[Vegan-commits] r2880 - in pkg/vegan: . inst tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Sep 4 08:49:31 CEST 2014
Author: jarioksa
Date: 2014-09-04 08:49:30 +0200 (Thu, 04 Sep 2014)
New Revision: 2880
Modified:
pkg/vegan/DESCRIPTION
pkg/vegan/inst/ChangeLog
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
Merge branch 'master' into r-forge-svn-local
Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION 2014-09-03 09:36:53 UTC (rev 2879)
+++ pkg/vegan/DESCRIPTION 2014-09-04 06:49:30 UTC (rev 2880)
@@ -1,7 +1,7 @@
Package: vegan
Title: Community Ecology Package
-Version: 2.1-41
-Date: December 12, 2013
+Version: 2.1-42
+Date: September 4, 2014
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
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2014-09-03 09:36:53 UTC (rev 2879)
+++ pkg/vegan/inst/ChangeLog 2014-09-04 06:49:30 UTC (rev 2880)
@@ -2,8 +2,18 @@
VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
-Version 2.1-41 (opened December 12, 2013)
+Version 2.1-42 (opened September 4, 2014)
+ * Opened a new version to prepare release 2.2-0.
+
+ * Moved main development from R-Forge to GitHub.com.
+
+ * NAMESPACE, DESCRIPTION: adapted to current R CMD check that has
+ more stringent tests on attaching and importing external packages
+ and using their functions.
+
+Version 2.1-41 (closed September 4, 2014)
+
* ordiellipse, ordihull, ordispider: can now handle (omit) NA
cases in 'groups'. They were able to omit to NA cases in scores,
but having NA in 'groups' triggered really cryptic error
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2014-09-03 09:36:53 UTC (rev 2879)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2014-09-04 06:49:30 UTC (rev 2880)
@@ -1,5 +1,5 @@
-R Under development (unstable) (2014-01-12 r64752) -- "Unsuffered Consequences"
+R Under development (unstable) (2014-09-03 r66516) -- "Unsuffered Consequences"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -153,26 +153,20 @@
> ef <- envfit(mod ~ pH, varechem, permutations = 0)
> plot(ef)
> ordisurf(mod ~ pH, varechem, knots = 1, add = TRUE)
-Loading required package: mgcv
-Loading required package: nlme
-This is mgcv 1.7-27. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x1a4dcf8>
+<environment: 0x5c946e8>
Total model degrees of freedom 3
-REML score: -3.185099
+REML score: -3.185099
>
>
>
> cleanEx()
-
-detaching ‘package:mgcv’, ‘package:nlme’
-
> nameEx("MOStest")
> ### * MOStest
>
@@ -236,7 +230,6 @@
2.5 % 97.5 %
5.255827 6.782979
> confint(mod)
-Loading required package: MASS
2.5 % 97.5 %
5.816021 6.574378
> plot(profile(mod))
@@ -245,9 +238,6 @@
>
> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
> cleanEx()
-
-detaching ‘package:MASS’
-
> nameEx("RsquareAdj")
> ### * RsquareAdj
>
@@ -1240,9 +1230,9 @@
> dis[c(2, 20)] <- NA
> mod2 <- betadisper(dis, groups) ## warnings
Warning in betadisper(dis, groups) :
- Missing observations due to 'group' removed.
+ missing observations due to 'group' removed
Warning in betadisper(dis, groups) :
- Missing observations due to 'd' removed.
+ missing observations due to 'd' removed
> mod2
Homogeneity of multivariate dispersions
@@ -1297,9 +1287,9 @@
> ## Using group centroids
> mod3 <- betadisper(dis, groups, type = "centroid")
Warning in betadisper(dis, groups, type = "centroid") :
- Missing observations due to 'group' removed.
+ missing observations due to 'group' removed
Warning in betadisper(dis, groups, type = "centroid") :
- Missing observations due to 'd' removed.
+ missing observations due to 'd' removed
> mod3
Homogeneity of multivariate dispersions
@@ -5037,21 +5027,18 @@
> vare.dist <- vegdist(varespec)
> vare.mds <- monoMDS(vare.dist)
> with(varechem, ordisurf(vare.mds, Baresoil, bubble = 5))
-Loading required package: mgcv
-Loading required package: nlme
-This is mgcv 1.7-27. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE)
-<environment: 0x9968520>
+<environment: 0x77c4478>
Estimated degrees of freedom:
5.63 total = 6.63
-REML score: 92.96761
+REML score: 92.96761
>
> ## as above but without the extra penalties on smooth terms,
> ## and using GCV smoothness selection (old behaviour of `ordisurf()`):
@@ -5063,23 +5050,23 @@
Formula:
y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE)
-<environment: 0xa291388>
+<environment: 0x8afa6c0>
Estimated degrees of freedom:
6.45 total = 7.45
-GCV score: 144.0039
+GCV score: 144.0039
>
> ## Cover of Cladina arbuscula
> fit <- with(varespec, ordisurf(vare.mds, Cladarbu, family=quasipoisson))
> ## Get fitted values
> calibrate(fit)
1 2 3 4 5 6 7 8
-21.253963 5.675210 3.679486 3.898355 9.643787 7.698255 7.729282 9.758092
+21.254026 5.675259 3.679616 3.898510 9.643821 7.698310 7.729203 9.758046
9 10 11 12 13 14 15 16
- 2.743203 29.700504 11.971986 8.310916 5.390556 24.906203 11.006871 25.330570
+ 2.743212 29.700556 11.971747 8.310960 5.390564 24.905994 11.007652 25.330656
17 18 19 20 21 22 23 24
- 6.520735 9.410672 4.519645 4.090901 11.558075 4.314814 11.693769 14.244150
+ 6.520708 9.410616 4.519672 4.090948 11.557930 4.314850 11.693692 14.243453
>
> ## Variable selection via additional shrinkage penalties
> ## This allows non-significant smooths to be selected out
@@ -5094,12 +5081,12 @@
Formula:
y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE)
-<environment: 0xa202b48>
+<environment: 0x97119c8>
Estimated degrees of freedom:
5.63 total = 6.63
-REML score: 92.96761
+REML score: 92.96761
> ## - option 2: use a basis with shrinkage
> with(varechem,
+ ordisurf(vare.mds, Baresoil, method = "REML", bs = "ts"))
@@ -5109,12 +5096,12 @@
Formula:
y ~ s(x1, x2, k = 10, bs = "ts", fx = FALSE)
-<environment: 0x99e3890>
+<environment: 0x7a3cfd0>
Estimated degrees of freedom:
4.43 total = 5.43
-REML score: 96.2345
+REML score: 96.2345
> ## or bs = "cs" with `isotropic = FALSE`
>
> ## Plot method
@@ -5123,6 +5110,9 @@
> ## Plotting the "gam" object
> plot(fit, what = "gam") ## 'col' and 'cex' not passed on
> ## or via plot.gam directly
+> library(mgcv)
+Loading required package: nlme
+This is mgcv 1.8-2. For overview type 'help("mgcv-package")'.
> plot.gam(fit, cex = 2, pch = 1, col = "blue")
> ## 'col' effects all objects drawn...
>
@@ -5135,12 +5125,12 @@
Formula:
y ~ s(x1, x2, k = 10, bs = "ds", fx = FALSE)
-<environment: 0x9f10bb8>
+<environment: 0x95af318>
Estimated degrees of freedom:
5.63 total = 6.63
-REML score: 93.17149
+REML score: 93.17149
>
> ## A fixed degrees of freedom smooth, must use 'select = FALSE'
> with(varechem, ordisurf(vare.mds, Baresoil, knots = 4,
@@ -5151,12 +5141,12 @@
Formula:
y ~ s(x1, x2, k = 4, bs = "tp", fx = TRUE)
-<environment: 0x8ba13d8>
+<environment: 0x7bccf50>
Estimated degrees of freedom:
3 total = 4
-REML score: 81.86011
+REML score: 81.86011
>
> ## An anisotropic smoother with cubic regression spline bases
> with(varechem, ordisurf(vare.mds, Baresoil, isotropic = FALSE,
@@ -5168,12 +5158,12 @@
Formula:
y ~ te(x1, x2, k = c(4, 4), bs = c("cr", "cr"), fx = c(FALSE,
FALSE))
-<environment: 0x98f4090>
+<environment: 0x8a73740>
Estimated degrees of freedom:
2.99 total = 3.99
-REML score: 90.861
+REML score: 90.86099
>
> ## An anisotropic smoother with cubic regression spline with
> ## shrinkage bases & different degrees of freedom in each dimension
@@ -5187,12 +5177,12 @@
Formula:
y ~ te(x1, x2, k = c(3, 4), bs = c("cs", "cs"), fx = c(TRUE,
TRUE))
-<environment: 0x9a7a810>
+<environment: 0x86bea20>
Estimated degrees of freedom:
11 total = 12
-REML score: 39.58245
+REML score: 39.58245
>
>
>
@@ -5322,21 +5312,18 @@
> op <- par(mfrow=c(1,3))
> ## Map of PCNMs in the sample plot
> ordisurf(mite.xy, scores(pcnm1, choi=1), bubble = 4, main = "PCNM 1")
-Loading required package: mgcv
-Loading required package: nlme
-This is mgcv 1.7-27. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE)
-<environment: 0x6b7a770>
+<environment: 0x9eca308>
Estimated degrees of freedom:
8.71 total = 9.71
-REML score: -120.7705
+REML score: -120.7705
> ordisurf(mite.xy, scores(pcnm1, choi=2), bubble = 4, main = "PCNM 2")
Family: gaussian
@@ -5344,12 +5331,12 @@
Formula:
y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE)
-<environment: 0x9576da8>
+<environment: 0x8adb928>
Estimated degrees of freedom:
7.18 total = 8.18
-REML score: -103.4662
+REML score: -103.4662
> ordisurf(mite.xy, scores(pcnm1, choi=3), bubble = 4, main = "PCNM 3")
Family: gaussian
@@ -5357,12 +5344,12 @@
Formula:
y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE)
-<environment: 0x987ebd8>
+<environment: 0x86d11e0>
Estimated degrees of freedom:
8.32 total = 9.32
-REML score: -94.19053
+REML score: -94.19053
> par(op)
> ## Plot first PCNMs against each other
> ordisplom(pcnm1, choices=1:4)
@@ -5379,9 +5366,6 @@
>
> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
> cleanEx()
-
-detaching ‘package:mgcv’, ‘package:nlme’
-
> nameEx("permatfull")
> ### * permatfull
>
@@ -6340,6 +6324,32 @@
>
>
> cleanEx()
+> nameEx("reorder.hclust")
+> ### * reorder.hclust
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: reorder.hclust
+> ### Title: Reorder a Hierarchical Clustering Tree
+> ### Aliases: reorder.hclust rev.hclust
+> ### Keywords: multivariate
+>
+> ### ** Examples
+>
+> data(mite, mite.env)
+> hc <- hclust(vegdist(wisconsin(sqrt(mite))))
+> ohc <- with(mite.env, reorder(hc, WatrCont))
+> plot(hc)
+> plot(ohc)
+> ## Slightly different from reordered 'dendrogram' which ignores group
+> ## sizes in assessing means.
+> den <- as.dendrogram(hc)
+> den <- with(mite.env, reorder(den, WatrCont, agglo.FUN = mean))
+> plot(den)
+>
+>
+>
+> cleanEx()
> nameEx("scores")
> ### * scores
>
@@ -6384,6 +6394,28 @@
>
>
> cleanEx()
+> nameEx("scores.hclust")
+> ### * scores.hclust
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: scores.hclust
+> ### Title: Coordinates of Leaves and Internal Nodes in a hclust Tree
+> ### Aliases: scores.hclust
+> ### Keywords: multivariate
+>
+> ### ** Examples
+>
+> ## Show values that were used in reordering a tree
+> data(mite, mite.env)
+> hc <- hclust(vegdist(mite))
+> hc <- with(mite.env, reorder(hc, WatrCont))
+> with(mite.env, plot(hc, labels=round(WatrCont), cex=0.7))
+> ordilabel(scores(hc), label=round(hc$value), cex=0.7)
+>
+>
+>
+> cleanEx()
> nameEx("screeplot.cca")
> ### * screeplot.cca
>
@@ -6750,8 +6782,8 @@
>
> ### Name: spantree
> ### Title: Minimum Spanning Tree
-> ### Aliases: spantree cophenetic.spantree plot.spantree lines.spantree
-> ### spandepth
+> ### Aliases: spantree cophenetic.spantree as.hclust.spantree plot.spantree
+> ### lines.spantree spandepth
> ### Keywords: multivariate
>
> ### ** Examples
@@ -6761,7 +6793,6 @@
> tr <- spantree(dis)
> ## Add tree to a metric scaling
> plot(tr, cmdscale(dis), type = "t")
-Loading required package: MASS
> ## Find a configuration to display the tree neatly
> plot(tr, type = "t")
Initial stress : 0.03111
@@ -6777,13 +6808,12 @@
stress after 20 iters: 0.01139, magic = 0.500
stress after 30 iters: 0.01118, magic = 0.500
stress after 40 iters: 0.01114, magic = 0.500
+> ## Plot as a dendrogram
+> plot(as.hclust(tr))
>
>
>
> cleanEx()
-
-detaching ‘package:MASS’
-
> nameEx("specaccum")
> ### * specaccum
>
@@ -7146,50 +7176,50 @@
> mod <- taxondive(dune, taxdis)
> mod
Species Delta Delta* Lambda+ Delta+ S Delta+
-1 5.000 25.201 32.401 1583.249 51.705 258.53
-2 10.000 60.573 66.438 1415.833 66.779 667.79
-3 10.000 46.754 51.874 1385.449 70.835 708.35
-4 13.000 58.307 63.293 1249.469 73.461 954.99
-5 14.000 72.023 76.967 1013.850 77.581 1086.14
-6 11.000 76.352 83.052 856.565 80.779 888.57
-7 13.000 71.005 76.286 896.552 79.375 1031.87
-8 12.000 62.880 67.464 906.057 77.412 928.95
-9 13.000 60.341 64.619 1081.914 73.544 956.07
-10 12.000 68.919 74.532 1023.714 77.748 932.97
-11 9.000 76.140 85.057 553.804 82.412 741.71
-12 9.000 71.195 79.626 669.623 83.756 753.80
-13 10.000 57.210 65.101 848.964 77.901 779.01
-14 7.000 78.441 90.207 279.757 88.808 621.66
-15 8.000 77.813 87.496 330.572 88.150 705.20
-16 8.000 62.725 72.154 875.566 77.140 617.12
-17 7.000 64.823 72.409 1204.103 70.968 496.77
-18 9.000 76.626 85.656 599.550 81.260 731.34
-19 9.000 73.340 81.198 480.065 83.218 748.96
-20 8.000 79.807 88.993 390.726 89.385 715.08
-Expected 74.594 71.431 79.644
+1 5.000 25.009 32.154 1592.777 51.545 257.73
+2 10.000 60.493 66.350 1426.590 66.687 666.87
+3 10.000 46.599 51.702 1395.603 70.748 707.47
+4 13.000 58.199 63.176 1258.772 73.403 954.24
+5 14.000 72.045 76.990 1018.677 77.602 1086.43
+6 11.000 76.415 83.121 858.170 80.843 889.27
+7 13.000 70.250 75.475 970.358 78.397 1019.17
+8 12.000 59.126 63.436 1079.722 74.787 897.44
+9 13.000 56.948 60.985 1220.760 71.160 925.08
+10 12.000 68.902 74.513 1028.527 77.762 933.14
+11 9.000 76.201 85.126 552.357 82.538 742.84
+12 9.000 69.555 77.792 760.886 82.614 743.52
+13 10.000 55.296 62.923 935.943 76.657 766.57
+14 7.000 77.609 89.250 341.499 88.182 617.27
+15 8.000 74.924 84.249 473.604 86.558 692.47
+16 8.000 57.843 66.539 1111.251 73.360 586.88
+17 7.000 64.823 72.408 1209.057 70.974 496.82
+18 9.000 76.731 85.773 596.607 81.401 732.61
+19 9.000 73.449 81.318 476.221 83.371 750.34
+20 8.000 78.076 87.063 520.623 87.922 703.38
+Expected 73.289 70.182 78.712
> summary(mod)
Delta Delta* Delta+ sd(Delta+) z(Delta+) Pr(>|z|)
-1 25.2010 32.4013 51.7051 8.9683 -3.1153 0.001837 **
-2 60.5731 66.4375 66.7793 4.2930 -2.9967 0.002729 **
-3 46.7535 51.8745 70.8346 4.2930 -2.0520 0.040165 *
-4 58.3066 63.2933 73.4609 3.2021 -1.9310 0.053486 .
-5 72.0231 76.9667 77.5814 2.9323 -0.7034 0.481792
-6 76.3523 83.0524 80.7792 3.8687 0.2934 0.769200
-7 71.0050 76.2863 79.3749 3.2021 -0.0840 0.933019
-8 62.8802 67.4643 77.4124 3.5104 -0.6357 0.524956
-9 60.3414 64.6193 73.5437 3.2021 -1.9051 0.056762 .
-10 68.9193 74.5319 77.7475 3.5104 -0.5403 0.589023
-11 76.1400 85.0573 82.4117 4.8067 0.5758 0.564763
-12 71.1954 79.6265 83.7558 4.8067 0.8554 0.392326
-13 57.2101 65.1011 77.9007 4.2930 -0.4061 0.684669
-14 78.4412 90.2074 88.8084 6.2696 1.4617 0.143819
-15 77.8128 87.4962 88.1501 5.4461 1.5619 0.118320
-16 62.7252 72.1545 77.1396 5.4461 -0.4599 0.645611
-17 64.8233 72.4091 70.9677 6.2696 -1.3839 0.166399
-18 76.6264 85.6556 81.2596 4.8067 0.3361 0.736794
-19 73.3403 81.1982 83.2181 4.8067 0.7436 0.457145
-20 79.8067 88.9931 89.3845 5.4461 1.7885 0.073693 .
-Expected 74.5941 71.4315 79.6440
+1 25.0089 32.1543 51.5455 9.5637 -2.8405 0.004504 **
+2 60.4931 66.3497 66.6869 4.6664 -2.5769 0.009970 **
+3 46.5985 51.7024 70.7475 4.6664 -1.7067 0.087881 .
+4 58.1988 63.1763 73.4033 3.5073 -1.5135 0.130150
+5 72.0452 76.9903 77.6024 3.2187 -0.3446 0.730386
+6 76.4148 83.1205 80.8430 4.2170 0.5054 0.613259
+7 70.2500 75.4752 78.3974 3.5073 -0.0896 0.928626
+8 59.1259 63.4363 74.7865 3.8361 -1.0232 0.306220
+9 56.9481 60.9854 71.1597 3.5073 -2.1532 0.031303 *
+10 68.9021 74.5133 77.7617 3.8361 -0.2476 0.804432
+11 76.2014 85.1259 82.5379 5.2089 0.7346 0.462605
+12 69.5554 77.7922 82.6136 5.2089 0.7491 0.453792
+13 55.2961 62.9232 76.6566 4.6664 -0.4404 0.659657
+14 77.6087 89.2500 88.1818 6.7459 1.4039 0.160362
+15 74.9245 84.2485 86.5584 5.8818 1.3341 0.182178
+16 57.8435 66.5389 73.3604 5.8818 -0.9098 0.362936
+17 64.8225 72.4081 70.9740 6.7459 -1.1470 0.251377
+18 76.7314 85.7730 81.4015 5.2089 0.5164 0.605570
+19 73.4487 81.3182 83.3712 5.2089 0.8945 0.371029
+20 78.0762 87.0634 87.9221 5.8818 1.5659 0.117368
+Expected 73.2888 70.1816 78.7116
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> plot(mod)
@@ -7933,21 +7963,18 @@
> with(dune.env, ordiellipse(mod, Management, label = TRUE))
> ## add fitted surface of diversity to the model
> ordisurf(mod, diversity(dune), add = TRUE)
-Loading required package: mgcv
-Loading required package: nlme
-This is mgcv 1.7-27. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE)
-<environment: 0x84b2db8>
+<environment: 0x974c070>
Estimated degrees of freedom:
1.28 total = 2.28
-REML score: 3.006229
+REML score: 3.00623
> ### Example 3: analysis of dissimilarites a.k.a. non-parametric
> ### permutational anova
> adonis(dune ~ ., dune.env)
@@ -7985,9 +8012,6 @@
>
>
> cleanEx()
-
-detaching ‘package:mgcv’, ‘package:nlme’
-
> nameEx("vegandocs")
> ### * vegandocs
>
@@ -8495,7 +8519,7 @@
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 27.424 0.147 27.577 0 0
+Time elapsed: 35.834 7.734 41.19 0 0.001
> grDevices::dev.off()
null device
1
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