[Vegan-commits] r2019 - pkg/vegan/tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Dec 12 09:37:44 CET 2011
Author: jarioksa
Date: 2011-12-12 09:37:43 +0100 (Mon, 12 Dec 2011)
New Revision: 2019
Modified:
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
update
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-12-11 18:30:06 UTC (rev 2018)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-12-12 08:37:43 UTC (rev 2019)
@@ -1,8 +1,8 @@
-R version 2.14.0 Patched (2011-11-05 r57575)
+R Under development (unstable) (2011-12-11 r57866)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
-Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit)
+Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -154,14 +154,14 @@
> plot(ef)
> ordisurf(mod ~ pH, varechem, knots = 1, add = TRUE)
Loading required package: mgcv
-This is mgcv 1.7-10. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-11. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x101fb3ad8>
+<environment: 0x2a7ab40>
Total model degrees of freedom 3
GCV score: 0.0427924
@@ -3942,7 +3942,7 @@
> ### Name: nestedtemp
> ### Title: Nestedness Indices for Communities of Islands or Patches
> ### Aliases: nestedtemp nestedchecker nestedn0 nesteddisc nestednodf
-> ### plot.nestedtemp
+> ### nestedbetasor nestedbetajac plot.nestedtemp
> ### Keywords: univar
>
> ### ** Examples
@@ -4696,17 +4696,17 @@
> vare.mds <- monoMDS(vare.dist)
> with(varechem, ordisurf(vare.mds, Baresoil, bubble = 5))
Loading required package: mgcv
-This is mgcv 1.7-10. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-11. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x109f03a28>
+<environment: 0x8ad2b48>
Estimated degrees of freedom:
-6.4351 total = 7.435071
+6.4351 total = 7.43507
GCV score: 144.1236
>
@@ -4719,7 +4719,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x109004d48>
+<environment: 0x995d978>
Estimated degrees of freedom:
6.1039 total = 7.103853
@@ -4731,13 +4731,13 @@
> ## Get fitted values
> calibrate(fit)
1 2 3 4 5 6 7
-22.0644614 6.0132251 3.6350483 4.1019742 9.0030989 5.9202601 8.6399184
+22.0644615 6.0132250 3.6350484 4.1019743 9.0030990 5.9202602 8.6399182
8 9 10 11 12 13 14
-11.0719303 0.6561781 35.2282118 10.4346331 7.2900018 5.5710617 24.6503110
+11.0719302 0.6561783 35.2282116 10.4346331 7.2900019 5.5710617 24.6503109
15 16 17 18 19 20 21
-18.8754521 29.7286543 5.6158934 9.5869716 3.2876267 2.7111721 10.7832857
+18.8754520 29.7286540 5.6158934 9.5869715 3.2876268 2.7111723 10.7832857
22 23 24
- 3.0020413 9.8128952 7.3656932
+ 3.0020415 9.8128952 7.3656934
>
> ## Plot method
> plot(fit, what = "contour")
@@ -4868,14 +4868,14 @@
> ## Map of PCNMs in the sample plot
> ordisurf(mite.xy, scores(pcnm1, choi=1), bubble = 4, main = "PCNM 1")
Loading required package: mgcv
-This is mgcv 1.7-10. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-11. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x109ae36b0>
+<environment: 0x8dbccd8>
Estimated degrees of freedom:
8.9275 total = 9.927492
@@ -4888,7 +4888,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10abfbc78>
+<environment: 0x999e6a8>
Estimated degrees of freedom:
7.7529 total = 8.75294
@@ -4901,7 +4901,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x109acbc08>
+<environment: 0x936c760>
Estimated degrees of freedom:
8.8962 total = 9.89616
@@ -5667,8 +5667,8 @@
[2,] 0.1169579 0.9931369
Translation of averages:
- [,1] [,2]
-[1,] 1.047183e-17 -1.381645e-17
+ [,1] [,2]
+[1,] 1.79048e-17 9.246476e-19
Scaling of target:
[1] 0.6736868
@@ -6509,7 +6509,7 @@
Salrep 0.7118892 8.654457e-02
Achmil 1.5948052 8.449914e-01
Poatri 0.7367577 7.099165e-01
-Chealb 1.9479718 2.220446e-16
+Chealb 1.9479718 6.661338e-16
Elyrep 0.5160932 5.135604e-01
Sagpro 1.3031750 1.019154e+00
Plalan 1.7013794 6.393173e-01
@@ -7163,14 +7163,14 @@
> ## add fitted surface of diversity to the model
> ordisurf(mod, diversity(dune), add = TRUE)
Loading required package: mgcv
-This is mgcv 1.7-10. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-11. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x108e4e190>
+<environment: 0x9403288>
Estimated degrees of freedom:
2 total = 3
@@ -7613,13 +7613,13 @@
> ## Eigevalues are numerically similar
> ca$CA$eig - ord$eig
CA1 CA2 CA3 CA4 CA5
- 9.992007e-16 -6.106227e-16 8.881784e-16 -2.775558e-17 2.220446e-16
+-7.771561e-16 -2.220446e-16 6.106227e-16 -3.608225e-16 -1.110223e-16
CA6 CA7 CA8 CA9 CA10
- 9.714451e-17 9.714451e-17 4.163336e-17 -1.387779e-17 8.326673e-17
+ 1.387779e-17 9.714451e-17 1.387779e-17 2.775558e-17 1.318390e-16
CA11 CA12 CA13 CA14 CA15
- 7.632783e-17 1.040834e-16 -2.081668e-17 4.510281e-17 1.908196e-17
+ 9.714451e-17 6.938894e-18 -6.938894e-18 3.122502e-17 0.000000e+00
CA16 CA17 CA18 CA19
--1.908196e-17 0.000000e+00 7.025630e-17 2.125036e-17
+-3.295975e-17 2.428613e-17 2.862294e-17 5.637851e-18
> ## Configurations are similar when site scores are scaled by
> ## eigenvalues in CA
> procrustes(ord, ca, choices=1:19, scaling = 1)
@@ -7628,7 +7628,7 @@
procrustes(X = ord, Y = ca, choices = 1:19, scaling = 1)
Procrustes sum of squares:
--4.263e-14
+ 0
> plot(procrustes(ord, ca, choices=1:2, scaling=1))
> ## Reconstruction of non-Euclidean distances with negative eigenvalues
@@ -7646,7 +7646,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 108.43 2.371 111.048 0 0
+Time elapsed: 25.593 0.132 25.82 0 0
> grDevices::dev.off()
null device
1
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