[Vegan-commits] r1990 - pkg/vegan/tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Nov 12 12:21:12 CET 2011
Author: gsimpson
Date: 2011-11-12 12:21:12 +0100 (Sat, 12 Nov 2011)
New Revision: 1990
Modified:
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
update checks following r1988
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-11-12 10:54:57 UTC (rev 1989)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-11-12 11:21:12 UTC (rev 1990)
@@ -1,8 +1,8 @@
-R version 2.14.0 RC (2011-10-29 r57474)
+R version 2.14.0 Patched (2011-11-04 r57571)
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 1.7-9. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-10. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x101faf2d8>
+<environment: 0x3745a78>
Total model degrees of freedom 3
GCV score: 0.0427924
@@ -585,8 +585,8 @@
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Management 3 1.4686 0.48953 3.2629 0.34161 0.01 **
-A1 1 0.4409 0.44089 2.9387 0.10256 0.02 *
-Management:A1 3 0.5892 0.19639 1.3090 0.13705 0.18
+A1 1 0.4409 0.44089 2.9387 0.10256 0.01 **
+Management:A1 3 0.5892 0.19639 1.3090 0.13705 0.01 **
Residuals 12 1.8004 0.15003 0.41878
Total 19 4.2990 1.00000
---
@@ -638,10 +638,10 @@
Call:
adonis(formula = Y ~ NO3, data = dat, permutations = 1000, strata = dat$field)
- Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
-NO3 1 0.055856 0.055856 4.0281 0.28714 0.008991 **
-Residuals 10 0.138667 0.013867 0.71286
-Total 11 0.194524 1.00000
+ Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
+NO3 1 0.055856 0.055856 4.0281 0.28714 0.000999 ***
+Residuals 10 0.138667 0.013867 0.71286
+Total 11 0.194524 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
@@ -651,10 +651,10 @@
Call:
adonis(formula = Y ~ NO3, data = dat, permutations = 1000)
- Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
-NO3 1 0.055856 0.055856 4.0281 0.28714 0.004995 **
-Residuals 10 0.138667 0.013867 0.71286
-Total 11 0.194524 1.00000
+ Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
+NO3 1 0.055856 0.055856 4.0281 0.28714 0.000999 ***
+Residuals 10 0.138667 0.013867 0.71286
+Total 11 0.194524 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
@@ -4688,17 +4688,17 @@
> vare.mds <- monoMDS(vare.dist)
> with(varechem, ordisurf(vare.mds, Baresoil, bubble = 5))
Loading required package: mgcv
-This is mgcv 1.7-9. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-10. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10a0c9000>
+<environment: 0x954e888>
Estimated degrees of freedom:
-6.4351 total = 7.435071
+6.4351 total = 7.43507
GCV score: 144.1236
>
@@ -4711,7 +4711,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x109adf6d0>
+<environment: 0x87cc510>
Estimated degrees of freedom:
6.1039 total = 7.103853
@@ -4723,13 +4723,13 @@
> ## 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")
@@ -4860,14 +4860,14 @@
> ## 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 1.7-9. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-10. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10692bee0>
+<environment: 0x6407078>
Estimated degrees of freedom:
8.9275 total = 9.927492
@@ -4880,7 +4880,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x1096e8098>
+<environment: 0x916f818>
Estimated degrees of freedom:
7.7529 total = 8.75294
@@ -4893,7 +4893,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10a7e9830>
+<environment: 0x84c5758>
Estimated degrees of freedom:
8.8962 total = 9.89616
@@ -5659,8 +5659,8 @@
[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
@@ -6501,7 +6501,7 @@
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
@@ -7155,14 +7155,14 @@
> ## add fitted surface of diversity to the model
> ordisurf(mod, diversity(dune), add = TRUE)
Loading required package: mgcv
-This is mgcv 1.7-9. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-10. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10952b190>
+<environment: 0x8a4dc68>
Estimated degrees of freedom:
2 total = 3
@@ -7175,14 +7175,14 @@
Call:
adonis(formula = dune ~ ., data = dune.env)
- Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
-A1 1 0.7230 0.72295 5.2038 0.16817 0.002 **
-Moisture 3 1.1871 0.39569 2.8482 0.27613 0.003 **
-Management 3 0.9036 0.30121 2.1681 0.21019 0.025 *
-Use 2 0.0921 0.04606 0.3315 0.02143 0.976
-Manure 3 0.4208 0.14026 1.0096 0.09787 0.490
-Residuals 7 0.9725 0.13893 0.22621
-Total 19 4.2990 1.00000
+ Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
+A1 1 0.7230 0.72295 5.2038 0.16817 0.001 ***
+Moisture 3 1.1871 0.39569 2.8482 0.27613 0.001 ***
+Management 3 0.9036 0.30121 2.1681 0.21019 0.001 ***
+Use 2 0.0921 0.04606 0.3315 0.02143 0.001 ***
+Manure 3 0.4208 0.14026 1.0096 0.09787 0.001 ***
+Residuals 7 0.9725 0.13893 0.22621
+Total 19 4.2990 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> adonis(dune ~ Management + Moisture, dune.env)
@@ -7192,7 +7192,7 @@
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Management 3 1.4686 0.48953 3.7907 0.34161 0.001 ***
-Moisture 3 1.1516 0.38387 2.9726 0.26788 0.003 **
+Moisture 3 1.1516 0.38387 2.9726 0.26788 0.001 ***
Residuals 13 1.6788 0.12914 0.39051
Total 19 4.2990 1.00000
---
@@ -7605,13 +7605,13 @@
> ## 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)
@@ -7620,7 +7620,7 @@
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
@@ -7638,7 +7638,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 81.081 1.732 83.592 0 0
+Time elapsed: 49.21 0.408 50.131 0 0
> grDevices::dev.off()
null device
1
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