 2013-08-01 13:43:23 UTC (rev 2578) @@ -199,10 +199,7 @@ mode="integer", fun=function(x, n, nr, nc, cs, rs, rf, cf, s, fill, thin) { indshuffle <- function(x) { - out <- integer(length(x)) - tmp <- table(sample.int(length(x), sum(x), replace = TRUE)) - out[as.integer(names(tmp))] <- as.integer(tmp) - out + drop(rmultinom(1, sum(x), rep(1, length(x)))) } nz <- as.integer(x[x > 0]) out <- array(unlist(r2dtable(fill, rf, cf)), c(nr, nc, n)) @@ -256,10 +253,7 @@ mode="integer", fun=function(x, n, nr, nc, cs, rs, rf, cf, s, fill, thin) { indshuffle <- function(x) { - out <- integer(length(x)) - tmp <- table(sample.int(length(x), sum(x), replace = TRUE)) - out[as.integer(names(tmp))] <- as.integer(tmp) - out + drop(rmultinom(1, sum(x), rep(1, length(x)))) } I <- seq_len(nr) out <- array(unlist(r2dtable(fill, rf, cf)), c(nr, nc, n)) @@ -281,10 +275,7 @@ mode="integer", fun=function(x, n, nr, nc, cs, rs, rf, cf, s, fill, thin) { indshuffle <- function(x) { - out <- integer(length(x)) - tmp <- table(sample.int(length(x), sum(x), replace = TRUE)) - out[as.integer(names(tmp))] <- as.integer(tmp) - out + drop(rmultinom(1, sum(x), rep(1, length(x)))) } J <- seq_len(nc) out <- array(unlist(r2dtable(fill, rf, cf)), c(nr, nc, n)) @@ -357,10 +348,7 @@ mode="integer", fun=function(x, n, nr, nc, rs, cs, rf, cf, s, fill, thin) { indshuffle <- function(x) { - out <- integer(length(x)) - tmp <- table(sample.int(length(x), sum(x), replace = TRUE)) - out[as.integer(names(tmp))] <- as.integer(tmp) - out + drop(rmultinom(1, sum(x), rep(1, length(x)))) } out <- matrix(0L, nr * nc, n) for (k in seq_len(n)) @@ -372,10 +360,7 @@ mode="integer", fun=function(x, n, nr, nc, rs, cs, rf, cf, s, fill, thin) { indshuffle <- function(x) { - out <- integer(length(x)) - tmp <- table(sample.int(length(x), sum(x), replace = TRUE)) - out[as.integer(names(tmp))] <- as.integer(tmp) - out + drop(rmultinom(1, sum(x), rep(1, length(x)))) } out <- array(0L, c(nr, nc, n)) J <- seq_len(nc) @@ -388,10 +373,7 @@ mode="integer", fun=function(x, n, nr, nc, rs, cs, rf, cf, s, fill, thin) { indshuffle <- function(x) { - out <- integer(length(x)) - tmp <- table(sample.int(length(x), sum(x), replace = TRUE)) - out[as.integer(names(tmp))] <- as.integer(tmp) - out + drop(rmultinom(1, sum(x), rep(1, length(x)))) } out <- array(0L, c(nr, nc, n)) I <- seq_len(nr) @@ -404,10 +386,7 @@ mode="integer", fun=function(x, n, nr, nc, rs, cs, rf, cf, s, fill, thin) { indshuffle <- function(x) { - out <- integer(length(x)) - tmp <- table(sample.int(length(x), sum(x), replace = TRUE)) - out[as.integer(names(tmp))] <- as.integer(tmp) - out + drop(rmultinom(1, sum(x), rep(1, length(x)))) } out <- matrix(0L, nr * nc, n) for (k in seq_len(n)) { @@ -421,10 +400,7 @@ mode="integer", fun=function(x, n, nr, nc, rs, cs, rf, cf, s, fill, thin) { indshuffle <- function(x) { - out <- integer(length(x)) - tmp <- table(sample.int(length(x), sum(x), replace = TRUE)) - out[as.integer(names(tmp))] <- as.integer(tmp) - out + drop(rmultinom(1, sum(x), rep(1, length(x)))) } out <- array(0L, c(nr, nc, n)) J <- seq_len(nc) @@ -439,10 +415,7 @@ mode="integer", fun=function(x, n, nr, nc, rs, cs, rf, cf, s, fill, thin) { indshuffle <- function(x) { - out <- integer(length(x)) - tmp <- table(sample.int(length(x), sum(x), replace = TRUE)) - out[as.integer(names(tmp))] <- as.integer(tmp) - out + drop(rmultinom(1, sum(x), rep(1, length(x)))) } out <- array(0L, c(nr, nc, n)) I <- seq_len(nr) Modified: pkg/vegan/inst/ChangeLog =================================================================== --- pkg/vegan/inst/ChangeLog 2013-07-28 05:04:40 UTC (rev 2577) +++ pkg/vegan/inst/ChangeLog 2013-08-01 13:43:23 UTC (rev 2578) @@ -13,6 +13,14 @@ Ecology Progress Series_, 320, 11?27. The basic development was made in github.com and merged to R-Forge. + * nullmodel: replaced internal indshuffle() function in + make.commsim() with much faster stats::rmultinom(). The + rmultinom() function takes argument 'n' for the number of random + vectors, and using this could be still faster, but we only + generate one vector in time. Using 'n' would require better + analysis of individual nullmodels. The commit changes random + sequences, but passes tests. + * oecosimu: Gained argument 'batchsize' to set the maximum size of simulated nullmodels (in Mb). If a larger object would be produced, the analysis is broken into several batches to avoid Modified: pkg/vegan/tests/oecosimu-tests.Rout.save =================================================================== --- pkg/vegan/tests/oecosimu-tests.Rout.save 2013-07-28 05:04:40 UTC (rev 2577) +++ pkg/vegan/tests/oecosimu-tests.Rout.save 2013-08-01 13:43:23 UTC (rev 2578) @@ -1,8 +1,8 @@ -R Under development (unstable) (2013-01-31 r61792) -- "Unsuffered Consequences" +R version 2.15.3 (2013-03-01) -- "Security Blanket" Copyright (C) 2013 The R Foundation for Statistical Computing ISBN 3-900051-07-0 -Platform: x86_64-unknown-linux-gnu (64-bit) +Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. @@ -626,56 +626,56 @@ --> margin none shuffle ind <-- grand sum: [1] TRUE -row sums: [1] "Mean relative difference: 0.3935785" -col sums: [1] "Mean relative difference: 1.181426" -fill: [1] "Mean relative difference: 0.5952064" -row freqs: [1] "Mean relative difference: 0.5952064" -col freqs: [1] "Mean relative difference: 0.5952064" +row sums: [1] "Mean relative difference: 0.4053168" +col sums: [1] "Mean relative difference: 1.1797" +fill: [1] "Mean relative difference: 0.5960133" +row freqs: [1] "Mean relative difference: 0.5960133" +col freqs: [1] "Mean relative difference: 0.6122867" Brachy PHTH HPAV RARD SSTR Protopl MEGR MPRO TVIE HMIN HMIN2 NPRA -8 3 2 3 9 0 1 5 6 3 4 5 0 -9 3 3 4 3 4 5 4 7 4 5 2 2 -11 4 2 7 3 2 2 4 4 6 3 3 7 -14 2 5 6 2 6 1 3 5 2 4 2 3 -15 2 0 6 1 5 2 2 1 2 5 4 4 -19 2 3 6 10 5 3 2 2 1 4 3 2 -25 6 3 5 4 3 4 5 2 2 1 6 2 -30 9 3 1 5 6 3 4 7 6 4 3 4 -32 5 0 3 3 3 6 5 5 3 4 2 9 -33 4 5 1 5 5 1 1 6 4 3 4 4 -34 4 2 6 7 4 5 6 6 5 2 6 3 -35 5 9 5 6 2 5 3 4 7 3 2 3 -36 3 2 5 5 0 5 3 1 1 8 4 3 -37 7 2 5 7 8 2 3 2 4 3 6 3 -38 2 7 4 3 7 3 4 1 3 4 6 3 -39 3 4 4 2 1 3 3 4 0 2 6 4 -40 3 4 2 6 3 2 5 3 3 3 5 2 -41 2 3 3 3 5 4 5 3 6 4 2 6 -42 7 4 3 3 5 5 3 4 5 4 1 4 -43 4 4 2 3 5 6 2 7 7 3 2 7 -44 5 6 4 3 4 1 6 2 5 5 2 8 -45 3 4 4 2 4 6 2 0 2 4 6 6 -46 1 3 6 5 2 3 2 4 0 5 2 6 -47 5 2 3 5 5 1 6 5 4 4 0 3 -48 2 7 2 5 6 7 3 2 2 3 1 5 -49 5 2 4 4 4 4 4 1 4 7 3 3 -50 3 6 2 7 2 1 10 2 3 5 2 3 -51 2 5 7 2 4 8 6 1 3 1 2 5 -52 2 2 0 1 2 5 3 3 3 2 3 3 -53 3 6 6 5 4 5 5 6 4 8 1 4 -54 7 3 1 5 1 2 4 4 8 4 2 9 -55 5 3 6 8 1 5 1 3 5 4 6 6 -56 4 3 4 5 3 4 3 6 5 5 4 4 -57 2 3 2 0 6 6 1 8 5 3 3 1 -58 4 6 4 6 5 4 1 6 6 5 7 3 -59 2 5 6 2 3 6 5 6 6 5 4 5 -60 1 2 2 1 3 5 5 6 6 3 5 2 -61 2 1 2 3 3 3 4 2 1 5 4 6 -62 7 6 2 2 0 0 2 3 2 5 1 4 -63 8 2 6 4 3 0 3 4 6 5 7 5 -64 0 4 6 1 6 8 3 4 3 0 4 6 -66 3 8 2 7 3 4 4 7 6 0 3 1 -67 6 3 1 3 3 1 3 6 3 5 9 5 -68 5 4 8 6 4 1 0 6 2 5 4 1 +8 8 6 5 2 5 2 3 2 3 4 1 6 +9 4 3 4 11 2 5 3 4 3 2 6 3 +11 7 3 5 2 2 4 3 3 6 5 2 2 +14 2 7 1 3 5 1 4 5 7 6 8 6 +15 6 1 4 6 1 2 6 2 3 4 1 3 +19 4 6 2 5 5 8 4 7 3 5 3 3 +25 3 4 8 4 3 2 5 1 2 4 5 4 +30 2 5 4 3 1 4 2 8 5 2 2 1 +32 2 2 5 3 5 4 5 4 4 4 4 5 +33 1 4 3 2 2 7 4 1 3 3 2 1 +34 1 3 1 4 4 2 4 7 2 5 5 2 +35 4 5 3 8 10 6 2 6 5 1 6 3 +36 5 2 3 5 5 4 2 5 2 2 3 5 +37 2 5 5 5 5 1 6 5 3 3 1 2 +38 2 5 5 4 2 3 2 8 2 4 5 3 +39 2 8 7 2 2 4 5 5 6 2 1 5 +40 4 4 3 4 3 3 4 0 2 1 4 5 +41 5 7 5 3 4 3 2 2 6 4 2 6 +42 5 7 1 6 3 5 2 2 0 5 4 5 +43 8 7 2 4 1 1 4 2 2 1 7 3 +44 2 6 3 4 7 4 1 8 1 2 4 9 +45 6 4 3 1 5 3 3 3 3 1 6 5 +46 1 3 2 9 2 2 0 6 3 4 4 2 +47 5 7 5 4 3 8 2 4 1 5 5 5 +48 4 2 3 8 3 5 3 7 5 1 4 3 +49 6 4 1 3 5 4 3 3 3 3 6 2 +50 4 2 0 4 4 3 1 3 6 2 2 2 +51 1 1 3 2 4 1 3 5 2 5 6 5 +52 4 3 5 3 5 5 2 6 3 2 4 5 +53 3 4 9 5 2 0 2 5 3 3 2 2 +54 7 0 6 3 4 6 4 6 4 6 2 5 +55 0 5 2 8 5 3 4 6 2 4 3 2 +56 3 1 5 5 1 2 5 2 6 3 2 4 +57 3 5 5 2 1 4 4 5 4 3 5 2 +58 4 7 5 6 3 3 2 1 2 3 1 7 +59 2 3 1 0 5 5 2 6 4 5 6 6 +60 3 1 4 5 4 8 6 3 2 6 3 5 +61 4 4 2 4 4 6 6 6 6 4 6 4 +62 6 4 4 0 5 1 3 4 3 7 0 5 +63 4 5 2 3 2 3 4 4 2 3 3 2 +64 5 3 3 4 5 3 4 2 3 3 3 4 +66 2 6 3 4 2 4 1 5 2 1 5 5 +67 4 1 2 4 3 3 4 4 1 5 2 1 +68 3 5 6 3 6 4 4 4 1 6 1 1 --> margin none shuffle samp <-- grand sum: [1] TRUE @@ -732,109 +732,109 @@ --> margin none shuffle both <-- grand sum: [1] TRUE -row sums: [1] "Mean relative difference: 0.4619368" -col sums: [1] "Mean relative difference: 1.228379" +row sums: [1] "Mean relative difference: 0.4389986" +col sums: [1] "Mean relative difference: 1.20342" fill: [1] TRUE -row freqs: [1] "Mean relative difference: 0.3531599" -col freqs: [1] "Mean relative difference: 0.6381579" +row freqs: [1] "Mean relative difference: 0.3670669" +col freqs: [1] "Mean relative difference: 0.5723684" Brachy PHTH HPAV RARD SSTR Protopl MEGR MPRO TVIE HMIN HMIN2 NPRA -8 0 0 0 14 0 0 9 16 7 5 0 0 -9 0 11 0 0 0 6 0 0 10 0 0 0 -11 5 0 0 13 0 0 0 0 0 12 0 0 -14 0 0 0 12 0 0 6 11 19 0 0 0 -15 0 0 0 6 0 6 0 0 7 0 13 9 -19 0 0 11 0 16 0 9 0 0 0 0 0 -25 0 12 5 0 0 0 0 0 13 0 0 0 -30 0 0 0 7 8 0 6 0 5 9 0 12 -32 6 14 0 11 0 10 12 0 12 0 8 0 -33 7 0 0 0 0 12 8 0 0 0 8 0 -34 9 0 0 0 0 10 0 0 0 0 0 11 -35 0 0 8 5 12 8 0 0 0 0 0 0 -36 0 0 0 0 0 7 0 0 0 11 10 0 -37 0 0 0 0 6 13 0 0 5 0 0 0 -38 7 9 0 0 0 0 15 6 0 11 8 0 -39 0 0 0 0 0 0 0 9 0 11 0 0 -40 11 0 0 6 6 11 0 8 0 0 0 11 -41 0 0 0 10 0 0 0 7 0 0 0 14 -42 0 14 0 7 0 0 12 10 10 0 6 0 -43 8 13 0 4 0 11 8 0 0 0 0 0 -44 11 7 8 11 0 12 11 16 0 0 0 0 -45 0 8 0 0 0 8 0 14 0 9 0 0 -46 0 0 0 2 14 9 0 0 12 14 0 0 -47 0 0 0 0 0 0 0 0 0 0 6 0 -48 0 9 0 11 0 0 11 0 7 0 0 0 -49 0 11 0 0 4 0 12 10 0 8 0 0 -50 0 9 0 0 16 0 0 0 0 0 0 0 -51 0 0 9 10 0 8 8 0 8 15 0 8 -52 0 0 0 10 11 3 11 10 0 10 0 0 -53 12 7 0 0 0 8 8 0 7 0 6 9 -54 8 6 8 9 0 0 0 6 6 0 11 0 -55 0 0 0 14 10 8 0 0 10 0 0 0 -56 11 0 0 0 0 0 0 0 0 0 0 0 -57 0 7 11 0 0 0 10 10 8 0 0 5 -58 9 0 0 8 0 11 14 0 0 0 0 10 -59 13 0 0 0 0 10 7 9 8 0 9 6 -60 6 0 0 0 0 11 9 0 10 0 0 6 -61 9 0 0 7 0 0 0 0 8 19 5 0 -62 0 0 0 0 0 0 0 6 0 16 0 10 -63 0 0 0 0 13 0 0 10 0 0 11 12 -64 0 0 0 0 0 6 13 13 10 0 0 8 -66 0 0 0 0 0 9 7 0 0 0 8 0 -67 0 0 0 0 0 0 0 0 0 0 13 8 -68 0 0 9 0 0 7 14 9 6 9 0 0 +8 0 7 9 7 6 12 0 10 0 0 0 0 +9 10 0 12 0 11 0 8 0 7 0 7 0 +11 6 14 9 0 6 0 12 0 0 7 0 11 +14 0 13 7 0 0 0 0 0 0 0 0 10 +15 15 0 0 0 9 0 11 0 16 11 0 0 +19 0 8 9 8 0 0 11 12 9 0 12 0 +25 0 12 7 10 0 7 12 0 0 10 0 12 +30 7 0 0 8 0 10 0 8 9 0 0 0 +32 8 0 0 0 0 0 11 0 0 0 0 0 +33 11 6 0 8 0 9 0 0 0 0 0 0 +34 0 15 9 7 0 13 5 7 0 11 0 0 +35 11 0 0 0 0 9 0 0 5 0 0 0 +36 0 0 10 9 9 0 0 9 0 7 4 0 +37 9 0 0 13 0 8 0 0 0 0 0 0 +38 10 7 10 9 10 0 10 0 14 11 6 0 +39 8 0 0 9 0 0 0 0 0 10 0 8 +40 0 8 0 0 0 0 12 0 0 0 11 0 +41 0 0 11 0 13 0 5 10 13 0 0 13 +42 0 7 7 0 0 11 16 11 11 14 0 7 +43 9 11 0 0 6 0 0 0 0 0 11 13 +44 9 0 0 7 14 8 0 7 10 0 7 0 +45 0 0 0 0 0 0 7 0 11 0 0 0 +46 9 9 0 0 0 9 7 0 0 0 0 0 +47 0 7 0 7 10 0 7 10 11 0 0 0 +48 9 7 0 9 12 0 12 8 7 10 10 0 +49 0 0 8 0 0 6 0 0 0 0 0 0 +50 0 0 9 11 8 15 0 0 15 9 0 7 +51 0 0 0 0 0 10 0 0 0 6 0 17 +52 0 8 0 0 3 0 0 10 8 0 0 10 +53 0 0 0 0 0 0 12 7 0 0 10 8 +54 9 6 10 0 6 6 0 0 7 14 0 0 +55 7 0 0 0 0 9 0 0 12 0 0 0 +56 0 0 8 0 0 17 10 8 0 0 0 0 +57 0 13 0 0 17 11 16 0 0 8 8 11 +58 0 4 12 0 6 0 0 0 0 15 12 8 +59 0 7 0 0 0 0 9 0 0 10 0 12 +60 0 10 0 0 0 7 0 0 0 0 0 0 +61 0 0 16 7 0 10 0 6 0 0 0 0 +62 11 0 4 0 5 9 11 8 0 12 0 9 +63 0 0 0 0 6 0 0 0 9 11 0 0 +64 0 0 2 7 0 0 0 0 10 3 0 0 +66 0 0 0 0 5 0 11 0 0 0 0 8 +67 0 0 0 11 0 0 9 0 6 0 8 0 +68 13 0 0 0 0 0 9 0 0 0 0 10 --> margin rows shuffle ind <-- grand sum: [1] TRUE row sums: [1] TRUE -col sums: [1] "Mean relative difference: 1.181426" -fill: [1] "Mean relative difference: 0.5700141" -row freqs: [1] "Mean relative difference: 0.5700141" -col freqs: [1] "Mean relative difference: 0.5909753" +col sums: [1] "Mean relative difference: 1.1797" +fill: [1] "Mean relative difference: 0.5715292" +row freqs: [1] "Mean relative difference: 0.5715292" +col freqs: [1] "Mean relative difference: 0.6076233" Brachy PHTH HPAV RARD SSTR Protopl MEGR MPRO TVIE HMIN HMIN2 NPRA -8 4 4 7 3 3 3 2 3 3 4 4 4 -9 3 1 3 6 6 1 5 4 1 4 3 1 -11 5 6 5 10 5 5 9 12 6 4 7 9 -14 7 7 6 10 5 2 7 8 9 6 10 9 -15 4 1 2 3 1 0 3 1 1 4 2 2 -19 3 3 6 3 6 4 2 5 7 2 3 3 -25 6 3 2 5 5 5 3 3 6 3 2 4 -30 2 5 2 3 1 3 1 3 3 1 5 3 -32 0 2 1 1 1 4 4 3 1 1 3 3 -33 7 7 4 5 4 2 5 3 1 3 5 7 -34 5 11 3 8 6 6 2 9 2 4 7 5 -35 3 2 2 6 2 4 8 4 4 3 2 6 -36 8 4 4 4 3 2 6 3 3 1 4 5 -37 5 3 6 6 4 4 1 4 5 3 4 5 -38 4 6 6 4 4 8 7 6 1 5 6 6 -39 1 4 1 2 2 6 2 1 3 2 3 4 -40 4 7 2 2 7 4 5 4 9 4 4 5 -41 0 3 3 1 0 2 2 2 3 5 0 2 -42 3 0 6 1 7 3 4 8 5 4 3 4 -43 5 8 3 5 4 6 7 3 7 8 4 2 -44 0 3 2 1 0 0 1 2 1 0 2 4 -45 1 4 5 4 5 3 3 4 5 4 3 8 -46 7 3 4 4 6 7 1 3 1 4 5 5 -47 6 1 1 5 3 2 6 3 4 5 2 4 -48 4 1 2 4 1 1 3 6 6 9 4 4 -49 2 2 4 3 3 5 5 3 1 4 3 6 -50 3 6 4 6 10 9 4 5 2 5 6 4 -51 4 1 1 3 3 2 2 3 2 3 0 4 -52 4 5 3 3 5 3 1 5 6 3 3 1 -53 4 4 7 6 3 2 4 2 6 5 5 0 -54 3 1 3 1 2 2 0 2 0 1 1 1 -55 2 1 1 3 0 0 0 2 2 2 2 1 -56 4 4 9 3 2 3 4 3 3 3 2 2 -57 0 0 0 0 0 0 1 0 0 1 0 1 -58 6 3 3 2 1 3 4 5 5 0 6 3 -59 4 2 6 3 2 0 2 4 5 1 3 1 -60 7 3 1 1 2 5 3 4 5 5 2 2 -61 2 0 1 1 1 0 2 2 2 2 1 1 -62 0 0 0 0 1 0 0 1 0 0 1 0 -63 2 1 2 3 3 2 3 0 3 4 0 2 -64 0 1 8 1 1 1 3 4 3 2 2 3 -66 5 5 5 4 3 4 1 1 3 7 1 6 -67 15 23 23 30 24 28 16 21 19 26 22 25 -68 3 2 2 3 3 2 4 3 4 4 2 2 +8 7 4 6 2 6 4 2 2 2 1 1 4 +9 4 2 2 4 5 4 5 1 4 3 5 3 +11 5 6 4 2 6 6 1 8 2 9 11 5 +14 9 12 6 9 4 6 6 7 5 10 7 4 +15 4 4 3 2 2 2 3 7 4 3 3 1 +19 0 2 4 4 4 3 4 2 2 4 1 5 +25 5 1 3 4 0 1 3 5 4 4 5 2 +30 3 0 3 2 1 7 4 3 2 1 4 0 +32 4 3 3 1 1 4 1 4 3 1 1 3 +33 4 4 2 4 3 5 2 7 1 8 4 1 +34 3 7 3 8 4 9 5 6 4 7 5 5 +35 3 1 4 3 5 2 2 3 4 2 5 4 +36 2 3 4 2 1 4 6 1 2 1 4 6 +37 2 9 1 4 6 2 4 2 5 6 3 2 +38 4 8 1 4 5 7 3 3 9 5 3 9 +39 1 4 4 1 4 1 3 1 6 5 3 2 +40 3 3 5 9 1 4 7 5 7 6 1 2 +41 4 3 3 3 3 2 2 0 3 1 4 2 +42 4 4 6 3 1 5 3 2 6 4 3 3 +43 3 3 6 2 8 4 6 4 4 5 1 4 +44 2 2 0 1 2 2 3 0 2 1 2 3 +45 6 7 3 8 3 2 2 4 5 8 1 4 +46 5 4 7 2 2 5 3 7 6 7 3 4 +47 4 4 3 3 1 5 2 3 4 6 5 4 +48 5 4 4 4 3 1 3 4 0 4 2 4 +49 2 6 1 1 0 1 6 5 3 2 1 2 +50 3 4 6 4 6 1 6 6 4 5 5 4 +51 0 2 2 7 3 3 4 5 7 4 3 5 +52 2 3 8 1 7 2 4 3 3 5 2 3 +53 5 7 3 5 3 5 3 6 7 4 4 5 +54 1 0 3 1 0 2 3 1 1 1 1 0 +55 0 1 2 2 3 5 0 1 2 0 2 3 +56 2 4 2 2 2 2 2 3 7 1 3 5 +57 0 1 0 0 0 0 1 0 0 1 0 0 +58 5 3 3 4 2 5 9 3 4 3 3 2 +59 7 2 2 2 4 3 0 1 2 1 3 3 +60 5 7 3 4 6 2 3 3 7 1 6 2 +61 2 0 1 1 1 1 1 1 1 2 1 4 +62 0 0 0 0 0 0 1 0 0 1 0 1 +63 3 2 0 3 3 2 2 1 1 0 4 1 +64 2 3 6 3 2 3 2 1 2 1 0 1 +66 2 1 6 2 4 2 2 4 5 1 1 2 +67 15 24 21 18 36 22 25 21 18 21 19 28 +68 6 4 4 2 0 4 6 1 1 1 4 6 --> margin rows shuffle samp <-- grand sum: [1] TRUE @@ -892,108 +892,108 @@ --> margin rows shuffle both <-- grand sum: [1] TRUE row sums: [1] TRUE -col sums: [1] "Mean relative difference: 1.223546" +col sums: [1] "Mean relative difference: 1.251856" fill: [1] TRUE row freqs: [1] TRUE -col freqs: [1] "Mean relative difference: 0.6239168" +col freqs: [1] "Mean relative difference: 0.6503497" Brachy PHTH HPAV RARD SSTR Protopl MEGR MPRO TVIE HMIN HMIN2 NPRA -8 3 6 0 5 4 6 0 4 0 8 11 3 -9 7 0 7 0 5 0 0 0 10 0 0 7 -11 11 9 9 7 0 6 0 7 9 0 13 6 -14 0 11 17 11 12 11 0 8 12 0 19 11 -15 0 0 5 6 3 6 3 5 5 0 10 0 -19 6 0 4 0 6 0 0 5 0 0 3 0 -25 0 0 4 6 5 0 0 0 0 6 0 0 -30 3 6 2 6 4 4 3 0 0 7 4 2 -32 0 0 8 0 0 4 8 8 2 0 4 0 -33 0 0 8 8 0 0 8 8 0 0 10 6 -34 10 4 12 0 0 0 0 7 7 0 8 0 -35 0 5 7 4 0 0 0 9 8 3 8 0 -36 5 0 0 0 6 9 8 0 9 8 0 5 -37 10 16 8 0 0 11 0 11 8 0 0 5 -38 0 0 12 0 0 0 13 0 11 15 0 0 -39 8 10 0 5 8 0 4 12 6 0 0 0 -40 9 0 0 8 0 0 0 20 0 14 11 0 -41 3 9 9 0 0 0 0 7 8 0 0 0 -42 0 0 0 0 13 18 0 0 0 18 0 12 -43 16 14 0 0 0 0 11 0 0 0 12 15 -44 0 0 0 0 0 0 10 0 0 0 0 0 -45 7 0 0 0 0 16 10 0 0 0 7 0 -46 0 14 0 0 9 6 0 0 0 0 0 0 -47 8 15 0 0 0 9 0 10 0 0 10 0 -48 0 0 0 0 0 0 12 0 0 0 9 8 -49 0 8 0 8 0 0 0 0 0 0 7 0 -50 0 0 0 0 0 0 0 0 0 0 0 9 -51 0 0 0 7 0 0 0 0 0 7 9 0 -52 11 7 7 0 0 6 0 6 0 0 12 12 -53 0 8 8 0 13 14 11 10 0 0 0 0 -54 5 0 0 0 0 0 0 2 7 0 6 0 -55 0 0 7 0 4 7 0 0 3 0 0 0 -56 9 0 13 9 0 0 12 0 11 0 0 0 -57 1 0 0 0 0 1 0 0 2 0 0 0 -58 0 0 0 0 9 10 0 11 0 0 11 0 -59 0 0 0 0 0 15 14 0 9 0 8 0 -60 0 8 0 0 9 0 0 14 0 0 16 0 -61 0 4 0 0 0 0 0 4 0 0 0 0 -62 0 0 0 0 0 3 0 0 0 0 0 0 -63 0 0 0 0 5 0 0 5 6 5 8 0 -64 7 12 0 8 0 9 0 8 3 7 0 8 -66 0 10 0 0 0 0 0 0 3 0 0 0 -67 0 0 0 0 0 0 0 0 0 139 0 0 -68 0 6 0 0 0 0 0 0 12 0 0 7 +8 6 0 6 0 0 9 4 0 0 4 0 10 +9 0 6 8 3 9 0 0 0 0 0 9 6 +11 5 6 0 0 10 0 4 5 7 0 11 0 +14 9 0 12 8 13 0 0 13 13 13 15 0 +15 0 6 0 4 0 6 2 0 0 0 8 7 +19 4 0 0 6 2 8 3 0 0 0 3 4 +25 0 0 5 0 3 7 9 7 4 0 0 0 +30 4 3 0 3 0 0 5 6 5 5 3 8 +32 0 8 0 0 3 8 0 2 0 11 0 6 +33 11 0 0 0 0 0 0 0 8 12 0 7 +34 10 9 0 0 9 8 12 0 0 0 10 0 +35 6 5 0 9 0 2 0 0 4 0 0 0 +36 6 5 8 0 0 0 6 0 0 0 4 12 +37 0 0 0 7 8 0 0 12 10 0 13 0 +38 0 8 14 15 14 0 0 13 12 0 0 0 +39 9 0 0 4 8 0 8 0 9 0 0 13 +40 0 0 0 0 10 14 0 0 0 0 0 0 +41 0 3 9 0 0 0 0 0 0 9 7 0 +42 21 0 0 0 12 17 0 0 15 0 15 0 +43 0 0 0 0 0 13 17 0 12 0 0 13 +44 0 13 0 0 0 0 0 0 0 17 0 0 +45 0 0 6 10 9 8 0 8 6 16 0 9 +46 0 0 0 8 9 13 0 12 0 7 0 4 +47 13 5 13 9 0 0 9 0 0 0 6 7 +48 0 0 8 0 0 0 0 0 12 11 12 0 +49 0 7 0 10 0 0 0 8 14 0 7 8 +50 0 0 0 10 13 11 0 0 0 0 18 13 +51 0 5 0 7 0 6 0 0 5 7 0 11 +52 0 0 0 0 5 12 0 0 0 0 0 0 +53 9 0 5 0 7 0 0 8 0 0 0 12 +54 0 0 0 11 0 0 0 0 6 4 5 0 +55 0 0 6 3 0 0 7 8 0 0 9 0 +56 13 0 14 0 0 0 7 0 13 9 0 0 +57 0 0 0 0 0 0 0 1 0 0 0 0 +58 16 0 0 10 10 0 0 9 0 0 0 0 +59 0 0 18 0 13 0 0 0 0 0 0 13 +60 0 0 0 9 0 10 13 0 0 0 0 15 +61 0 0 3 8 0 0 0 0 5 0 0 0 [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/vegan -r 2578 From noreply at r-forge.r-project.org Fri Aug 2 07:29:42 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 2 Aug 2013 07:29:42 +0200 (CEST) Subject: [Vegan-commits] r2579 - in pkg/vegan: R tests Message-ID: <20130802052942.2BBC518532D@r-forge.r-project.org> Author: jarioksa Date: 2013-08-02 07:29:41 +0200 (Fri, 02 Aug 2013) New Revision: 2579 Modified: pkg/vegan/R/make.commsim.R pkg/vegan/tests/oecosimu-tests.Rout.save Log: remove redundant sample() of random vectors Modified: pkg/vegan/R/make.commsim.R =================================================================== --- pkg/vegan/R/make.commsim.R 2013-08-01 13:43:23 UTC (rev 2578) +++ pkg/vegan/R/make.commsim.R 2013-08-02 05:29:41 UTC (rev 2579) @@ -207,7 +207,7 @@ for (k in seq_len(n)) { out[,,k] <- .C("quasiswap", m = out[,,k], nr, nc, PACKAGE = "vegan")$m - out[,,k][out[,,k] > 0] <- sample(indshuffle(nz - 1L) + 1L) # we assume that length(nz)>1 + out[,,k][out[,,k] > 0] <- indshuffle(nz - 1L) + 1L # we assume that length(nz)>1 } out }), @@ -266,7 +266,7 @@ if (length(nz) == 1) out[i,,k][out[i,,k] > 0] <- nz if (length(nz) > 1) - out[i,,k][out[i,,k] > 0] <- sample(indshuffle(nz - 1L) + 1L) + out[i,,k][out[i,,k] > 0] <- indshuffle(nz - 1L) + 1L } } out @@ -288,7 +288,7 @@ if (length(nz) == 1) out[,j,k][out[,j,k] > 0] <- nz if (length(nz) > 1) - out[,j,k][out[,j,k] > 0] <- sample(indshuffle(nz - 1L) + 1L) + out[,j,k][out[,j,k] > 0] <- indshuffle(nz - 1L) + 1L } } out Modified: pkg/vegan/tests/oecosimu-tests.Rout.save =================================================================== --- pkg/vegan/tests/oecosimu-tests.Rout.save 2013-08-01 13:43:23 UTC (rev 2578) +++ pkg/vegan/tests/oecosimu-tests.Rout.save 2013-08-02 05:29:41 UTC (rev 2579) @@ -1564,55 +1564,55 @@ --> margin rows shuffle both <-- grand sum: [1] TRUE row sums: [1] TRUE -col sums: [1] "Mean relative difference: 0.7018816" +col sums: [1] "Mean relative difference: 0.677024" fill: [1] TRUE row freqs: [1] TRUE col freqs: [1] TRUE Brachy PHTH HPAV RARD SSTR Protopl MEGR MPRO TVIE HMIN HMIN2 NPRA -8 3 0 8 0 7 4 0 0 0 0 4 3 -9 12 0 5 5 0 13 10 0 0 0 0 6 -11 12 0 8 11 0 0 5 7 5 9 0 9 -14 13 12 13 0 0 0 0 0 12 14 13 8 -15 3 0 10 0 0 0 0 0 6 2 0 5 -19 9 0 7 0 0 0 0 4 0 8 3 0 -25 5 7 6 0 0 0 0 0 6 6 0 0 -30 4 2 5 0 0 0 0 2 2 0 3 6 -32 8 8 8 0 0 0 0 0 2 0 0 6 -33 9 0 11 0 0 7 0 0 0 0 0 10 -34 11 0 7 8 0 8 6 0 4 7 4 10 -35 3 4 4 0 0 0 0 0 0 9 4 7 -36 6 0 6 0 3 8 8 6 0 0 0 8 -37 9 11 7 0 11 0 0 0 0 0 0 5 -38 19 0 11 0 0 16 15 0 0 0 0 11 -39 9 0 6 0 0 0 10 0 0 0 0 8 -40 21 0 11 0 0 0 16 0 14 0 0 0 -41 0 10 6 0 0 0 0 0 0 0 0 9 -42 17 0 18 0 0 16 0 0 0 0 0 0 -43 12 0 13 0 0 0 14 0 16 15 0 0 -44 0 0 15 0 0 0 0 0 0 0 0 11 -45 6 0 12 0 0 0 10 0 0 0 0 0 -46 11 0 9 0 0 0 0 12 4 8 0 0 -47 0 0 11 0 0 0 8 0 0 0 0 6 -48 9 0 12 0 0 0 0 0 0 0 0 0 -49 8 0 10 0 0 0 10 0 0 0 0 0 -50 13 0 9 0 0 0 0 0 0 0 0 14 -51 11 0 7 0 0 0 0 0 0 0 0 0 -52 13 0 11 0 0 0 0 0 0 5 0 0 -53 4 0 10 0 0 0 11 0 0 9 11 8 -54 7 0 4 0 0 0 0 0 0 5 0 0 -55 0 0 5 0 0 0 6 0 0 7 0 8 -56 9 0 7 0 0 0 0 0 0 0 0 7 -57 0 0 1 0 0 0 0 0 0 0 0 0 -58 0 0 13 0 0 0 8 0 0 5 0 0 -59 14 0 0 0 0 0 11 0 0 0 0 0 -60 9 0 0 0 0 0 0 0 11 0 0 7 -61 4 0 7 5 0 0 0 0 0 0 0 4 -62 1 0 0 0 0 0 0 0 2 0 0 0 -63 6 3 10 0 0 0 9 0 8 1 0 4 -64 8 0 0 0 0 0 12 0 6 0 0 6 -66 17 0 6 4 0 0 8 0 7 9 9 9 -67 0 0 136 0 0 0 0 0 0 135 0 0 -68 11 0 9 0 0 0 0 0 4 0 6 8 +8 8 0 3 0 5 14 0 0 0 0 5 5 +9 7 0 4 12 0 10 10 0 0 0 0 4 +11 6 0 8 13 0 0 8 8 12 8 0 9 +14 14 11 9 0 0 0 0 0 15 15 13 10 +15 5 0 6 0 0 0 0 0 5 5 0 7 +19 5 0 5 0 0 0 0 4 0 4 6 0 +25 5 6 5 0 0 0 0 0 9 6 0 0 +30 5 5 1 0 0 0 0 6 2 0 3 5 +32 6 4 3 0 0 0 0 0 8 0 0 3 +33 7 0 4 0 0 8 0 0 0 0 0 13 +34 9 0 11 10 0 7 11 0 6 13 12 9 +35 6 5 10 0 0 0 0 0 0 10 3 10 +36 8 0 7 0 13 6 4 4 0 0 0 9 +37 14 11 7 0 8 0 0 0 0 0 0 8 +38 17 0 14 0 0 20 12 0 0 0 0 12 +39 7 0 8 0 0 0 8 0 0 0 0 10 +40 14 0 10 0 0 0 12 0 15 0 0 0 +41 0 4 8 0 0 0 0 0 0 0 0 8 +42 15 0 14 0 0 15 0 0 0 0 0 0 +43 12 0 17 0 0 0 11 0 11 15 0 0 +44 0 0 9 0 0 0 0 0 0 0 0 15 +45 13 0 12 0 0 0 6 0 0 0 0 0 +46 10 0 10 0 0 0 0 8 8 15 0 0 +47 0 0 12 0 0 0 8 0 0 0 0 8 +48 12 0 9 0 0 0 0 0 0 0 0 0 +49 7 0 13 0 0 0 7 0 0 0 0 0 +50 12 0 8 0 0 0 0 0 0 0 0 16 +51 2 0 7 0 0 0 0 0 0 0 0 0 +52 4 0 8 0 0 0 0 0 0 11 0 0 +53 11 0 6 0 0 0 10 0 0 9 7 7 +54 7 0 6 0 0 0 0 0 0 4 0 0 +55 0 0 5 0 0 0 6 0 0 2 0 7 +56 10 0 10 0 0 0 0 0 0 0 0 10 +57 0 0 2 0 0 0 0 0 0 0 0 0 +58 0 0 10 0 0 0 10 0 0 5 0 0 +59 15 0 0 0 0 0 13 0 0 0 0 0 +60 3 0 0 0 0 0 0 0 9 0 0 8 +61 4 0 5 6 0 0 0 0 0 0 0 5 +62 3 0 0 0 0 0 0 0 3 0 0 0 +63 6 5 4 0 0 0 7 0 3 4 0 10 +64 8 0 0 0 0 0 5 0 7 0 0 7 +66 8 0 7 10 0 0 11 0 5 7 7 9 +67 0 0 119 0 0 0 0 0 0 134 0 0 +68 11 0 7 0 0 0 0 0 7 0 7 12 *** swsh *** --> margin columns shuffle samp <-- @@ -1671,56 +1671,56 @@ *** swsh *** --> margin columns shuffle both <-- grand sum: [1] TRUE -row sums: [1] "Mean relative difference: 0.378733" +row sums: [1] "Mean relative difference: 0.3752805" col sums: [1] TRUE fill: [1] TRUE row freqs: [1] TRUE col freqs: [1] TRUE Brachy PHTH HPAV RARD SSTR Protopl MEGR MPRO TVIE HMIN HMIN2 NPRA -8 8 0 9 0 1 1 0 0 0 0 3 4 -9 6 0 10 7 0 1 5 0 0 0 0 3 -11 8 0 19 1 0 0 4 2 3 10 0 3 -14 12 2 9 0 0 0 0 0 2 11 9 1 -15 7 0 10 0 0 0 0 0 1 12 0 4 -19 5 0 11 0 0 0 0 1 0 13 6 0 -25 8 2 10 0 0 0 0 0 3 9 0 0 -30 7 3 7 0 0 0 0 1 2 0 7 5 -32 8 3 14 0 0 0 0 0 2 0 0 1 -33 9 0 8 0 0 2 0 0 0 0 0 1 -34 11 0 14 5 0 1 5 0 2 10 6 2 -35 8 7 14 0 0 0 0 0 0 8 6 2 -36 11 0 7 0 1 2 5 1 0 0 0 3 -37 7 2 10 0 2 0 0 0 0 0 0 2 -38 13 0 12 0 0 1 6 0 0 0 0 5 -39 8 0 8 0 0 0 4 0 0 0 0 3 -40 8 0 7 0 0 0 9 0 2 0 0 0 -41 0 4 11 0 0 0 0 0 0 0 0 4 -42 5 0 13 0 0 1 0 0 0 0 0 0 -43 10 0 8 0 0 0 6 0 2 11 0 0 -44 0 0 8 0 0 0 0 0 0 0 0 5 -45 6 0 11 0 0 0 7 0 0 0 0 0 -46 6 0 10 0 0 0 0 1 4 12 0 0 -47 0 0 17 0 0 0 6 0 0 0 0 6 -48 13 0 8 0 0 0 0 0 0 0 0 0 -49 6 0 8 0 0 0 3 0 0 0 0 0 -50 9 0 6 0 0 0 0 0 0 0 0 5 -51 5 0 15 0 0 0 0 0 0 0 0 0 -52 11 0 13 0 0 0 0 0 0 10 0 0 -53 4 0 11 0 0 0 5 0 0 10 7 1 -54 6 0 10 0 0 0 0 0 0 9 0 0 -55 0 0 11 0 0 0 4 0 0 7 0 4 -56 6 0 8 0 0 0 0 0 0 0 0 2 -57 0 0 8 0 0 0 0 0 0 0 0 0 -58 0 0 14 0 0 0 2 0 0 8 0 0 -59 5 0 0 0 0 0 1 0 0 0 0 0 -60 5 0 0 0 0 0 0 0 3 0 0 2 -61 4 0 12 1 0 0 0 0 0 0 0 1 -62 9 0 0 0 0 0 0 0 1 0 0 0 -63 17 4 19 0 0 0 7 0 6 18 0 1 -64 8 0 0 0 0 0 3 0 5 0 0 3 -66 13 0 11 2 0 0 6 0 1 10 7 1 -67 0 0 8 0 0 0 0 0 0 11 0 0 -68 7 0 11 0 0 0 0 0 2 0 7 2 +8 11 0 9 0 2 1 0 0 0 0 5 3 +9 5 0 10 3 0 2 3 0 0 0 0 6 +11 7 0 9 3 0 0 3 1 4 10 0 1 +14 17 3 5 0 0 0 0 0 2 14 7 3 +15 7 0 13 0 0 0 0 0 2 14 0 1 +19 8 0 16 0 0 0 0 1 0 8 10 0 +25 5 5 7 0 0 0 0 0 5 11 0 0 +30 9 3 6 0 0 0 0 1 1 0 7 1 +32 7 3 16 0 0 0 0 0 2 0 0 4 +33 8 0 10 0 0 1 0 0 0 0 0 1 +34 4 0 15 3 0 1 7 0 2 11 4 5 +35 9 5 10 0 0 0 0 0 0 13 7 3 +36 6 0 15 0 1 1 2 1 0 0 0 5 +37 8 3 10 0 1 0 0 0 0 0 0 2 +38 6 0 11 0 0 2 5 0 0 0 0 7 +39 5 0 11 0 0 0 5 0 0 0 0 1 +40 9 0 13 0 0 0 4 0 4 0 0 0 +41 0 3 10 0 0 0 0 0 0 0 0 1 +42 8 0 8 0 0 1 0 0 0 0 0 0 +43 8 0 14 0 0 0 4 0 2 11 0 0 +44 0 0 14 0 0 0 0 0 0 0 0 5 +45 13 0 12 0 0 0 4 0 0 0 0 0 +46 8 0 9 0 0 0 0 2 3 11 0 0 +47 0 0 8 0 0 0 6 0 0 0 0 1 +48 4 0 9 0 0 0 0 0 0 0 0 0 +49 13 0 11 0 0 0 3 0 0 0 0 0 +50 11 0 15 0 0 0 0 0 0 0 0 1 +51 11 0 10 0 0 0 0 0 0 0 0 0 +52 5 0 6 0 0 0 0 0 0 4 0 0 +53 13 0 15 0 0 0 6 0 0 13 6 2 +54 6 0 11 0 0 0 0 0 0 6 0 0 +55 0 0 10 0 0 0 11 0 0 8 0 1 +56 7 0 7 0 0 0 0 0 0 0 0 3 +57 0 0 9 0 0 0 0 0 0 0 0 0 +58 0 0 17 0 0 0 10 0 0 11 0 0 +59 10 0 0 0 0 0 3 0 0 0 0 0 +60 6 0 0 0 0 0 0 0 1 0 0 5 +61 6 0 9 4 0 0 0 0 0 0 0 4 +62 6 0 0 0 0 0 0 0 2 0 0 0 +63 8 2 6 0 0 0 3 0 1 10 0 4 +64 12 0 0 0 0 0 6 0 4 0 0 2 +66 5 0 13 3 0 0 3 0 4 13 6 3 +67 0 0 10 0 0 0 0 0 0 11 0 0 +68 8 0 11 0 0 0 0 0 2 0 6 1 *** abuswap *** --> margin rows shuffle samp <-- @@ -1979,4 +1979,4 @@ > > proc.time() user system elapsed - 2.390 0.228 2.623 + 2.317 0.220 2.504 From noreply at r-forge.r-project.org Fri Aug 9 10:00:38 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 9 Aug 2013 10:00:38 +0200 (CEST) Subject: [Vegan-commits] r2580 - pkg/vegan/man Message-ID: <20130809080038.50CD118599D@r-forge.r-project.org> Author: jarioksa Date: 2013-08-09 10:00:37 +0200 (Fri, 09 Aug 2013) New Revision: 2580 Modified: pkg/vegan/man/specaccum.Rd Log: belated update of a literature reference Modified: pkg/vegan/man/specaccum.Rd =================================================================== --- pkg/vegan/man/specaccum.Rd 2013-08-02 05:29:41 UTC (rev 2579) +++ pkg/vegan/man/specaccum.Rd 2013-08-09 08:00:37 UTC (rev 2580) @@ -225,8 +225,8 @@ Kindt R., Van Damme, P. & Simons, A.J. (2006) Patterns of species richness at varying scales in western Kenya: planning for - agroecosystem diversification. \emph{Biodiversity and Conservation}, online - first: DOI 10.1007/s10531-005-0311-9 + agroecosystem diversification. \emph{Biodiversity and Conservation}, + 10: 3235--3249. Ugland, K.I., Gray, J.S. & Ellingsen, K.E. (2003). The species-accumulation curve and estimation of species richness. \emph{Journal From noreply at r-forge.r-project.org Fri Aug 9 10:13:48 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 9 Aug 2013 10:13:48 +0200 (CEST) Subject: [Vegan-commits] r2581 - pkg/vegan/man Message-ID: <20130809081348.710C0183F77@r-forge.r-project.org> Author: jarioksa Date: 2013-08-09 10:13:48 +0200 (Fri, 09 Aug 2013) New Revision: 2581 Modified: pkg/vegan/man/betadisper.Rd Log: update literature reference Modified: pkg/vegan/man/betadisper.Rd =================================================================== --- pkg/vegan/man/betadisper.Rd 2013-08-09 08:00:37 UTC (rev 2580) +++ pkg/vegan/man/betadisper.Rd 2013-08-09 08:13:48 UTC (rev 2581) @@ -146,7 +146,7 @@ will be biased downward. This bias matters most when comparing diversity among treatments with small, unequal numbers of samples. Setting \code{bias.adjust=TRUE} when using \code{betadisper} imposes a - \eqn{\sqrt{n/(n-1)}}{sqrt(n/(n-1))} correction (Stier et al. 2012). + \eqn{\sqrt{n/(n-1)}}{sqrt(n/(n-1))} correction (Stier et al. 2013). } \value{ The \code{anova} method returns an object of class \code{"anova"} @@ -214,9 +214,9 @@ Test of Homogeneity of Variance. \emph{Australian & New Zealand Journal of Statistics} \strong{42}, 81-?100. - Stier, A.C., Geange, S.W., Hanson, K.M., & Bolker, B.M. (2012) Predator - density and timing of arrival affect reef fish community assembly. Ms. - in revision, \emph{Oikos}. + Stier, A.C., Geange, S.W., Hanson, K.M., & Bolker, B.M. (2013) Predator + density and timing of arrival affect reef fish community + assembly. \emph{Ecology} \strong{94}, 1057--1068. } \author{Gavin L. Simpson; bias correction by Adrian Stier and Ben Bolker.} \seealso{\code{\link{permutest.betadisper}}, \code{\link[stats]{anova.lm}}, From noreply at r-forge.r-project.org Mon Aug 19 09:21:18 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 19 Aug 2013 09:21:18 +0200 (CEST) Subject: [Vegan-commits] r2582 - pkg/vegan Message-ID: <20130819072118.D301218514A@r-forge.r-project.org> Author: jarioksa Date: 2013-08-19 09:21:18 +0200 (Mon, 19 Aug 2013) New Revision: 2582 Modified: pkg/vegan/DESCRIPTION pkg/vegan/NAMESPACE Log: R-devel introduced more anal tests on suggests/imports etc. Modified: pkg/vegan/DESCRIPTION =================================================================== --- pkg/vegan/DESCRIPTION 2013-08-09 08:13:48 UTC (rev 2581) +++ pkg/vegan/DESCRIPTION 2013-08-19 07:21:18 UTC (rev 2582) @@ -8,7 +8,7 @@ Maintainer: Jari Oksanen Depends: permute (>= 0.7-4), R (>= 2.12.0) Imports: lattice -Suggests: MASS, mgcv, lattice, cluster, parallel, scatterplot3d, rgl, tcltk +Suggests: MASS, mgcv, cluster, parallel, scatterplot3d, rgl, tcltk Description: Ordination methods, diversity analysis and other functions for community and vegetation ecologists. License: GPL-2 Modified: pkg/vegan/NAMESPACE =================================================================== --- pkg/vegan/NAMESPACE 2013-08-09 08:13:48 UTC (rev 2581) +++ pkg/vegan/NAMESPACE 2013-08-19 07:21:18 UTC (rev 2582) @@ -63,8 +63,9 @@ ## Registration of S3 methods import(stats) import(graphics) +import(permute) importFrom(utils, head, tail, str) -importFrom(lattice, densityplot) +import(lattice) ## nobs only exists in R 2.13.0 -- import from permute with older R if (getRversion() < "2.13.0") { importFrom(permute, nobs) From noreply at r-forge.r-project.org Mon Aug 19 09:27:44 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 19 Aug 2013 09:27:44 +0200 (CEST) Subject: [Vegan-commits] r2583 - pkg/vegan/man Message-ID: <20130819072744.6BD8418514A@r-forge.r-project.org> Author: jarioksa Date: 2013-08-19 09:27:44 +0200 (Mon, 19 Aug 2013) New Revision: 2583 Modified: pkg/vegan/man/betadisper.Rd Log: TukeyHSD.aov is neither exported nor documented since R revision 63605 (2013-08-17) Modified: pkg/vegan/man/betadisper.Rd =================================================================== --- pkg/vegan/man/betadisper.Rd 2013-08-19 07:21:18 UTC (rev 2582) +++ pkg/vegan/man/betadisper.Rd 2013-08-19 07:27:44 UTC (rev 2583) @@ -128,7 +128,7 @@ comparison of group dispersions, is to calculate Tukey's Honest Significant Differences between groups, via \code{TukeyHSD.betadisper}. This is a simple wrapper to - \code{\link{TukeyHSD.aov}}. The user is directed to read the help file + \code{\link{TukeyHSD}}. The user is directed to read the help file for \code{\link{TukeyHSD}} before using this function. In particular, note the statement about using the function with unbalanced designs. From noreply at r-forge.r-project.org Mon Aug 19 09:36:39 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 19 Aug 2013 09:36:39 +0200 (CEST) Subject: [Vegan-commits] r2584 - pkg/vegan/R Message-ID: <20130819073640.0E39B18514A@r-forge.r-project.org> Author: jarioksa Date: 2013-08-19 09:36:39 +0200 (Mon, 19 Aug 2013) New Revision: 2584 Modified: pkg/vegan/R/prepanel.ordi3d.R Log: prepanel.default.cloud is exported from lattice Modified: pkg/vegan/R/prepanel.ordi3d.R =================================================================== --- pkg/vegan/R/prepanel.ordi3d.R 2013-08-19 07:27:44 UTC (rev 2583) +++ pkg/vegan/R/prepanel.ordi3d.R 2013-08-19 07:36:39 UTC (rev 2584) @@ -2,5 +2,5 @@ function(xlim = xlim, ylim = ylim, zlim = zlim, aspect = c(1,1), ...) { aspect = c(diff(ylim)/diff(xlim), diff(zlim)/diff(xlim)) - lattice:::prepanel.default.cloud(xlim = xlim, ylim = ylim, zlim = zlim, aspect = aspect, ...) + prepanel.default.cloud(xlim = xlim, ylim = ylim, zlim = zlim, aspect = aspect, ...) } From noreply at r-forge.r-project.org Mon Aug 19 09:45:39 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 19 Aug 2013 09:45:39 +0200 (CEST) Subject: [Vegan-commits] r2585 - pkg/vegan/R Message-ID: <20130819074539.53B021850AA@r-forge.r-project.org> Author: jarioksa Date: 2013-08-19 09:45:39 +0200 (Mon, 19 Aug 2013) New Revision: 2585 Modified: pkg/vegan/R/permutest.cca.R Log: vegan::: never needed within functions Modified: pkg/vegan/R/permutest.cca.R =================================================================== --- pkg/vegan/R/permutest.cca.R 2013-08-19 07:36:39 UTC (rev 2584) +++ pkg/vegan/R/permutest.cca.R 2013-08-19 07:45:39 UTC (rev 2585) @@ -110,7 +110,7 @@ else permutations <- t(sapply(1:permutations, - function(x) vegan:::permuted.index(N, strata=strata))) + function(x) permuted.index(N, strata=strata))) } nperm <- nrow(permutations) ## Parallel processing (similar as in oecosimu) From noreply at r-forge.r-project.org Mon Aug 19 10:50:29 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 19 Aug 2013 10:50:29 +0200 (CEST) Subject: [Vegan-commits] r2586 - in pkg/vegan: . R inst inst/doc man Message-ID: <20130819085029.DDD59185857@r-forge.r-project.org> 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 -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 Sz?cs'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}). -<>= -require(lattice, quietly=TRUE) -@ \begin{figure} <>= 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 From noreply at r-forge.r-project.org Mon Aug 19 15:29:51 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 19 Aug 2013 15:29:51 +0200 (CEST) Subject: [Vegan-commits] r2587 - pkg/vegan/man Message-ID: <20130819132951.4B0E8184DE2@r-forge.r-project.org> Author: jarioksa Date: 2013-08-19 15:29:50 +0200 (Mon, 19 Aug 2013) New Revision: 2587 Modified: pkg/vegan/man/anova.cca.Rd Log: print.anova is neither exported nor documented since R rev63619 (2013-08-19) Modified: pkg/vegan/man/anova.cca.Rd =================================================================== --- pkg/vegan/man/anova.cca.Rd 2013-08-19 08:50:29 UTC (rev 2586) +++ pkg/vegan/man/anova.cca.Rd 2013-08-19 13:29:50 UTC (rev 2587) @@ -139,9 +139,8 @@ \code{"permutest.cca"}, which has its own \code{print} method. The distribution of permuted \eqn{F} values can be inspected with \code{\link{density.permutest.cca}} function. The function - \code{anova.cca} calls \code{permutest.cca}, fills an - \code{\link{anova}} table and uses \code{\link{print.anova}} for - printing. + \code{anova.cca} calls \code{permutest.cca} and fills an + \code{\link{anova}} table. } \note{ From noreply at r-forge.r-project.org Fri Aug 23 08:45:23 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 23 Aug 2013 08:45:23 +0200 (CEST) Subject: [Vegan-commits] r2588 - in pkg/vegan: . R Message-ID: <20130823064524.03BE8185485@r-forge.r-project.org> Author: jarioksa Date: 2013-08-23 08:45:23 +0200 (Fri, 23 Aug 2013) New Revision: 2588 Modified: pkg/vegan/NAMESPACE pkg/vegan/R/vegandocs.R Log: startDynamicHelp and Rd2txt were exported from tools: no ::: needed Modified: pkg/vegan/NAMESPACE =================================================================== --- pkg/vegan/NAMESPACE 2013-08-19 13:29:50 UTC (rev 2587) +++ pkg/vegan/NAMESPACE 2013-08-23 06:45:23 UTC (rev 2588) @@ -65,6 +65,7 @@ import(graphics) import(permute) importFrom(utils, head, tail, str) +importFrom(tools, Rd2txt, startDynamicHelp) import(lattice) ## nobs only exists in R 2.13.0 -- import from permute with older R if (getRversion() < "2.13.0") { Modified: pkg/vegan/R/vegandocs.R =================================================================== --- pkg/vegan/R/vegandocs.R 2013-08-19 13:29:50 UTC (rev 2587) +++ pkg/vegan/R/vegandocs.R 2013-08-23 06:45:23 UTC (rev 2588) @@ -17,11 +17,11 @@ helptype <- getOption("help_type") if (length(helptype) && helptype == "html") { if (!tools:::httpdPort) - tools:::startDynamicHelp() + startDynamicHelp() browseURL(paste("http://127.0.0.1:", tools:::httpdPort, "/library/vegan/doc/NEWS.html", sep="")) } else { - file.show(tools:::Rd2txt(file.path(system.file(package="vegan"), + file.show(Rd2txt(file.path(system.file(package="vegan"), "NEWS.Rd"), tempfile())) } } else { From noreply at r-forge.r-project.org Fri Aug 23 13:49:17 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 23 Aug 2013 13:49:17 +0200 (CEST) Subject: [Vegan-commits] r2589 - in branches/2.0: R inst man Message-ID: <20130823114917.70297185AE1@r-forge.r-project.org> Author: jarioksa Date: 2013-08-23 13:49:17 +0200 (Fri, 23 Aug 2013) New Revision: 2589 Modified: branches/2.0/R/adipart.default.R branches/2.0/R/betadiver.R branches/2.0/R/hiersimu.default.R branches/2.0/R/multipart.default.R branches/2.0/R/orditkplot.R branches/2.0/R/vegandocs.R branches/2.0/R/vegdist.R branches/2.0/inst/ChangeLog branches/2.0/man/SSarrhenius.Rd branches/2.0/man/adipart.Rd branches/2.0/man/adonis.Rd branches/2.0/man/anova.cca.Rd branches/2.0/man/betadisper.Rd branches/2.0/man/cca.Rd branches/2.0/man/clamtest.Rd branches/2.0/man/density.adonis.Rd branches/2.0/man/eventstar.Rd branches/2.0/man/make.cepnames.Rd branches/2.0/man/mantel.correlog.Rd branches/2.0/man/model.matrix.cca.Rd branches/2.0/man/monoMDS.Rd branches/2.0/man/mrpp.Rd branches/2.0/man/multipart.Rd branches/2.0/man/nobs.adonis.Rd branches/2.0/man/ordistep.Rd branches/2.0/man/ordisurf.Rd branches/2.0/man/pcnm.Rd branches/2.0/man/prc.Rd branches/2.0/man/predict.cca.Rd branches/2.0/man/radfit.Rd branches/2.0/man/specaccum.Rd branches/2.0/man/vegan-package.Rd branches/2.0/man/vegdist.Rd Log: merge to 2.0-9 all itsy bitsy teenie weenie things that do not trigger conflicts Modified: branches/2.0/R/adipart.default.R =================================================================== --- branches/2.0/R/adipart.default.R 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/R/adipart.default.R 2013-08-23 11:49:17 UTC (rev 2589) @@ -24,7 +24,7 @@ ## check proper design of the model frame l1 <- sapply(rhs, function(z) length(unique(z))) if (!any(sapply(2:nlevs, function(z) l1[z] <= l1[z-1]))) - stop("number of levels are inapropriate, check sequence") + stop("number of levels are inappropriate, check sequence") rval <- list() rval[[1]] <- rhs[,nlevs] nCol <- nlevs - 1 Modified: branches/2.0/R/betadiver.R =================================================================== --- branches/2.0/R/betadiver.R 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/R/betadiver.R 2013-08-23 11:49:17 UTC (rev 2589) @@ -11,8 +11,8 @@ } beta <- list("w"="(b+c)/(2*a+b+c)", "-1"="(b+c)/(2*a+b+c)", "c"="(b+c)/2", "wb"="b+c", "r"="2*b*c/((a+b+c)^2-2*b*c)", - "I"="log(2*a+b+c)-2*a*log(2)/(2*a+b+c)-((a+b)*log(a+b)+(a+c)*log(a+c))/(2*a+b+c)", - "e"="exp(log(2*a+b+c)-2*a*log(2)/(2*a+b+c)-((a+b)*log(a+b)+(a+c)*log(a+c))/(2*a+b+c))-1", + "I"="log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) - ((a+b)*log(a+b) + (a+c)*log(a+c)) / (2*a+b+c)", + "e"="exp(log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) - ((a+b)*log(a+b) + (a+c)*log(a+c)) / (2*a+b+c))-1", "t"="(b+c)/(2*a+b+c)", "me"="(b+c)/(2*a+b+c)", "j"="a/(a+b+c)", "sor"="2*a/(2*a+b+c)", "m"="(2*a+b+c)*(b+c)/(a+b+c)", @@ -27,8 +27,9 @@ "z"="(log(2)-log(2*a+b+c)+log(a+b+c))/log(2)" ) if (help) { - for (i in 1:length(beta)) - cat(i, " \"", names(beta[i]),"\" = ", beta[[i]], "\n", sep="") + for (i in 1:length(beta)) + writeLines(strwrap(paste(i, " \"", names(beta[i]), + "\" = ", beta[[i]], "\n", sep=""))) return(invisible(NULL)) } x <- ifelse(x > 0, 1, 0) Modified: branches/2.0/R/hiersimu.default.R =================================================================== --- branches/2.0/R/hiersimu.default.R 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/R/hiersimu.default.R 2013-08-23 11:49:17 UTC (rev 2589) @@ -18,7 +18,7 @@ ## check proper design of the model frame l1 <- sapply(rhs, function(z) length(unique(z))) if (!any(sapply(2:nlevs, function(z) l1[z] <= l1[z-1]))) - stop("number of levels are inapropriate, check sequence") + stop("number of levels are inappropriate, check sequence") rval <- list() rval[[1]] <- rhs[,nlevs] nCol <- nlevs - 1 Modified: branches/2.0/R/multipart.default.R =================================================================== --- branches/2.0/R/multipart.default.R 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/R/multipart.default.R 2013-08-23 11:49:17 UTC (rev 2589) @@ -26,7 +26,7 @@ ## check proper design of the model frame l1 <- sapply(rhs, function(z) length(unique(z))) if (!any(sapply(2:nlevs, function(z) l1[z] <= l1[z-1]))) - stop("number of levels are inapropriate, check sequence") + stop("number of levels are inappropriate, check sequence") rval <- list() rval[[1]] <- rhs[,nlevs] nCol <- nlevs - 1 Modified: branches/2.0/R/orditkplot.R =================================================================== --- branches/2.0/R/orditkplot.R 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/R/orditkplot.R 2013-08-23 11:49:17 UTC (rev 2589) @@ -241,9 +241,6 @@ ## Should work also in R < 2.8.0 with no capabilities("tiff") if (!isTRUE(unname(capabilities("tiff")))) falt["tiff"] <- FALSE - ## bmp lives only in Windows - if (.Platform$OS.type != "windows") - falt["bmp"] <- FALSE ftypes <- ftypes[falt] fname <- tkgetSaveFile(filetypes=ftypes) if(tclvalue(fname) == "") Modified: branches/2.0/R/vegandocs.R =================================================================== --- branches/2.0/R/vegandocs.R 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/R/vegandocs.R 2013-08-23 11:49:17 UTC (rev 2589) @@ -17,11 +17,11 @@ helptype <- getOption("help_type") if (length(helptype) && helptype == "html") { if (!tools:::httpdPort) - tools:::startDynamicHelp() + startDynamicHelp() browseURL(paste("http://127.0.0.1:", tools:::httpdPort, "/library/vegan/doc/NEWS.html", sep="")) } else { - file.show(tools:::Rd2txt(file.path(system.file(package="vegan"), + file.show(Rd2txt(file.path(system.file(package="vegan"), "NEWS.Rd"), tempfile())) } } else { Modified: branches/2.0/R/vegdist.R =================================================================== --- branches/2.0/R/vegdist.R 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/R/vegdist.R 2013-08-23 11:49:17 UTC (rev 2589) @@ -21,7 +21,7 @@ warning("results may be meaningless because data have negative entries in method ", dQuote(inm)) if (method == 11 && any(colSums(x) == 0)) - warning("data have empty species which influence the results im method ", + warning("data have empty species which influence the results in method ", dQuote(inm)) if (method == 6) # gower, but no altGower x <- decostand(x, "range", 2, na.rm = TRUE, ...) Modified: branches/2.0/inst/ChangeLog =================================================================== --- branches/2.0/inst/ChangeLog 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/inst/ChangeLog 2013-08-23 11:49:17 UTC (rev 2589) @@ -2,8 +2,22 @@ VEGAN RELEASE VERSIONS at http://cran.r-project.org/ -Version 2.0-8 (opened March 19, 2013) +Version 2.0-9 (opened August 23, 2013) + * merge r2588: remove unneeded utils::: in vegandocs (some remain). + * merge r2583,7: remove cross-references to disappear in R-3.0-2. + * merge r2580,1: literature refs in specaccum.Rd and + betadisper.Rd. + * merge r2571: aspell fixes in Rd files (stressplot.wmcscale.Rd, + commsim.Rd and nullmodel.Rd did not exist in 2.0 and were + excluded). + * merge r2570: aspell fixes in R files. + * merge r2568: aspell fixes in Rd files. + * merge r2564: line wrapping in betadiver(help=TRUE). + * merge r2558: ordiktplot bmp device in all platforms. + +Version 2.0-8 (released July 10, 2013) + * merge r2540: remove hard-coded inconsolata fonts. * merge r2539: stressplot return data in input order. * merge r2538: use expression(R^2) in stressplot. Modified: branches/2.0/man/SSarrhenius.Rd =================================================================== --- branches/2.0/man/SSarrhenius.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/SSarrhenius.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -58,8 +58,8 @@ The Lomolino model (\code{SSlomolino}) is \code{Asym/(1 + slope^log(xmid/area))} (Lomolino 2000, Dengler 2009). Parameter \code{Asym} is the asymptotic maximum number of species, - \code{slope} is the maximum slope of increse of richness, and - \code{xmid} is the area where half of the maximum richess is + \code{slope} is the maximum slope of increase of richness, and + \code{xmid} is the area where half of the maximum richness is achieved. In addition to these models, several other models studied by Dengler Modified: branches/2.0/man/adipart.Rd =================================================================== --- branches/2.0/man/adipart.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/adipart.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -36,7 +36,7 @@ gamma diversities.} \item{formula}{A two sided model formula in the form \code{y ~ x}, where \code{y} is the community data matrix with samples as rows and - species as column. Right hand side (\code{x}) must grouping vaiables + species as column. Right hand side (\code{x}) must grouping variables referring to levels of sampling hierarchy, terms from right to left will be treated as nested (first column is the lowest, last is the highest level, at least two levels specified). Interaction terms are Modified: branches/2.0/man/adonis.Rd =================================================================== --- branches/2.0/man/adonis.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/adonis.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -127,7 +127,7 @@ \item{coef.sites}{ matrix of coefficients of the linear model, with rows representing sources of variation and columns representing sites; each column represents a fit of a sites distances (from all - other sites) to the linear model.These are what you get when you + other sites) to the linear model. These are what you get when you fit distances of one site to your predictors. } \item{f.perms}{ an \eqn{N} by \eqn{m} matrix of the null \eqn{F} Modified: branches/2.0/man/anova.cca.Rd =================================================================== --- branches/2.0/man/anova.cca.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/anova.cca.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -132,9 +132,8 @@ \code{"permutest.cca"}, which has its own \code{print} method. The distribution of permuted \eqn{F} values can be inspected with \code{\link{density.permutest.cca}} function. The function - \code{anova.cca} calls \code{permutest.cca}, fills an - \code{\link{anova}} table and uses \code{\link{print.anova}} for - printing. + \code{anova.cca} calls \code{permutest.cca} and fills an + \code{\link{anova}} table. } \note{ Modified: branches/2.0/man/betadisper.Rd =================================================================== --- branches/2.0/man/betadisper.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/betadisper.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -128,7 +128,7 @@ comparison of group dispersions, is to calculate Tukey's Honest Significant Differences between groups, via \code{TukeyHSD.betadisper}. This is a simple wrapper to - \code{\link{TukeyHSD.aov}}. The user is directed to read the help file + \code{\link{TukeyHSD}}. The user is directed to read the help file for \code{\link{TukeyHSD}} before using this function. In particular, note the statement about using the function with unbalanced designs. @@ -146,7 +146,7 @@ will be biased downward. This bias matters most when comparing diversity among treatments with small, unequal numbers of samples. Setting \code{bias.adjust=TRUE} when using \code{betadisper} imposes a - \eqn{\sqrt{n/(n-1)}}{sqrt(n/(n-1))} correction (Stier et al. 2012). + \eqn{\sqrt{n/(n-1)}}{sqrt(n/(n-1))} correction (Stier et al. 2013). } \value{ The \code{anova} method returns an object of class \code{"anova"} @@ -214,9 +214,9 @@ Test of Homogeneity of Variance. \emph{Australian & New Zealand Journal of Statistics} \strong{42}, 81-?100. - Stier, A.C., Geange, S.W., Hanson, K.M., & Bolker, B.M. (2012) Predator - density and timing of arrival affect reef fish community assembly. Ms. - in revision, \emph{Oikos}. + Stier, A.C., Geange, S.W., Hanson, K.M., & Bolker, B.M. (2013) Predator + density and timing of arrival affect reef fish community + assembly. \emph{Ecology} \strong{94}, 1057--1068. } \author{Gavin L. Simpson; bias correction by Adrian Stier and Ben Bolker.} \seealso{\code{\link{permutest.betadisper}}, \code{\link[stats]{anova.lm}}, Modified: branches/2.0/man/cca.Rd =================================================================== --- branches/2.0/man/cca.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/cca.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -228,7 +228,7 @@ finding influence statistics (\code{\link{lm.influence}}, \code{\link{cooks.distance}} etc.). - Permutation based signficance for the overall model, single + Permutation based significance for the overall model, single constraining variables or axes can be found with \code{\link{anova.cca}}. Automatic model building with \R{} \code{\link{step}} function is possible with @@ -239,7 +239,7 @@ \code{\link{simulate.cca}}. Separate methods based on constrained ordination model are principal - response curves (\code{\link{prc}}) and variance partioning between + response curves (\code{\link{prc}}) and variance partitioning between several components (\code{\link{varpart}}). Design decisions are explained in \code{\link{vignette}} Modified: branches/2.0/man/clamtest.Rd =================================================================== --- branches/2.0/man/clamtest.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/clamtest.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -132,7 +132,7 @@ \item The original authors suggest that multiple testing adjustment for multiple testing should be based on the number of points (\code{npoints}) used to draw the critical lines on the plot, - whereas the adjustment should be based on the number tests (i.e, + whereas the adjustment should be based on the number tests (i.e., tested species). The function uses the same numerical values as the original paper, but there is no automatic connection between \code{npoints} and \code{alpha} arguments, but you must work out Modified: branches/2.0/man/density.adonis.Rd =================================================================== --- branches/2.0/man/density.adonis.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/density.adonis.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -72,10 +72,10 @@ standard \code{plot} of \code{densiy} objects, but can also add a vertical line for the observed statistic. - Functions that can return several permuted statistics simultaenously + Functions that can return several permuted statistics simultaneously also have \code{\link[lattice]{densityplot}} method - (\code{\link{adonis}}, \code{\link{oecosimu}} and diversity partioning - functions based on \code{oecosimu}). The standard + (\code{\link{adonis}}, \code{\link{oecosimu}} and diversity + partitioning functions based on \code{oecosimu}). The standard \code{\link{density}} can only handle univariate data, and a warning is issued if the function is used for a model with several observed statistics. The \code{\link[lattice]{densityplot}} method is available Modified: branches/2.0/man/eventstar.Rd =================================================================== --- branches/2.0/man/eventstar.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/eventstar.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -34,7 +34,7 @@ The \eqn{q^\ast}{q*} index represents the scale parameter of the one parameter Tsallis diversity family that leads to the greatest deviation from the maximum equitability given the relative -abundance vactor of a community. +abundance vector of a community. The value of \eqn{q^\ast}{q*} is found by identifying the minimum of the evenness profile over scaling factor \eqn{q}{q} by Modified: branches/2.0/man/make.cepnames.Rd =================================================================== --- branches/2.0/man/make.cepnames.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/make.cepnames.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -26,7 +26,7 @@ formed by taking four first letters of the generic name and four first letters of the specific or subspecific epithet. The current function first makes valid \R names using \code{\link{make.names}}, - and then splits these into elemets. The CEP name is made by taking + and then splits these into elements. The CEP name is made by taking the four first letters of the first element, and four first letters of the last (default) or the second element (with \code{seconditem = TRUE}). If there was only one name element, it is Modified: branches/2.0/man/mantel.correlog.Rd =================================================================== --- branches/2.0/man/mantel.correlog.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/mantel.correlog.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -168,4 +168,5 @@ } -\keyword{ multivariate } \ No newline at end of file +\keyword{ multivariate } + Modified: branches/2.0/man/model.matrix.cca.Rd =================================================================== --- branches/2.0/man/model.matrix.cca.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/model.matrix.cca.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -37,8 +37,8 @@ of the original model are unavailable. } \value{ - Returns a data frame (\code{model.frame}) or an unnnamed matrix or a list - of two matrices called \code{Constraints} and \code{Conditions} + Returns a data frame (\code{model.frame}) or an unnamed matrix or a + list of two matrices called \code{Constraints} and \code{Conditions} (\code{model.matrix}). } \author{ Modified: branches/2.0/man/monoMDS.Rd =================================================================== --- branches/2.0/man/monoMDS.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/monoMDS.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -137,7 +137,7 @@ square and to rotate the axes (argument \code{pc}) to principal 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 fuction + parallel to a given environmental variable using function \code{\link{metaMDSrotate}}. } Modified: branches/2.0/man/mrpp.Rd =================================================================== --- branches/2.0/man/mrpp.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/mrpp.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -98,7 +98,7 @@ counts. Function \code{summary} finds the within-class, between-class and overall means of these dissimilarities, and the MRPP statistics with all \code{weight.type} options and the Classification Strength, - CS (Van Sickle and Hughes, 2000). CS is defined for dissimiliraties as + CS (Van Sickle and Hughes, 2000). CS is defined for dissimilirities as \eqn{\bar{B} - \bar{W}}{Bbar-Wbar}, where \eqn{\bar{B}}{Bbar} is the mean between cluster dissimilarity and \eqn{\bar{W}}{Wbar} is the mean within cluster dissimilarity with \code{weight.type = 1}. The function @@ -113,7 +113,7 @@ function \code{\link{hclust}}. The terminal segments hang to within-cluster dissimilarity. If some of the clusters are more heterogeneous than the combined class, the leaf segment are reversed. - The histograms are based on dissimilarites, but ore otherwise similar + The histograms are based on dissimilarities, but ore otherwise similar to those of Van Sickle and Hughes (2000): horizontal line is drawn at the level of mean between-cluster dissimilarity and vertical lines connect within-cluster dissimilarities to this line. } Modified: branches/2.0/man/multipart.Rd =================================================================== --- branches/2.0/man/multipart.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/multipart.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -25,7 +25,7 @@ all rows are in the same group in the second level.} \item{formula}{A two sided model formula in the form \code{y ~ x}, where \code{y} is the community data matrix with samples as rows and species as column. Right - hand side (\code{x}) must grouping vaiables referring to levels of sampling hierarchy, + hand side (\code{x}) must grouping variables referring to levels of sampling hierarchy, terms from right to left will be treated as nested (first column is the lowest, last is the highest level, at least two levels specified). Interaction terms are not allowed.} \item{data}{A data frame where to look for variables defined in the right hand side Modified: branches/2.0/man/nobs.adonis.Rd =================================================================== --- branches/2.0/man/nobs.adonis.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/nobs.adonis.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -38,7 +38,7 @@ \code{\link{isomap}}, \code{\link{metaMDS}}, \code{\link{pcnm}}, \code{\link{procrustes}}, \code{\link{radfit}}, \code{\link{varpart}} and \code{\link{wcmdscale}}. } \value{ A - single number, normally an interger, giving the number of + single number, normally an integer, giving the number of observations. } \author{ Modified: branches/2.0/man/ordistep.Rd =================================================================== --- branches/2.0/man/ordistep.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/ordistep.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -99,7 +99,7 @@ al. 2008). The second criterion is ignored with option \code{R2step = FALSE}, and the third criterion can be ignored setting \code{Pin = 1} (or higher). The \code{direction} has choices - \code{"forward"} and \code{"both"}, but it is very excepctional that a + \code{"forward"} and \code{"both"}, but it is very exceptional that a term is dropped with the adjusted \eqn{R^2}{R2} criterion. Function uses adjusted \eqn{R^2}{R2} as the criterion, and it cannot be used if the criterion cannot be calculated. Therefore it is unavailable for Modified: branches/2.0/man/ordisurf.Rd =================================================================== --- branches/2.0/man/ordisurf.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/ordisurf.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -42,7 +42,7 @@ if \code{knots = 2} the function will fit a quadratic trend surface instead of a smooth surface. A vector of length 2 is allowed when \code{isotropic = FALSE}, with the first and second elements of - \code{knots} refering to the first and second of ordination + \code{knots} referring to the first and second of ordination dimensions (as indicated by \code{choices}) respectively.} \item{family}{Error distribution in \code{\link[mgcv]{gam}}.} \item{col}{ Colour of contours. } Modified: branches/2.0/man/pcnm.Rd =================================================================== --- branches/2.0/man/pcnm.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/pcnm.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -33,9 +33,9 @@ distance has a huge influence on the PCNM vectors. The default is to use the longest distance to keep data connected. The distances above truncation threshold are given an arbitrary value of 4 times - threshold. For regular data, the first PCNM vectorsshow a wide scale + threshold. For regular data, the first PCNM vectors show a wide scale variation and later PCNM vectors show smaller scale variation (Borcard - & Legendre 2002), but for irregular data the intepretation is not as + & Legendre 2002), but for irregular data the interpretation is not as clear. The PCNM functions are used to express distances in rectangular form @@ -51,7 +51,7 @@ The function is based on \code{pcnm} function in Dray's unreleased \pkg{spacemakeR} package. The differences are that the current - function usesr \code{\link{spantree}} as an internal support + function uses \code{\link{spantree}} as an internal support function. The current function also can use prior weights for rows by using weighted metric scaling of \code{\link{wcmdscale}}. The use of row weights allows finding orthonormal PCNMs also for correspondence Modified: branches/2.0/man/prc.Rd =================================================================== --- branches/2.0/man/prc.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/prc.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -102,7 +102,7 @@ \section{Warning }{The first level of \code{treatment} must be the control: use function \code{\link{relevel}} to guarantee the correct - refence level. The current version will ignore user setting of + reference level. The current version will ignore user setting of \code{\link{contrasts}} and always use treatment contrasts (\code{\link{contr.treatment}}). The \code{time} must be an unordered factor. } Modified: branches/2.0/man/predict.cca.Rd =================================================================== --- branches/2.0/man/predict.cca.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/predict.cca.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -112,7 +112,7 @@ for sites from environmental data. In that case the new data frame must contain all constraining and conditioning environmental variables of the model formula. With \code{type = "response"} or - \code{type = "working"} the new data must contain envinronmental variables + \code{type = "working"} the new data must contain environmental variables if constrained component is desired, and community data matrix if residual or unconstrained component is desired. With these types, the function uses \code{newdata} to find new \code{"lc"} (constrained) or Modified: branches/2.0/man/radfit.Rd =================================================================== --- branches/2.0/man/radfit.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/radfit.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -197,7 +197,7 @@ \code{\link{coef}}, \code{\link{deviance}}, \code{\link{logLik}}. In addition the fit results can be accessed with \code{\link{fitted}}, \code{\link{predict}} and \code{\link{residuals}} (inheriting from - \code{\link{residuals.glm}}).The graphical functions were discussed + \code{\link{residuals.glm}}). The graphical functions were discussed above in Details. } Modified: branches/2.0/man/specaccum.Rd =================================================================== --- branches/2.0/man/specaccum.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/specaccum.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -191,8 +191,8 @@ Kindt R., Van Damme, P. & Simons, A.J. (2006) Patterns of species richness at varying scales in western Kenya: planning for - agroecosystem diversification. \emph{Biodiversity and Conservation}, online - first: DOI 10.1007/s10531-005-0311-9 + agroecosystem diversification. \emph{Biodiversity and Conservation}, + 10: 3235--3249. Ugland, K.I., Gray, J.S. & Ellingsen, K.E. (2003). The species-accumulation curve and estimation of species richness. \emph{Journal Modified: branches/2.0/man/vegan-package.Rd =================================================================== --- branches/2.0/man/vegan-package.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/vegan-package.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -107,4 +107,5 @@ \keyword{ spatial } \keyword{ nonparametric } \keyword{ htest } -\keyword{ regression } \ No newline at end of file +\keyword{ regression } + Modified: branches/2.0/man/vegdist.Rd =================================================================== --- branches/2.0/man/vegdist.Rd 2013-08-23 06:45:23 UTC (rev 2588) +++ branches/2.0/man/vegdist.Rd 2013-08-23 11:49:17 UTC (rev 2589) @@ -175,7 +175,7 @@ prob(j)}, or based on the probability of observing at least \eqn{j} species in shared in compared communities. The current function uses analytic result from hypergeometric distribution - (\code{\link{phyper}}) to find the probablities. This probability + (\code{\link{phyper}}) to find the probabilities. This probability (and the index) is dependent on the number of species missing in both sites, and adding all-zero species to the data or removing missing species from the data will influence the index. The probability (and From noreply at r-forge.r-project.org Fri Aug 23 13:56:39 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 23 Aug 2013 13:56:39 +0200 (CEST) Subject: [Vegan-commits] r2590 - pkg/vegan/man Message-ID: <20130823115639.9A82F1856A3@r-forge.r-project.org> Author: jarioksa Date: 2013-08-23 13:56:39 +0200 (Fri, 23 Aug 2013) New Revision: 2590 Modified: pkg/vegan/man/adipart.Rd pkg/vegan/man/mrpp.Rd pkg/vegan/man/multipart.Rd Log: aspell does not find all typos Modified: pkg/vegan/man/adipart.Rd =================================================================== --- pkg/vegan/man/adipart.Rd 2013-08-23 11:49:17 UTC (rev 2589) +++ pkg/vegan/man/adipart.Rd 2013-08-23 11:56:39 UTC (rev 2590) @@ -36,7 +36,7 @@ gamma diversities.} \item{formula}{A two sided model formula in the form \code{y ~ x}, where \code{y} is the community data matrix with samples as rows and - species as column. Right hand side (\code{x}) must grouping variables + species as column. Right hand side (\code{x}) must be grouping variables referring to levels of sampling hierarchy, terms from right to left will be treated as nested (first column is the lowest, last is the highest level, at least two levels specified). Interaction terms are Modified: pkg/vegan/man/mrpp.Rd =================================================================== --- pkg/vegan/man/mrpp.Rd 2013-08-23 11:49:17 UTC (rev 2589) +++ pkg/vegan/man/mrpp.Rd 2013-08-23 11:56:39 UTC (rev 2590) @@ -103,7 +103,7 @@ counts. Function \code{summary} finds the within-class, between-class and overall means of these dissimilarities, and the MRPP statistics with all \code{weight.type} options and the Classification Strength, - CS (Van Sickle and Hughes, 2000). CS is defined for dissimilirities as + CS (Van Sickle and Hughes, 2000). CS is defined for dissimilarities as \eqn{\bar{B} - \bar{W}}{Bbar-Wbar}, where \eqn{\bar{B}}{Bbar} is the mean between cluster dissimilarity and \eqn{\bar{W}}{Wbar} is the mean within cluster dissimilarity with \code{weight.type = 1}. The function Modified: pkg/vegan/man/multipart.Rd =================================================================== --- pkg/vegan/man/multipart.Rd 2013-08-23 11:49:17 UTC (rev 2589) +++ pkg/vegan/man/multipart.Rd 2013-08-23 11:56:39 UTC (rev 2590) @@ -25,7 +25,7 @@ all rows are in the same group in the second level.} \item{formula}{A two sided model formula in the form \code{y ~ x}, where \code{y} is the community data matrix with samples as rows and species as column. Right - hand side (\code{x}) must grouping variables referring to levels of sampling hierarchy, + hand side (\code{x}) must be grouping variables referring to levels of sampling hierarchy, terms from right to left will be treated as nested (first column is the lowest, last is the highest level, at least two levels specified). Interaction terms are not allowed.} \item{data}{A data frame where to look for variables defined in the right hand side From noreply at r-forge.r-project.org Fri Aug 23 14:01:41 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 23 Aug 2013 14:01:41 +0200 (CEST) Subject: [Vegan-commits] r2591 - in branches/2.0: inst man Message-ID: <20130823120141.9C69C1856A3@r-forge.r-project.org> Author: jarioksa Date: 2013-08-23 14:01:41 +0200 (Fri, 23 Aug 2013) New Revision: 2591 Modified: branches/2.0/inst/ChangeLog branches/2.0/man/adipart.Rd branches/2.0/man/mrpp.Rd branches/2.0/man/multipart.Rd Log: merge r2590 (typos) Modified: branches/2.0/inst/ChangeLog =================================================================== --- branches/2.0/inst/ChangeLog 2013-08-23 11:56:39 UTC (rev 2590) +++ branches/2.0/inst/ChangeLog 2013-08-23 12:01:41 UTC (rev 2591) @@ -4,6 +4,7 @@ Version 2.0-9 (opened August 23, 2013) + * merge 2590: typos. * merge r2588: remove unneeded utils::: in vegandocs (some remain). * merge r2583,7: remove cross-references to disappear in R-3.0-2. * merge r2580,1: literature refs in specaccum.Rd and Modified: branches/2.0/man/adipart.Rd =================================================================== --- branches/2.0/man/adipart.Rd 2013-08-23 11:56:39 UTC (rev 2590) +++ branches/2.0/man/adipart.Rd 2013-08-23 12:01:41 UTC (rev 2591) @@ -36,7 +36,7 @@ gamma diversities.} \item{formula}{A two sided model formula in the form \code{y ~ x}, where \code{y} is the community data matrix with samples as rows and - species as column. Right hand side (\code{x}) must grouping variables + species as column. Right hand side (\code{x}) must be grouping variables referring to levels of sampling hierarchy, terms from right to left will be treated as nested (first column is the lowest, last is the highest level, at least two levels specified). Interaction terms are Modified: branches/2.0/man/mrpp.Rd =================================================================== --- branches/2.0/man/mrpp.Rd 2013-08-23 11:56:39 UTC (rev 2590) +++ branches/2.0/man/mrpp.Rd 2013-08-23 12:01:41 UTC (rev 2591) @@ -98,7 +98,7 @@ counts. Function \code{summary} finds the within-class, between-class and overall means of these dissimilarities, and the MRPP statistics with all \code{weight.type} options and the Classification Strength, - CS (Van Sickle and Hughes, 2000). CS is defined for dissimilirities as + CS (Van Sickle and Hughes, 2000). CS is defined for dissimilarities as \eqn{\bar{B} - \bar{W}}{Bbar-Wbar}, where \eqn{\bar{B}}{Bbar} is the mean between cluster dissimilarity and \eqn{\bar{W}}{Wbar} is the mean within cluster dissimilarity with \code{weight.type = 1}. The function Modified: branches/2.0/man/multipart.Rd =================================================================== --- branches/2.0/man/multipart.Rd 2013-08-23 11:56:39 UTC (rev 2590) +++ branches/2.0/man/multipart.Rd 2013-08-23 12:01:41 UTC (rev 2591) @@ -25,7 +25,7 @@ all rows are in the same group in the second level.} \item{formula}{A two sided model formula in the form \code{y ~ x}, where \code{y} is the community data matrix with samples as rows and species as column. Right - hand side (\code{x}) must grouping variables referring to levels of sampling hierarchy, + hand side (\code{x}) must be grouping variables referring to levels of sampling hierarchy, terms from right to left will be treated as nested (first column is the lowest, last is the highest level, at least two levels specified). Interaction terms are not allowed.} \item{data}{A data frame where to look for variables defined in the right hand side From noreply at r-forge.r-project.org Sun Aug 25 17:16:16 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sun, 25 Aug 2013 17:16:16 +0200 (CEST) Subject: [Vegan-commits] r2592 - pkg/vegan/man Message-ID: <20130825151616.D19261858CF@r-forge.r-project.org> Author: jarioksa Date: 2013-08-25 17:16:16 +0200 (Sun, 25 Aug 2013) New Revision: 2592 Modified: pkg/vegan/man/varpart.Rd Log: more vocal about using adjusted R2 in varpart + edits Modified: pkg/vegan/man/varpart.Rd =================================================================== --- pkg/vegan/man/varpart.Rd 2013-08-23 12:01:41 UTC (rev 2591) +++ pkg/vegan/man/varpart.Rd 2013-08-25 15:16:16 UTC (rev 2592) @@ -10,12 +10,13 @@ \title{Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices } -\description{ The function partitions the variation of response table Y -with respect to two, three, or four explanatory tables, using -redundancy analysis ordination (RDA). If Y contains a single -vector, partitioning is by partial regression. Collinear variables in the -explanatory tables do NOT have to be removed prior to -partitioning. +\description{ + The function partitions the variation of response table Y with + respect to two, three, or four explanatory tables, using adjusted + \eqn{R^2}{R-squared} in redundancy analysis ordination (RDA). If Y + contains a single vector, partitioning is by partial regression. + Collinear variables in the explanatory tables do NOT have to be + removed prior to partitioning. } \usage{ @@ -65,17 +66,14 @@ effects. If \code{Y} is a multicolumn data frame or matrix, the partitioning is based on redundancy analysis (RDA, see \code{\link{rda}}), and if \code{Y} is a single variable, the - partitioning is based on linear regression. A simplified, fast - version of RDA is used (function \code{simpleRDA2}). The actual - calculations are done in functions \code{varpart2} to \code{varpart4}, - but these are not intended to be called directly by the user. + partitioning is based on linear regression. - The function primarily uses adjusted R squares to assess the partitions - explained by the explanatory tables and their combinations, because - this is the only unbiased method (Peres-Neto - et al., 2006). The raw R squares for basic fractions are also - displayed, but these are biased estimates of variation explained by - the explanatory table. + The function primarily uses adjusted \eqn{R^2}{R-squared} to assess + the partitions explained by the explanatory tables and their + combinations, because this is the only unbiased method (Peres-Neto + et al., 2006). The raw \eqn{R^2}{R-squared} for basic fractions are + also displayed, but these are biased estimates of variation + explained by the explanatory table. The identifiable fractions are designated by lower case alphabets. The meaning of the symbols can be found in the separate document @@ -151,9 +149,9 @@ \itemize{ \item{Df}{Degrees of freedom of numerator of the \eqn{F}-statistic for the fraction.} - \item{R.square}{Raw R-squared. This is calculated only for + \item{R.square}{Raw \eqn{R^2}{R-squared}. This is calculated only for \code{fract} and this is \code{NA} in other items.} - \item{Adj.R.square}{Adjusted R-squared.} + \item{Adj.R.square}{Adjusted \eqn{R^2}{R-squared}.} \item{Testable}{If the fraction can be expressed as a (partial) RDA model, it is directly \code{Testable}, and this field is \code{TRUE}. In that case the fraction label also gives the @@ -186,35 +184,47 @@ \author{ Pierre Legendre, Departement de Sciences Biologiques, Universite de Montreal, Canada. Adapted to \pkg{vegan} by Jari Oksanen. } -\note{You can use command \code{\link{vegandocs}} to display document - "partitioning.pdf" which presents -Venn diagrams showing the fraction names in partitioning the variation of -Y with respect to 2, 3, and 4 tables of explanatory variables, as well -as the equations used in variation partitioning. +\note{ -The functions frequently give negative estimates of variation. Adjusted -R-squares can be negative for any fraction; -unadjusted R squares of testable fractions always will be non-negative. -Non-testable fractions cannot be found directly, but by subtracting -different models, and these subtraction results can be negative. -The fractions are orthogonal, or linearly independent, but more -complicated or nonlinear dependencies can cause negative non-testable -fractions. + You can use command \code{\link{vegandocs}} to display document + "partitioning.pdf" which presents Venn diagrams showing the fraction + names in partitioning the variation of Y with respect to 2, 3, and 4 + tables of explanatory variables, as well as the equations used in + variation partitioning. -The current function will only use RDA in multivariate partitioning. It -is much more complicated to estimate the adjusted R-squares for CCA, and -unbiased analysis of CCA is not currently implemented. + The functions frequently give negative estimates of variation. + Adjusted \eqn{R^2}{R-squared} can be negative for any fraction; + unadjusted \eqn{R^2}{R-squared} of testable fractions always will be + non-negative. Non-testable fractions cannot be found directly, but + by subtracting different models, and these subtraction results can + be negative. The fractions are orthogonal, or linearly independent, + but more complicated or nonlinear dependencies can cause negative + non-testable fractions. + + The current function will only use RDA in multivariate + partitioning. It is much more complicated to estimate the adjusted + R-squares for CCA, and unbiased analysis of CCA is not currently + implemented. + + A simplified, fast version of RDA is used (function + \code{simpleRDA2}). The actual calculations are done in functions + \code{varpart2} to \code{varpart4}, but these are not intended to be + called directly by the user. + } -\seealso{ +\seealso{ For analysing testable fractions, see \code{\link{rda}} and \code{\link{anova.cca}}. For data transformation, see \code{\link{decostand}}. Function \code{\link{inertcomp}} gives (unadjusted) components of variation for each species or site - separately. - } + separately. Function \code{\link{rda}} displays unadjusted + components in its output, but \code{\link{RsquareAdj}} will give + adjusted \eqn{R^2}{R-squared} that are similar to the current + function also for partial models. +} - \examples{ +\examples{ data(mite) data(mite.env) data(mite.pcnm) From noreply at r-forge.r-project.org Mon Aug 26 08:53:47 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 26 Aug 2013 08:53:47 +0200 (CEST) Subject: [Vegan-commits] r2593 - pkg/vegan/R Message-ID: <20130826065347.7D6851855A4@r-forge.r-project.org> Author: jarioksa Date: 2013-08-26 08:53:47 +0200 (Mon, 26 Aug 2013) New Revision: 2593 Modified: pkg/vegan/R/anova.ccabyaxis.R Log: remove a case of stats::: Modified: pkg/vegan/R/anova.ccabyaxis.R =================================================================== --- pkg/vegan/R/anova.ccabyaxis.R 2013-08-25 15:16:16 UTC (rev 2592) +++ pkg/vegan/R/anova.ccabyaxis.R 2013-08-26 06:53:47 UTC (rev 2593) @@ -10,7 +10,8 @@ ## Handle missing values in scores, both "omit" and "exclude" to ## match dims with data. if (!is.null(object$na.action)) { - u <- stats:::napredict.exclude(object$na.action, object$CCA$u) + u <- napredict(structure(object$na.action, class="exclude"), + object$CCA$u) } else { u <- object$CCA$u } From noreply at r-forge.r-project.org Mon Aug 26 09:11:27 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 26 Aug 2013 09:11:27 +0200 (CEST) Subject: [Vegan-commits] r2594 - branches/2.0 Message-ID: <20130826071128.093061853D7@r-forge.r-project.org> Author: jarioksa Date: 2013-08-26 09:11:27 +0200 (Mon, 26 Aug 2013) New Revision: 2594 Modified: branches/2.0/NAMESPACE Log: vegandocs tools::: removal needs NAMESPACE update Modified: branches/2.0/NAMESPACE =================================================================== --- branches/2.0/NAMESPACE 2013-08-26 06:53:47 UTC (rev 2593) +++ branches/2.0/NAMESPACE 2013-08-26 07:11:27 UTC (rev 2594) @@ -64,6 +64,7 @@ import(graphics) importFrom(utils, head, tail) importFrom(lattice, densityplot) +importFrom(tools, Rd2txt, startDynamicHelp) ## nobs only exists in R 2.13.0 -- import from permute with older R if (getRversion() < "2.13.0") { importFrom(permute, nobs) From noreply at r-forge.r-project.org Mon Aug 26 09:29:17 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 26 Aug 2013 09:29:17 +0200 (CEST) Subject: [Vegan-commits] r2595 - in branches/2.0: . R inst inst/doc man Message-ID: <20130826072917.195DC184976@r-forge.r-project.org> Author: jarioksa Date: 2013-08-26 09:29:16 +0200 (Mon, 26 Aug 2013) New Revision: 2595 Modified: branches/2.0/DESCRIPTION branches/2.0/NAMESPACE branches/2.0/R/density.anosim.R branches/2.0/R/densityplot.oecosimu.R branches/2.0/R/ordicloud.R branches/2.0/R/ordiresids.R branches/2.0/R/ordisplom.R branches/2.0/R/ordixyplot.R branches/2.0/R/plot.poolaccum.R branches/2.0/R/plot.radfit.frame.R branches/2.0/R/plot.renyi.R branches/2.0/R/plot.renyiaccum.R branches/2.0/R/prepanel.ordi3d.R branches/2.0/R/radlattice.R branches/2.0/inst/ChangeLog branches/2.0/inst/doc/diversity-vegan.Rnw branches/2.0/man/adonis.Rd branches/2.0/man/density.adonis.Rd branches/2.0/man/oecosimu.Rd Log: vegan 2.0-9 depends on lattice (merge 2584,6 + edit NAMESPACE) Modified: branches/2.0/DESCRIPTION =================================================================== --- branches/2.0/DESCRIPTION 2013-08-26 07:11:27 UTC (rev 2594) +++ branches/2.0/DESCRIPTION 2013-08-26 07:29:16 UTC (rev 2595) @@ -1,14 +1,13 @@ Package: vegan Title: Community Ecology Package Version: 2.0-9 -Date: July 10, 2013 +Date: August 26, 2013 Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Helene Wagner Maintainer: Jari Oksanen -Depends: permute -Imports: lattice -Suggests: MASS, mgcv, lattice, cluster, scatterplot3d, rgl, tcltk +Depends: lattice, permute +Suggests: MASS, mgcv, cluster, scatterplot3d, rgl, tcltk Description: Ordination methods, diversity analysis and other functions for community and vegetation ecologists. License: GPL-2 Modified: branches/2.0/NAMESPACE =================================================================== --- branches/2.0/NAMESPACE 2013-08-26 07:11:27 UTC (rev 2594) +++ branches/2.0/NAMESPACE 2013-08-26 07:29:16 UTC (rev 2595) @@ -62,8 +62,9 @@ ## Registration of S3 methods import(stats) import(graphics) +import(lattice) +import(permute) importFrom(utils, head, tail) -importFrom(lattice, densityplot) importFrom(tools, Rd2txt, startDynamicHelp) ## nobs only exists in R 2.13.0 -- import from permute with older R if (getRversion() < "2.13.0") { Modified: branches/2.0/R/density.anosim.R =================================================================== --- branches/2.0/R/density.anosim.R 2013-08-26 07:11:27 UTC (rev 2594) +++ branches/2.0/R/density.anosim.R 2013-08-26 07:29:16 UTC (rev 2595) @@ -39,7 +39,6 @@ `densityplot.adonis` <- function(x, data, xlab = "Null", ...) { - require(lattice) || stop("requires package 'lattice'") obs <- x$aov.tab$F.Model obs <- obs[!is.na(obs)] sim <- rbind(obs, x$f.perms) Modified: branches/2.0/R/densityplot.oecosimu.R =================================================================== --- branches/2.0/R/densityplot.oecosimu.R 2013-08-26 07:11:27 UTC (rev 2594) +++ branches/2.0/R/densityplot.oecosimu.R 2013-08-26 07:29:16 UTC (rev 2595) @@ -1,7 +1,6 @@ `densityplot.oecosimu` <- function(x, data, xlab = "Simulated", ...) { - require(lattice) || stop("requires package 'lattice'") obs <- x$oecosimu$statistic sim <- rbind(obs, t(x$oecosimu$simulated)) nm <- names(obs)[col(sim)] Modified: branches/2.0/R/ordicloud.R =================================================================== --- branches/2.0/R/ordicloud.R 2013-08-26 07:11:27 UTC (rev 2594) +++ branches/2.0/R/ordicloud.R 2013-08-26 07:29:16 UTC (rev 2595) @@ -4,7 +4,6 @@ prepanel = "prepanel.ordi3d", ...) { localCloud <- function(..., shrink, origin, scaling) cloud(...) - require(lattice) || stop("requires package 'lattice'") x <- as.data.frame(scores(x, display = display, choices = choices, ...)) if (!is.null(data)) x <- cbind(x, data) Modified: branches/2.0/R/ordiresids.R =================================================================== --- branches/2.0/R/ordiresids.R 2013-08-26 07:11:27 UTC (rev 2594) +++ branches/2.0/R/ordiresids.R 2013-08-26 07:29:16 UTC (rev 2595) @@ -2,7 +2,6 @@ function(x, kind = c("residuals", "scale", "qqmath"), residuals = "working", type = c("p", "smooth", "g"), formula, ...) { - require(lattice) || stop("requires package lattice") kind <- match.arg(kind) if (!inherits(x, "cca") || is.null(x$CCA) || x$CCA$rank == 0) stop("function is only available for constrained ordination") Modified: branches/2.0/R/ordisplom.R =================================================================== --- branches/2.0/R/ordisplom.R 2013-08-26 07:11:27 UTC (rev 2594) +++ branches/2.0/R/ordisplom.R 2013-08-26 07:29:16 UTC (rev 2595) @@ -3,7 +3,6 @@ panel = "panel.ordi", type = "p", ...) { localSplom <- function(..., shrink, origin, scaling) splom(...) - require(lattice) || stop("requires package 'lattice'") x <- as.data.frame(scores(x, display = display, choices = choices, ...)) if (is.null(data)) data <- x Modified: branches/2.0/R/ordixyplot.R =================================================================== --- branches/2.0/R/ordixyplot.R 2013-08-26 07:11:27 UTC (rev 2594) +++ branches/2.0/R/ordixyplot.R 2013-08-26 07:29:16 UTC (rev 2595) @@ -4,7 +4,6 @@ type = c("p", "biplot"), ...) { localXyplot <- function(..., shrink, origin, scaling) xyplot(...) - require(lattice) || stop("requires package 'lattice'") p <- as.data.frame(scores(x, display = display, choices = choices, ...)) if (!is.null(data)) p <- cbind(p, data) Modified: branches/2.0/R/plot.poolaccum.R =================================================================== --- branches/2.0/R/plot.poolaccum.R 2013-08-26 07:11:27 UTC (rev 2594) +++ branches/2.0/R/plot.poolaccum.R 2013-08-26 07:29:16 UTC (rev 2595) @@ -1,7 +1,6 @@ `plot.poolaccum` <- function(x, alpha = 0.05, type = c("l","g"), ...) { - require(lattice) || stop("Needs package 'lattice'") m <- summary(x, alpha = alpha, ...) n <- nrow(m[[1]]) Size <- as.vector(sapply(m, function(x) c(x[,1], x[,1], rev(x[,1])))) Modified: branches/2.0/R/plot.radfit.frame.R =================================================================== --- branches/2.0/R/plot.radfit.frame.R 2013-08-26 07:11:27 UTC (rev 2594) +++ branches/2.0/R/plot.radfit.frame.R 2013-08-26 07:29:16 UTC (rev 2595) @@ -2,7 +2,6 @@ function (x, order.by, BIC = FALSE, model, legend = TRUE, as.table = TRUE, ...) { - require(lattice) modnam <- names(x[[1]]$models) if (!missing(model)) pick <- pmatch(model, modnam, nomatch = FALSE) Modified: branches/2.0/R/plot.renyi.R =================================================================== --- branches/2.0/R/plot.renyi.R 2013-08-26 07:11:27 UTC (rev 2594) +++ branches/2.0/R/plot.renyi.R 2013-08-26 07:29:16 UTC (rev 2595) @@ -1,7 +1,6 @@ `plot.renyi` <- function(x, ...) { - require(lattice) || stop("requires lattice") if (inherits(x, "data.frame")) { plt <- factor(rep(rownames(x), ncol(x)), levels=rownames(x)) alp <- factor(rep(colnames(x), each=nrow(x)), levels=colnames(x)) Modified: branches/2.0/R/plot.renyiaccum.R =================================================================== --- branches/2.0/R/plot.renyiaccum.R 2013-08-26 07:11:27 UTC (rev 2594) +++ branches/2.0/R/plot.renyiaccum.R 2013-08-26 07:29:16 UTC (rev 2595) @@ -1,7 +1,6 @@ `plot.renyiaccum` <- function (x, what=c("mean", "Qnt 0.025", "Qnt 0.975"), type = "l", ...) { - require(lattice) || stop("requires package lattice") if (any(what %in% colnames(x[,1,]))) x <- x[,,what] dm <- dim(x) Modified: branches/2.0/R/prepanel.ordi3d.R =================================================================== --- branches/2.0/R/prepanel.ordi3d.R 2013-08-26 07:11:27 UTC (rev 2594) +++ branches/2.0/R/prepanel.ordi3d.R 2013-08-26 07:29:16 UTC (rev 2595) @@ -2,5 +2,5 @@ function(xlim = xlim, ylim = ylim, zlim = zlim, aspect = c(1,1), ...) { aspect = c(diff(ylim)/diff(xlim), diff(zlim)/diff(xlim)) - lattice:::prepanel.default.cloud(xlim = xlim, ylim = ylim, zlim = zlim, aspect = aspect, ...) + prepanel.default.cloud(xlim = xlim, ylim = ylim, zlim = zlim, aspect = aspect, ...) } Modified: branches/2.0/R/radlattice.R =================================================================== --- branches/2.0/R/radlattice.R 2013-08-26 07:11:27 UTC (rev 2594) +++ branches/2.0/R/radlattice.R 2013-08-26 07:29:16 UTC (rev 2595) @@ -3,7 +3,6 @@ { if (!inherits(x, "radfit")) stop("function only works with 'radfit' results for single site") - require(lattice) || stop("requires package 'lattice'") y <- x$y fv <- unlist(fitted(x)) mods <- names(x$models) Modified: branches/2.0/inst/ChangeLog =================================================================== --- branches/2.0/inst/ChangeLog 2013-08-26 07:11:27 UTC (rev 2594) +++ branches/2.0/inst/ChangeLog 2013-08-26 07:29:16 UTC (rev 2595) @@ -6,6 +6,7 @@ * merge 2590: typos. * merge r2588: remove unneeded utils::: in vegandocs (some remain). + * merge 2584,6: vegan Depends on lattice, avoid lattice::: * merge r2583,7: remove cross-references to disappear in R-3.0-2. * merge r2580,1: literature refs in specaccum.Rd and betadisper.Rd. Modified: branches/2.0/inst/doc/diversity-vegan.Rnw =================================================================== --- branches/2.0/inst/doc/diversity-vegan.Rnw 2013-08-26 07:11:27 UTC (rev 2594) +++ branches/2.0/inst/doc/diversity-vegan.Rnw 2013-08-26 07:29:16 UTC (rev 2595) @@ -127,9 +127,6 @@ diversities are higher than in another site. We can inspect this graphically using the standard \code{plot} function for the \code{renyi} result (Fig. \ref{fig:renyi}). -<>= -require(lattice, quietly=TRUE) -@ \begin{SCfigure} <>= print(plot(R)) Modified: branches/2.0/man/adonis.Rd =================================================================== --- branches/2.0/man/adonis.Rd 2013-08-26 07:11:27 UTC (rev 2594) +++ branches/2.0/man/adonis.Rd 2013-08-26 07:29:16 UTC (rev 2595) @@ -199,7 +199,6 @@ Agropyron <- with(dat, as.numeric(field) + as.numeric(NO3)+2) +rnorm(12)/2 Schizachyrium <- with(dat, as.numeric(field) - as.numeric(NO3)+2) +rnorm(12)/2 total <- Agropyron + Schizachyrium -library(lattice) dotplot(total ~ NO3, dat, jitter.x=TRUE, groups=field, type=c('p','a'), xlab="NO3", auto.key=list(columns=3, lines=TRUE) ) Modified: branches/2.0/man/density.adonis.Rd =================================================================== --- branches/2.0/man/density.adonis.Rd 2013-08-26 07:11:27 UTC (rev 2594) +++ branches/2.0/man/density.adonis.Rd 2013-08-26 07:29:16 UTC (rev 2595) @@ -106,7 +106,6 @@ data(dune.env) mod <- adonis(dune ~ Management, data = dune.env) plot(density(mod)) -library(lattice) mod <- adonis(dune ~ Management * Moisture, dune.env) densityplot(mod) } Modified: branches/2.0/man/oecosimu.Rd =================================================================== --- branches/2.0/man/oecosimu.Rd 2013-08-26 07:11:27 UTC (rev 2594) +++ branches/2.0/man/oecosimu.Rd 2013-08-26 07:29:16 UTC (rev 2595) @@ -261,8 +261,7 @@ plot(as.ts(out)) lag.plot(as.ts(out)) acf(as.ts(out)) -## Density plot: needs lattice -require(lattice) +## Density plot densityplot(out, as.table = TRUE) ## Use quantitative null models to compare ## mean Bray-Curtis dissimilarities From noreply at r-forge.r-project.org Mon Aug 26 09:38:35 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 26 Aug 2013 09:38:35 +0200 (CEST) Subject: [Vegan-commits] r2596 - in branches/2.0: R inst Message-ID: <20130826073835.6891E184976@r-forge.r-project.org> Author: jarioksa Date: 2013-08-26 09:38:35 +0200 (Mon, 26 Aug 2013) New Revision: 2596 Modified: branches/2.0/R/anova.ccabyaxis.R branches/2.0/inst/ChangeLog Log: merge r2593: stats::: in anova.ccabyaxis Modified: branches/2.0/R/anova.ccabyaxis.R =================================================================== --- branches/2.0/R/anova.ccabyaxis.R 2013-08-26 07:29:16 UTC (rev 2595) +++ branches/2.0/R/anova.ccabyaxis.R 2013-08-26 07:38:35 UTC (rev 2596) @@ -10,7 +10,8 @@ ## Handle missing values in scores, both "omit" and "exclude" to ## match dims with data. if (!is.null(object$na.action)) { - u <- stats:::napredict.exclude(object$na.action, object$CCA$u) + u <- napredict(structure(object$na.action, class="exclude"), + object$CCA$u) } else { u <- object$CCA$u } Modified: branches/2.0/inst/ChangeLog =================================================================== --- branches/2.0/inst/ChangeLog 2013-08-26 07:29:16 UTC (rev 2595) +++ branches/2.0/inst/ChangeLog 2013-08-26 07:38:35 UTC (rev 2596) @@ -4,6 +4,7 @@ Version 2.0-9 (opened August 23, 2013) + * merge 2593: remove stats::: in anova.ccabyaxis(). * merge 2590: typos. * merge r2588: remove unneeded utils::: in vegandocs (some remain). * merge 2584,6: vegan Depends on lattice, avoid lattice::: From noreply at r-forge.r-project.org Wed Aug 28 10:56:55 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 28 Aug 2013 10:56:55 +0200 (CEST) Subject: [Vegan-commits] r2597 - in pkg/vegan: . inst inst/doc vignettes Message-ID: <20130828085655.AA458185C16@r-forge.r-project.org> Author: jarioksa Date: 2013-08-28 10:56:55 +0200 (Wed, 28 Aug 2013) New Revision: 2597 Added: pkg/vegan/vignettes/ pkg/vegan/vignettes/.install_extras pkg/vegan/vignettes/FAQ-vegan.texi pkg/vegan/vignettes/Makefile pkg/vegan/vignettes/decision-vegan.Rnw pkg/vegan/vignettes/diversity-vegan.Rnw pkg/vegan/vignettes/intro-vegan.Rnw pkg/vegan/vignettes/vegan.bib pkg/vegan/vignettes/vegan.sty Removed: pkg/vegan/.Rinstignore pkg/vegan/inst/doc/FAQ-vegan.texi pkg/vegan/inst/doc/Makefile pkg/vegan/inst/doc/decision-vegan.Rnw pkg/vegan/inst/doc/diversity-vegan.Rnw pkg/vegan/inst/doc/intro-vegan.Rnw pkg/vegan/inst/doc/vegan.bib pkg/vegan/inst/doc/vegan.sty Modified: pkg/vegan/DESCRIPTION pkg/vegan/inst/ChangeLog Log: move vignettes and friends from inst/doc/ to vignettes/ (depends on R >= 2.14.0) Deleted: pkg/vegan/.Rinstignore =================================================================== --- pkg/vegan/.Rinstignore 2013-08-26 07:38:35 UTC (rev 2596) +++ pkg/vegan/.Rinstignore 2013-08-28 08:56:55 UTC (rev 2597) @@ -1,5 +0,0 @@ -Makefile -.*tex$ -.*sty$ -.*bib$ -.*texi$ Modified: pkg/vegan/DESCRIPTION =================================================================== --- pkg/vegan/DESCRIPTION 2013-08-26 07:38:35 UTC (rev 2596) +++ pkg/vegan/DESCRIPTION 2013-08-28 08:56:55 UTC (rev 2597) @@ -1,12 +1,12 @@ Package: vegan Title: Community Ecology Package -Version: 2.1-33 -Date: August 19, 2013 +Version: 2.1-34 +Date: August 28, 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 -Depends: permute (>= 0.7-4), lattice, R (>= 2.12.0) +Depends: permute (>= 0.7-4), lattice, R (>= 2.14.0) Suggests: MASS, mgcv, cluster, parallel, scatterplot3d, rgl, tcltk Description: Ordination methods, diversity analysis and other functions for community and vegetation ecologists. Modified: pkg/vegan/inst/ChangeLog =================================================================== --- pkg/vegan/inst/ChangeLog 2013-08-26 07:38:35 UTC (rev 2596) +++ pkg/vegan/inst/ChangeLog 2013-08-28 08:56:55 UTC (rev 2597) @@ -2,10 +2,27 @@ VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/ -Version 2.1-33 (opened August 23, 2013) +Version 2.1-34 (opened August 28, 2013) + * DESCRIPTION, vignettes: R 3.0.2-to-be checks with --as-cran + requires (with a NOTE) the vignettes source files (Rnw) to be in + vignettes/ directory. Because Makefile is not executed in + inst/doc if vignettes/ directory is present, all other sources had + to be moved to vignettes/ as well with vignettes/.install_extras + to move those to inst/doc after building. This also made + /.Rinstignore unnecessary. The vignettes directory was introduced + and made recommended in R 2.14.0 so that the this version of vegan + depends on R >= 2.14.0. With this, some of the parallel code + that is also dependent on 2.14.0 could be simplified as no version + checking is necessary. + +Version 2.1-33 (closed August 28, 2013) + * DESCRIPTION: new dependence on lattice. Passes new strict R - checks with NOTE on unavoidable ':::' calls. + checks with NOTE on ':::' calls to tools:::httpdPort (to launch + reading vegan NEWS.html in existing browser window) and + parallel:::.reg to acces the defaultCluster in an unexported + function in parallel Namespace. Version 2.1-32 (closed August 19, 2013) Deleted: pkg/vegan/inst/doc/FAQ-vegan.texi =================================================================== --- pkg/vegan/inst/doc/FAQ-vegan.texi 2013-08-26 07:38:35 UTC (rev 2596) +++ pkg/vegan/inst/doc/FAQ-vegan.texi 2013-08-28 08:56:55 UTC (rev 2597) @@ -1,833 +0,0 @@ -\input texinfo - - at macro pkg {p} - at strong{\p\} - at end macro - - at c %**start of header - at setfilename FAQ- at pkg{vegan}.info - at settitle @pkg{vegan} FAQ - at setchapternewpage on - at set FAQ_YEAR 2013 - at afourpaper - at c %**end of header - - at copying - at ifnottex -This document contains answers to some of the most frequently asked -questions about R package @pkg{vegan}. -This is version of $Date$. - at end ifnottex - - at quotation -This work is licensed under the Creative Commons Attribution 3.0 -License. To view a copy of this license, visit - at uref{http://creativecommons.org/licenses/by/3.0/} or send a letter to -Creative Commons, 543 Howard Street, 5th Floor, San Francisco, -California, 94105, USA. - -Copyright @copyright{} 2008-2013 Jari Oksanen - at end quotation - at end copying - - at dircategory Programming - at direntry -* R @pkg{vegan} FAQ: (FAQ- at pkg{vegan}). FAQ for R package @pkg{vegan}. - at end direntry - - at finalout - - at titlepage - at title @pkg{vegan} @acronym{FAQ} - at subtitle Frequently Asked Questions on R package @pkg{vegan} - at subtitle Version of $Date$ - at author Jari Oksanen - - at vskip 0pt plus 1fill - at insertcopying - at end titlepage - - at ifnothtml - at contents - at end ifnothtml - - - at ifnottex - at node Top, Introduction, (dir), (dir) - at top @pkg{vegan} FAQ - at insertcopying - at end ifnottex - - - - - at menu -* Introduction:: -* Ordination:: -* Other analysis methods :: - at end menu - - at node Introduction, Ordination, Top, Top - at chapter Introduction - - at menu -* What is @pkg{vegan}?:: -* What is R?:: -* How to obtain @pkg{vegan} and R?:: -* What R packages @pkg{vegan} depends on?:: -* What other packages are available for ecologists?:: -* What other documentation is available for @pkg{vegan}?:: -* Is there a Graphical User Interface (GUI) for @pkg{vegan}?:: -* How to cite @pkg{vegan}?:: -* How to build @pkg{vegan} from sources?:: -* Are there binaries for devel versions?:: -* Can I use @pkg{vegan} in Mac?:: -* How to report a bug in @pkg{vegan}?:: -* Is it a bug or a feature?:: -* Can I contribute to @pkg{vegan}?:: -* Can I have write access to @pkg{vegan} repository?:: - at end menu - - at node What is @pkg{vegan}?, What is R?, Introduction, Introduction - at section What is @pkg{vegan}? - - at pkg{Vegan} is an R package for community ecologists. It contains the most -popular methods of multivariate analysis needed in analysing ecological -communities, and tools for diversity analysis, and other potentially -useful functions. @pkg{Vegan} is not self-contained but it must be run under -R statistical environment, and it also depends on many other R -packages. @pkg{Vegan} is @uref{http://www.gnu.org/philosophy/free-sw.html, free -software} and distributed under - at uref{http://www.gnu.org/licenses/gpl.html, ,GPL2 license}. - - at node What is R?, How to obtain @pkg{vegan} and R?, What is @pkg{vegan}?, Introduction - at section What is R? - -R is a system for statistical computation and graphics. It consists of -a language plus a run-time environment with graphics, a debugger, access -to certain system functions, and the ability to run programs stored in -script files. - -R has a home page at @uref{http://www.R-project.org/}. It is - at uref{http://www.gnu.org/philosophy/free-sw.html, free software} -distributed under a @acronym{GNU}-style - at uref{http://www.gnu.org/copyleft/copyleft.html, copyleft}, and an -official part of the @uref{http://www.gnu.org/, @acronym{GNU}} project -(``@acronym{GNU} S''). - - at node How to obtain @pkg{vegan} and R?, What R packages @pkg{vegan} depends on?, What is R?, Introduction - at section How to obtain @pkg{vegan} and R? - -Both R and latest release version of @pkg{vegan} can be obtained through - at uref{http://cran.r-project.org,,CRAN}. Unstable development version of - at pkg{vegan} can be obtained through - at uref{http://r-forge.r-project.org/projects/vegan/,,R-Forge}. - - - - at node What R packages @pkg{vegan} depends on?, What other packages are available for ecologists?, How to obtain @pkg{vegan} and R?, Introduction - at section What R packages @pkg{vegan} depends on? - - at pkg{Vegan} depends on the @pkg{permute} package which will provide -advanced and flexible permutation routines for vegan (but currently only -a small part of functions use @pkg{permute}). The @pkg{permute} package -is developed together with @pkg{vegan} in - at uref{http://vegan.r-forge.r-project.org/,,R-Forge}. - -Some individual @pkg{vegan} functions depend on packages @pkg{MASS}, - at pkg{mgcv}, @pkg{cluster}, @pkg{lattice} and @pkg{tcltk}. These all are -base or recommended R packages that should be available in every R -installation. In addition, some @pkg{vegan} functions @code{require} -non-standard R packages. @pkg{Vegan} declares these packages only as -suggested ones, and you can install @pkg{vegan} and use most of its -functions without these packages. The non-standard packages needed by -some @pkg{vegan} functions are: - at itemize - - at item Package @pkg{scatterplot3d} -is needed by @code{ordiplot3d} - - at item Package @pkg{rgl} -is needed by @code{ordirgl} -and @code{rgl.isomap} - - at end itemize - - at node What other packages are available for ecologists?, What other documentation is available for @pkg{vegan}?, What R packages @pkg{vegan} depends on?, Introduction - at section What other packages are available for ecologists? - - at acronym{CRAN} @uref{http://cran.r-project.org/src/contrib/Views/,,Task -Views} include entries like @code{Environmetrics}, @code{Multivariate} -and @code{Spatial} that describe several useful packages and functions. -If you install R package @pkg{ctv}, you can inspect Task Views from your -R session, and automatically install sets of most important packages. - - at node What other documentation is available for @pkg{vegan}?, Is there a Graphical User Interface (GUI) for @pkg{vegan}?, What other packages are available for ecologists?, Introduction - at section What other documentation is available for @pkg{vegan}? - - at pkg{Vegan} is a fully documented R package with standard help pages. These -are the most authoritative sources of documentation (and as a last -resource you can use the force and the read the source, as @pkg{vegan} is open -source). @pkg{Vegan} package ships with other documents which can be read -with @code{vegandocs} command (documented in the @pkg{vegan} help). The -documents included in the @pkg{vegan} package are - at itemize - at item - at pkg{Vegan} @code{NEWS} - at item - at pkg{Vegan} @code{ChangeLog}. - at item -This document (@code{FAQ-vegan.pdf}). - at item -Short introduction to basic ordination methods in @pkg{vegan} -(@code{intro-vegan.pdf}). - at item -Introduction to diversity methods in @pkg{vegan} (@code{diversity-vegan.pdf}). - at item -Discussion on design decisions in @pkg{vegan} (@code{decision-vegan.pdf}). - at item -Description of variance partition procedures in function - at code{varpart} (@code{partitioning.pdf}). - at end itemize - - -Web documents outside the package include: - at itemize - - at item - at uref{http://vegan.r-forge.r-project.org/}: @pkg{vegan} homepage. - at item - at uref{http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf}: @pkg{vegan} -tutorial. - - at end itemize - - at node Is there a Graphical User Interface (GUI) for @pkg{vegan}?, How to cite @pkg{vegan}?, What other documentation is available for @pkg{vegan}?, Introduction - at section Is there a Graphical User Interface (GUI) for @pkg{vegan}? - -Roeland Kindt has made package @pkg{BiodiversityR} which provides a -GUI for @pkg{vegan}. The package is available at - at uref{http://cran.r-project.org/src/contrib/Descriptions/BiodiversityR.html,,CRAN}. -It is not a mere GUI for @pkg{vegan}, but adds some new functions and -complements @pkg{vegan} functions in order to provide a -workbench for biodiversity analysis. You can install @pkg{BiodiversityR} using - at code{install.packages("BiodiversityR")} or graphical package -management menu in R. The GUI works on Windows, MacOS X and Linux. - - at node How to cite @pkg{vegan}?, How to build @pkg{vegan} from sources?, Is there a Graphical User Interface (GUI) for @pkg{vegan}?, Introduction - at section How to cite @pkg{vegan}? - -Use command @code{citation("vegan")} in R to see the recommended -citation to be used in publications. - - at node How to build @pkg{vegan} from sources?, Are there binaries for devel versions?, How to cite @pkg{vegan}?, Introduction - at section How to build @pkg{vegan} from sources? - -In general, you do not need to build @pkg{vegan} from sources, but binary -builds of release versions are available through - at uref{http://cran.r-project.org/,,CRAN} for Windows and MacOS X. If you -use some other operating systems, you may have to use source packages. - at pkg{Vegan} is a standard R package, and can be built like instructed in R -documentation. @pkg{Vegan} contains source files in C and @acronym{FORTRAN}, -and you need appropriate compilers (which may need more work in Windows -and MacOS X). - - at node Are there binaries for devel versions?, Can I use @pkg{vegan} in Mac?, How to build @pkg{vegan} from sources?, Introduction - at section Are there binaries for devel versions? - - at uref{http://r-forge.r-project.org/projects/vegan/,,R-Forge} runs daily -tests on the devel package, and if passed, it builds source package -together with Windows and MacOS X binaries. You can install those -packages within R with command - at code{install.packages("vegan", repos="http://r-forge.r-project.org/")}. -If you use GUI menu entry, you must select or define the R-Forge -repository. - - at node Can I use @pkg{vegan} in Mac?, How to report a bug in @pkg{vegan}?, Are there binaries for devel versions?, Introduction - at section Can I use @pkg{vegan} in Mac? - -Yes, you can, and @pkg{vegan} binaries are available for Mac through - at uref{http://cran.r-project.org,,CRAN}. However, in some cases you may -need to install extra tools packages available in - at uref{http://cran.r-project.org/bin/macosx/tools/,,MacOS tools} pages: -If you use function such as @code{orditkplot} that need @code{Tcl/Tk} -you may need to install @code{tcltk} package. If you use @pkg{vegan} -binaries from other places than from - at uref{http://cran.r-project.org,,CRAN}, you may also need to install - at code{gfortran} package. - - at node How to report a bug in @pkg{vegan}?, Is it a bug or a feature?, Can I use @pkg{vegan} in Mac?, Introduction - at section How to report a bug in @pkg{vegan}? - -If you think you have found a bug in @pkg{vegan}, you should report it to - at pkg{vegan} maintainers or developers. The bug report should be so detailed -that the bug can be replicated and corrected. Preferably, you should -send an example that causes a bug. If it needs a data set that is not -available in R, you should send a minimal data set as well. You also -should paste the output or error message in your message. You also -should specify which version of @pkg{vegan} you used. - -Bug reports are welcome: they are the only way to make @pkg{vegan} non-buggy. - -Please note that you shall not send bug reports to R mailing lists, -since @pkg{vegan} is not a standard R package. - -There also is a bug reporting tool at - at uref{http://r-forge.r-project.org/projects/vegan/,,R-Forge}, but you -need to register as a site user to report bugs (this is site policy). - - at node Is it a bug or a feature?, Can I contribute to @pkg{vegan}?, How to report a bug in @pkg{vegan}?, Introduction - at section Is it a bug or a feature? - -It is not necessarily a bug if some function gives different -results than you expect: That may be a deliberate design decision. It -may be useful to check the documentation of the function to see what -was the intended behaviour. It may also happen that function has an -argument to switch the behaviour to match your expectation. For -instance, function @code{vegdist} always calculates quantitative -indices (when this is possible). If you expect it to calculate a -binary index, you should use argument @code{binary = TRUE}. - - at node Can I contribute to @pkg{vegan}?, Can I have write access to @pkg{vegan} repository?, Is it a bug or a feature?, Introduction - at section Can I contribute to @pkg{vegan}? - - at pkg{Vegan} is dependent on user contribution. All feedback is welcome. If -you have problem with @pkg{vegan}, it may be as simple as incomplete -documentation, and we'll do our best to improve the documents. - -Feature requests also are welcome, but they are not necessarily -fulfilled. A new feature will be added if it is easy to do and it looks -useful to me or in general, or if you submit code. - -Contributed code and functions are welcome and more certain to be -included than mere requests. However, not all functions will be added, -but I they must be suitable for @pkg{vegan}. We also audit the code, and -typically we edit the code in @pkg{vegan} style for easier maintenance. All -included contributions will be credited. - - at node Can I have write access to @pkg{vegan} repository?, , Can I contribute to @pkg{vegan}?, Introduction - at section Can I have write access to @pkg{vegan} repository? - -The @pkg{vegan} development happens mainly in - at uref{http://r-forge.r-project.org/,,R-Forge} which uses subversion for -version control. Subversion is a centralized version control system, -and only @pkg{vegan} developers can have write access to the central -repository. However, the @uref{http://r-forge.r-project.org/,,R-Forge} -is mirrored in - at uref{https://github.com/jarioksa/vegan.git,,GitHub}. This is a -distributed version control system and freely accessible for anybody. We -suggest you develop your own ideas in - at uref{https://github.com/jarioksa/vegan.git,,GitHub} and send a pull -request to us for incorporating your changes in @pkg{vegan} releases. - - at node Ordination, Other analysis methods , Introduction, Top - at chapter Ordination - - at menu -* I have only numeric and positive data but @pkg{vegan} still complains:: -* Can I analyse binary or cover class data?:: -* Why dissimilarities in @pkg{vegan} differ from other sources?:: -* Why NMDS stress is sometimes 0.1 and sometimes 10?:: -* I get zero stress but no convergent solutions in @code{metaMDS}:: -* Zero dissimilarities in isoMDS:: -* I have heard that you cannot fit environmental vectors or surfaces to NMDS results which only have rank-order scores:: -* Where can I find numerical scores of ordination axes?:: -* How the RDA results are scaled?:: -* cca fails with ``data.frame expected'' or ``"site.env" missing'':: -* Variance explained by ordination axes:: -* Can I have random effects in constrained ordination or in @code{adonis}?:: -* Is it possible to have passive points in ordination?:: -* Class variables and dummies:: -* How are environmental arrows scaled?:: -* I want to use Helmert or sum contrasts:: -* What are aliased variables and how to see them?:: -* Plotting aliased variables:: -* Constrained permutations in @pkg{vegan}:: -* How to use different plotting symbols in ordination graphics?:: -* How to avoid cluttered ordination graphs?:: -* Can I flip an axis in ordination diagram?:: -* Can I zoom into an ordination plot?:: - at end menu - - at node I have only numeric and positive data but @pkg{vegan} still complains, Can I analyse binary or cover class data?, Ordination, Ordination - at comment node-name, next, previous, up - at section I have only numeric and positive data but @pkg{vegan} still complains - -You are wrong! Computers are painfully pedantic, and if they find -non-numeric or negative data entries, you really have them. Check your -data. Most common reasons for non-numeric data are that row names were -read as a non-numeric variable instead of being used as row names (check -argument @code{row.names} in reading the data), or that the column names -were interpreted as data (check argument @code{header = TRUE} in reading -the data). Another common reason is that you had empty cells in your -input data, and these were interpreted as missing values. - - at node Can I analyse binary or cover class data?, Why dissimilarities in @pkg{vegan} differ from other sources?, I have only numeric and positive data but @pkg{vegan} still complains, Ordination - at section Can I analyse binary or cover class data? - -Yes. Most @pkg{vegan} methods can handle binary data or cover abundance data. -Most statistical tests are based on permutation, and do not make -distributional assumptions. There are some methods (mainly in diversity -analysis) that need count data. These methods check that input data are -integers, but they may be fooled by cover class data. - - at node Why dissimilarities in @pkg{vegan} differ from other sources?, Why NMDS stress is sometimes 0.1 and sometimes 10?, Can I analyse binary or cover class data?, Ordination - at section Why dissimilarities in @pkg{vegan} differ from other sources? - -Most commonly the reason is that other software use presence--absence -data whereas @pkg{vegan} used quantitative data. Usually @pkg{vegan} indices are -quantitative, but you can use argument @code{binary = TRUE} to make them -presence--absence. However, the index name is the same in both cases, -although different names usually occur in literature. For instance, -Jaccard index actually refers to the binary index, but @pkg{vegan} uses -name @code{"jaccard"} for the quantitative index, too. - -Another reason may be that indices indeed are defined differently, -because people use same names for different indices. - - at node Why NMDS stress is sometimes 0.1 and sometimes 10?, I get zero stress but no convergent solutions in @code{metaMDS}, Why dissimilarities in @pkg{vegan} differ from other sources?, Ordination - at section Why @acronym{NMDS} stress is sometimes 0.1 and sometimes 10? - -Stress is a proportional measure of badness of fit. The proportions can -be expressed either as parts of one or as percents. Function - at code{isoMDS} (@pkg{MASS} package) uses percents, and function @code{monoMDS} -(@pkg{vegan} package) uses proportions, and therefore the same stress is 100 -times higher in @code{isoMDS}. The results of @code{goodness} function -also depend on the definition of stress, and the same @code{goodness} is -100 times higher in @code{isoMDS} than in @code{monoMDS}. Both of these -conventions are equally correct. - - at node I get zero stress but no convergent solutions in @code{metaMDS}, Zero dissimilarities in isoMDS, Why NMDS stress is sometimes 0.1 and sometimes 10?, Ordination - at section I get zero stress but no convergent solutions in @code{metaMDS} - -Most common reason is that you have too few observations for your - at acronym{NMDS}. For @code{n} observations (points) and @code{k} -dimensions you need to estimate @code{n*k} parameters (ordination -scores) using @code{n*(n-1)/2} dissimilarities. For @code{k} dimensions -you must have @code{n > 2*k + 1}, or for two dimensions at least six -points. In some degenerate situations you may need even a larger number -of points. If you have a lower number of points, you can find an -undefined number of perfect (stress is zero) but different solutions. -Conventional wisdom due to Kruskal is that you should have @code{n > 4*k -+ 1} points for @code{k} dimensions. A typical symptom of insufficient -data is that you have (nearly) zero stress but no two convergent -solutions. In those cases you should reduce the number of dimensions -(@code{k}) and with very small data sets you should not use @code{NMDS}, -but rely on metric methods. - -It seems that local and hybrid scaling with @code{monoMDS} have similar -lower limits in practice (although theoretically they could differ). -However, higher number of dimensions can be used in metric scaling, both -with @code{monoMDS} and in principal coordinates analysis -(@code{cmdscale} in @pkg{stats}, @code{wcmdscale} in @pkg{vegan}). - - at node Zero dissimilarities in isoMDS, I have heard that you cannot fit environmental vectors or surfaces to NMDS results which only have rank-order scores, I get zero stress but no convergent solutions in @code{metaMDS}, Ordination - at section Zero dissimilarities in isoMDS - -Function @code{metaMDS} uses function @code{monoMDS} as its default -method for @acronym{NMDS}, and this function can handle zero -dissimilarities. The alternative function @code{isoMDS} was the only -choice before @pkg{vegan} 2.0-0, and it cannot handle zero dissimilarities. If -you want to use @code{isoMDS}, you can use argument @code{zerodist = -"add"} in @code{metaMDS} to handle zero dissimilarities. With this -argument, zero dissimilarities are replaced with a small above zero -value, and they can be handled in @code{isoMDS}. This is a kluge, and -some people do not like this. A more principal solution is to remove -duplicate sites using R command @code{unique}. However, after some -standardizations or with some dissimilarity indices, originally -non-unique sites can have zero dissimilarity, and you have to resort to -the kluge (or work harder with your data). Usually it is better to use - at code{monoMDS}. - - at node I have heard that you cannot fit environmental vectors or surfaces to NMDS results which only have rank-order scores, Where can I find numerical scores of ordination axes?, Zero dissimilarities in isoMDS, Ordination - at section I have heard that you cannot fit environmental vectors or surfaces to NMDS results which only have rank-order scores - -Claims like this have indeed been at large in the Internet, but they are -based on grave misunderstanding and are plainly wrong. @acronym{NMDS} -ordination results are strictly metric, and in @pkg{vegan} - at code{metaMDS} and @code{monoMDS} they are even strictly Euclidean. The -method is called ``non-metric'' because the Euclidean distances in -ordination space have a non-metric rank-order relationship to community -dissimilarities. You can inspect this non-linear step curve using -function @code{stressplot} in @pkg{vegan}. Because the ordination scores -are strictly Euclidean, it is correct to use @pkg{vegan} functions - at code{envfit} and @code{ordisurf} with @acronym{NMDS} results. - - at node Where can I find numerical scores of ordination axes?, How the RDA results are scaled?, I have heard that you cannot fit environmental vectors or surfaces to NMDS results which only have rank-order scores, Ordination - at section Where can I find numerical scores of ordination axes? - -Normally you can use function @code{scores} to extract ordination scores -for any ordination method. The @code{scores} function can also find -ordination scores for many non- at pkg{vegan} functions such as for - at code{prcomp} and @code{princomp} and for some @pkg{ade4} functions. - -In some cases the ordination result object stores raw scores, and -the axes are also scaled appropriate when you access them with - at code{scores}. For instance, in @code{cca} and @code{rda} the -ordination object has only so-called normalized scores, and they are -scaled for ordination plots or for other use when they are accessed with - at code{scores}. - - at node How the RDA results are scaled?, cca fails with ``data.frame expected'' or ``"site.env" missing'', Where can I find numerical scores of ordination axes?, Ordination - at section How the @acronym{RDA} results are scaled? - -The scaling or @acronym{RDA} results indeed differ from most other -software packages. The scaling of @acronym{RDA} is such a complicated -issue that it cannot be explained in this @acronym{FAQ}, but it is -explained in a separate @acronym{pdf} document on ``Design decision and -implementation details in vegan'' that you can read with @pkg{vegan} -command @code{vegandocs("decision")}. - - at node cca fails with ``data.frame expected'' or ``"site.env" missing'', Variance explained by ordination axes, How the RDA results are scaled?, Ordination - at section cca fails with ``data.frame expected'' or ``"site.env" missing'' - -This is not a @pkg{vegan} error message, but it comes from the - at code{cca} function in the @pkg{ade4} package. There is an unfortunate -name clash, and if you have loaded @pkg{ade4} after @pkg{vegan}, the - at pkg{ade4} version of @code{cca} will mask the @pkg{vegan} version. You -can use the @pkg{vegan} version using command @code{vegan::cca()}. If -you do not need package @pkg{ade4}, you can detach it with command - at code{detach(package:ade4)}. - - at node Variance explained by ordination axes, Can I have random effects in constrained ordination or in @code{adonis}?, cca fails with ``data.frame expected'' or ``"site.env" missing'', Ordination - at section Variance explained by ordination axes. - -In general, @pkg{vegan} does not directly give any statistics on the -``variance explained'' by ordination axes or by the constrained axes. -This is a design decision: I think this information is normally useless -and often misleading. In community ordination, the goal typically is -not to explain the variance, but to find the ``gradients'' or main -trends in the data. The ``total variation'' often is meaningless, and -all proportions of meaningless values also are meaningless. Often a -better solution explains a smaller part of ``total variation''. For -instance, in unstandardized principal components analysis most of the -variance is generated by a small number of most abundant species, and -they are easy to ``explain'' because data really are not very -multivariate. If you standardize your data, all species are equally -important. The first axes explains much less of the ``total -variation'', but now they explain all species equally, and results -typically are much more useful for the whole community. Correspondence -analysis uses another measure of variation (which is not variance), and -again it typically explains a ``smaller proportion'' than principal -components but with a better result. Detrended correspondence analysis -and nonmetric multidimensional scaling even do not try to ``explain'' -the variation, but use other criteria. All methods are incommensurable, -and it is impossible to compare methods using ``explanation of -variation''. - -If you still want to get ``explanation of variation'' (or a deranged -editor requests that from you), it is possible to get this information -for some methods: - at itemize - at item Eigenvector methods: -Functions @code{rda}, @code{cca} and @code{capscale} give the variation -of conditional (partialled), constrained (canonical) and residual -components, but you must calculate the proportions by hand. Function - at code{eigenvals} extracts the eigenvalues, and - at code{summary(eigenvals(ord))} reports the proportions explained in the -result object @code{ord}. Function @code{RsquareAdj} gives the -R-squared and adjusted R-squared (if available) for constrained -components. Function @code{goodness} gives the same statistics for -individual species or sites (species are unavailable with - at code{capscale}). In addition, there is a special function - at code{varpart} for unbiased partitioning of variance between up to four -separate components in redundancy analysis. - - at item Detrended correspondence analysis (function @code{decorana}). -The total amount of variation is undefined in detrended correspondence -analysis, and therefore proportions from total are unknown and -undefined. @acronym{DCA} is not a method for decomposition of -variation, and therefore these proportions would not make sense either. - - at item Nonmetric multidimensional scaling. - at acronym{NMDS} is a method for nonlinear mapping, and the concept of -of variation explained does not make sense. However, 1 - stress^2 -transforms nonlinear stress into quantity analogous to squared -correlation coefficient. Function @code{stressplot} displays the -nonlinear fit and gives this statistic. - - at end itemize - - at node Can I have random effects in constrained ordination or in @code{adonis}?, Is it possible to have passive points in ordination?, Variance explained by ordination axes, Ordination - at section Can I have random effects in constrained ordination or in @code{adonis}? - -No. Strictly speaking, this is impossible. However, you can define -models that respond to similar goals as random effects models, although -they strictly speaking use only fixed effects. - -Constrained ordination functions @code{cca}, @code{rda} and - at code{capscale} can have @code{Condition()} terms in their formula. The - at code{Condition()} define partial terms that are fitted before other -constraints and can be used to remove the effects of background -variables, and their contribution to decomposing inertia (variance) is -reported separately. These partial terms are often regarded as similar -to random effects, but they are still fitted in the same way as other -terms and strictly speaking they are fixed terms. - -Function @code{adonis} evaluates terms sequentially. In a model with -right-hand-side @code{~ A + B} the effects of @code{A} are evaluated -first, and the effects of @code{B} after removing the effects of - at code{A}. Sequential tests are also available in @code{anova} function -for constrained ordination results by setting argument @code{by = "term"}. -In this way, the first terms can serve in a similar role as -random effects, although they are fitted in the same way as all other -terms, and strictly speaking they are fixed terms. - -The permutation tests can usually have a @code{strata} argument which -restricts the permutations within levels of a factor given in the -argument. This can be used to restrict the permutations within levels of -factor regarded as a random term. More structured permutations are -available with the @pkg{permute} package. - -A major reason why real random effects models are impossible in most - at pkg{vegan} functions is that their tests are based on the permutation -of the data. The data are given, that is fixed, and therefore -permutation tests are basically tests of fixed terms on fixed data. -Random effect terms would require permutations of data with a random -component instead of the given, fixed data, and such tests are not -available in @pkg{vegan}. - - at node Is it possible to have passive points in ordination?, Class variables and dummies, Can I have random effects in constrained ordination or in @code{adonis}?, Ordination - at section Is it possible to have passive points in ordination? - - at pkg{Vegan} does not have a concept of passive points, or a point that should -only little influence the ordination results. However, you can add -points to eigenvector methods using @code{predict} functions with [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/vegan -r 2597 From noreply at r-forge.r-project.org Wed Aug 28 14:41:04 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 28 Aug 2013 14:41:04 +0200 (CEST) Subject: [Vegan-commits] r2598 - in pkg/vegan: R inst Message-ID: <20130828124109.C7905185CBA@r-forge.r-project.org> Author: jarioksa Date: 2013-08-28 14:41:00 +0200 (Wed, 28 Aug 2013) New Revision: 2598 Modified: pkg/vegan/R/as.mlm.cca.R pkg/vegan/R/as.mlm.rda.R pkg/vegan/R/eigenvals.R pkg/vegan/R/intersetcor.R pkg/vegan/inst/ChangeLog Log: remove R < 2.12.1 tweaks Modified: pkg/vegan/R/as.mlm.cca.R =================================================================== --- pkg/vegan/R/as.mlm.cca.R 2013-08-28 08:56:55 UTC (rev 2597) +++ pkg/vegan/R/as.mlm.cca.R 2013-08-28 12:41:00 UTC (rev 2598) @@ -5,10 +5,6 @@ wa <- x$CCA$wa wa <- sweep(wa, 1, sqrt(w), "*") X <- qr.X(x$CCA$QR) - ## qr.X gives wrong column names now, and they are fixed here - ## (hopefully fixed in 2.12.1, but that's only a wish). - if (getRversion() <= "2.12.0") - colnames(X)[x$CCA$QR$pivot] <- colnames(X) lm(wa ~ . - 1, data = as.data.frame(X)) } Modified: pkg/vegan/R/as.mlm.rda.R =================================================================== --- pkg/vegan/R/as.mlm.rda.R 2013-08-28 08:56:55 UTC (rev 2597) +++ pkg/vegan/R/as.mlm.rda.R 2013-08-28 12:41:00 UTC (rev 2598) @@ -2,10 +2,6 @@ function (x) { X <- qr.X(x$CCA$QR) - ## We hope that column names will be fixed in R 2.12.1 (but - ## perhaps in vain). - if (getRversion() <= "2.12.0") - colnames(X)[x$CCA$QR$pivot] <- colnames(X) lm(x$CCA$wa ~ . - 1, data = as.data.frame(X)) } Modified: pkg/vegan/R/eigenvals.R =================================================================== --- pkg/vegan/R/eigenvals.R 2013-08-28 08:56:55 UTC (rev 2597) +++ pkg/vegan/R/eigenvals.R 2013-08-28 12:41:00 UTC (rev 2598) @@ -20,8 +20,7 @@ else if (length(x) == 3 && all(names(x) %in% c("d", "u", "v"))) out <- x$d^2 ## cmdscale() will return all eigenvalues from R 2.12.1 - else if (getRversion() > "2.12.0" && - all(c("points","eig","GOF") %in% names(x))) + else if (all(c("points","eig","GOF") %in% names(x))) out <- x$eig } class(out) <- "eigenvals" Modified: pkg/vegan/R/intersetcor.R =================================================================== --- pkg/vegan/R/intersetcor.R 2013-08-28 08:56:55 UTC (rev 2597) +++ pkg/vegan/R/intersetcor.R 2013-08-28 12:41:00 UTC (rev 2598) @@ -8,8 +8,5 @@ wa <- sweep(object$CCA$wa, 1, sqrt(w), "*") } X <- qr.X(object$CCA$QR) - ## current R (2.12.0) uses wrong column names in pivoted qr.X() - if (getRversion() <= "2.12.0") - colnames(X)[object$CCA$QR$pivot] <- colnames(X) cor(X, wa) } Modified: pkg/vegan/inst/ChangeLog =================================================================== --- pkg/vegan/inst/ChangeLog 2013-08-28 08:56:55 UTC (rev 2597) +++ pkg/vegan/inst/ChangeLog 2013-08-28 12:41:00 UTC (rev 2598) @@ -4,6 +4,8 @@ Version 2.1-34 (opened August 28, 2013) + * DESCRIPTION: dependent on R >= 2.14.0. + * DESCRIPTION, vignettes: R 3.0.2-to-be checks with --as-cran requires (with a NOTE) the vignettes source files (Rnw) to be in vignettes/ directory. Because Makefile is not executed in @@ -12,9 +14,11 @@ to move those to inst/doc after building. This also made /.Rinstignore unnecessary. The vignettes directory was introduced and made recommended in R 2.14.0 so that the this version of vegan - depends on R >= 2.14.0. With this, some of the parallel code - that is also dependent on 2.14.0 could be simplified as no version - checking is necessary. + depends on R >= 2.14.0. + + * tweaks for R < 2.12.1 removed: code to fix buggy naming of + columns in qr.X before 2.12.1 (as.mlm.cca/rda, intersetcor), and + change in the cmdscale() output (eigenvals.default). Version 2.1-33 (closed August 28, 2013) @@ -22,7 +26,7 @@ checks with NOTE on ':::' calls to tools:::httpdPort (to launch reading vegan NEWS.html in existing browser window) and parallel:::.reg to acces the defaultCluster in an unexported - function in parallel Namespace. + environment within 'parallel' Namespace. Version 2.1-32 (closed August 19, 2013) From noreply at r-forge.r-project.org Wed Aug 28 14:46:35 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 28 Aug 2013 14:46:35 +0200 (CEST) Subject: [Vegan-commits] r2599 - in pkg/vegan: R inst Message-ID: <20130828124635.A6E51185738@r-forge.r-project.org> Author: jarioksa Date: 2013-08-28 14:46:34 +0200 (Wed, 28 Aug 2013) New Revision: 2599 Modified: pkg/vegan/R/capscale.R pkg/vegan/inst/ChangeLog Log: remove tweak against changed cmdscale output in R 2.13.0 (depend on newer R) Modified: pkg/vegan/R/capscale.R =================================================================== --- pkg/vegan/R/capscale.R 2013-08-28 12:41:00 UTC (rev 2598) +++ pkg/vegan/R/capscale.R 2013-08-28 12:46:34 UTC (rev 2599) @@ -79,8 +79,6 @@ if (add) { X <- cmdscale(X, k = k, eig = TRUE, add = add) ## All eigenvalues *should* be positive, but see that they are - if (getRversion() < "2.13.0") - X$points <- X$points[, X$eig[-(k+1)] > 0] X$eig <- X$eig[X$eig > 0] } else Modified: pkg/vegan/inst/ChangeLog =================================================================== --- pkg/vegan/inst/ChangeLog 2013-08-28 12:41:00 UTC (rev 2598) +++ pkg/vegan/inst/ChangeLog 2013-08-28 12:46:34 UTC (rev 2599) @@ -19,6 +19,9 @@ * tweaks for R < 2.12.1 removed: code to fix buggy naming of columns in qr.X before 2.12.1 (as.mlm.cca/rda, intersetcor), and change in the cmdscale() output (eigenvals.default). + + * tweak for R < 2.13.0 removed: change in cmdscale() output + (capscale). Version 2.1-33 (closed August 28, 2013) From noreply at r-forge.r-project.org Thu Aug 29 10:15:17 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 29 Aug 2013 10:15:17 +0200 (CEST) Subject: [Vegan-commits] r2600 - in pkg/vegan: R inst Message-ID: <20130829081517.1A6E1184D58@r-forge.r-project.org> Author: jarioksa Date: 2013-08-29 10:15:16 +0200 (Thu, 29 Aug 2013) New Revision: 2600 Modified: pkg/vegan/R/vegandocs.R pkg/vegan/inst/ChangeLog Log: avoid using tools::: Modified: pkg/vegan/R/vegandocs.R =================================================================== --- pkg/vegan/R/vegandocs.R 2013-08-28 12:46:34 UTC (rev 2599) +++ pkg/vegan/R/vegandocs.R 2013-08-29 08:15:16 UTC (rev 2600) @@ -16,10 +16,9 @@ ## Try html helptype <- getOption("help_type") if (length(helptype) && helptype == "html") { - if (!tools:::httpdPort) - startDynamicHelp() - browseURL(paste("http://127.0.0.1:", tools:::httpdPort, - "/library/vegan/doc/NEWS.html", sep="")) + browseURL(paste("file://", + system.file(package="vegan", "doc", "NEWS.html"), + sep="")) } else { file.show(Rd2txt(file.path(system.file(package="vegan"), "NEWS.Rd"), tempfile())) Modified: pkg/vegan/inst/ChangeLog =================================================================== --- pkg/vegan/inst/ChangeLog 2013-08-28 12:46:34 UTC (rev 2599) +++ pkg/vegan/inst/ChangeLog 2013-08-29 08:15:16 UTC (rev 2600) @@ -22,6 +22,10 @@ * tweak for R < 2.13.0 removed: change in cmdscale() output (capscale). + + * vegandocs: does not use unexported tools:::httpdPort. Now only + remaining ':::' case is querying default cluster in the + environment parallel:::.reg. Version 2.1-33 (closed August 28, 2013)