[Vegan-commits] r1812 - pkg/vegan/tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Sep 9 11:51:21 CEST 2011
Author: jarioksa
Date: 2011-09-09 11:51:20 +0200 (Fri, 09 Sep 2011)
New Revision: 1812
Modified:
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
update tests for r1811 (permatswap bug)
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-09-09 09:50:21 UTC (rev 1811)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-09-09 09:51:20 UTC (rev 1812)
@@ -23,7 +23,7 @@
> options(warn = 1)
> library('vegan')
Loading required package: permute
-This is vegan 2.0-0
+This is vegan 2.1-0
>
> assign(".oldSearch", search(), pos = 'CheckExEnv')
> cleanEx()
@@ -161,7 +161,7 @@
Formula:
y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x100c0cb08>
+<environment: 0x1009b4d90>
Total model degrees of freedom 3
GCV score: 0.0427924
@@ -4772,7 +4772,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x106a22f10>
+<environment: 0x106d2e878>
Estimated degrees of freedom:
6.4351 total = 7.435071
@@ -4788,7 +4788,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x107df0520>
+<environment: 0x1063f4df0>
Estimated degrees of freedom:
6.1039 total = 7.103853
@@ -4944,7 +4944,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x107a64f10>
+<environment: 0x105a75038>
Estimated degrees of freedom:
8.9275 total = 9.927492
@@ -4957,7 +4957,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x106b59208>
+<environment: 0x1068d7d40>
Estimated degrees of freedom:
7.7529 total = 8.75294
@@ -4970,7 +4970,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x106060608>
+<environment: 0x105afc0a8>
Estimated degrees of freedom:
8.8962 total = 9.89616
@@ -5041,17 +5041,17 @@
Matrix fill retained: 100 %
Row sums retained: 100 %
Column sums retained: 100 %
-Row incidences retained: 6.06 %
-Column incidences retained: 4.04 %
+Row incidences retained: 2.02 %
+Column incidences retained: 6.06 %
Bray-Curtis dissimilarities among original and permuted matrices:
Min. 1st Qu. Median Mean 3rd Qu. Max.
- 0.2333 0.3667 0.4000 0.4189 0.4667 0.6000
+ 0.2000 0.3667 0.4333 0.4202 0.4667 0.6333
Chi-squared for original matrix: 18.55)
Chi-squared values among expected and permuted matrices:
Min. 1st Qu. Median Mean 3rd Qu. Max.
- 16.16 19.22 21.07 21.56 23.61 32.19
+ 15.63 19.38 21.19 21.53 23.44 29.08
> ## Unrestricted permutation retaining
> ## row/columns sums but not matrix fill:
> x2 <- permatfull(m)
@@ -5071,20 +5071,20 @@
Number of permuted matrices: 99
Matrix sums retained: 100 %
-Matrix fill retained: 9.09 %
+Matrix fill retained: 18.18 %
Row sums retained: 100 %
Column sums retained: 100 %
-Row incidences retained: 1.01 %
-Column incidences retained: 0 %
+Row incidences retained: 0 %
+Column incidences retained: 1.01 %
Bray-Curtis dissimilarities among original and permuted matrices:
Min. 1st Qu. Median Mean 3rd Qu. Max.
- 0.2000 0.3333 0.4000 0.3889 0.4333 0.6000
+ 0.1667 0.3333 0.4000 0.3754 0.4333 0.5667
Chi-squared for original matrix: 18.55)
Chi-squared values among expected and permuted matrices:
Min. 1st Qu. Median Mean 3rd Qu. Max.
- 5.157 12.430 14.860 15.260 17.600 26.940
+ 7.857 12.640 15.650 16.410 20.240 33.150
> ## Unrestricted permutation of presence-absence type
> ## not retaining row/columns sums:
> x3 <- permatfull(m, "none", mtype="prab")
@@ -5119,12 +5119,12 @@
Bray-Curtis dissimilarities among original and permuted matrices:
Min. 1st Qu. Median Mean 3rd Qu. Max.
- 0.2000 0.3333 0.3333 0.3663 0.4000 0.6000
+ 0.2000 0.3333 0.4000 0.3643 0.4000 0.5333
Chi-squared for original matrix: 8.4)
Chi-squared values among expected and permuted matrices:
Min. 1st Qu. Median Mean 3rd Qu. Max.
- 6.854 13.600 15.940 15.500 17.670 21.330
+ 8.354 13.340 15.060 15.280 17.180 21.330
> ## Restricted permutation,
> ## check sums within strata:
> x4 <- permatfull(m, strata=c(1,1,2,2))
@@ -5144,21 +5144,21 @@
Number of permuted matrices: 99
Matrix sums retained: 100 %
-Matrix fill retained: 53.54 %
+Matrix fill retained: 49.49 %
Row sums retained: 100 %
Column sums retained: 100 %
-Row incidences retained: 1.01 %
-Column incidences retained: 2.02 %
+Row incidences retained: 7.07 %
+Column incidences retained: 3.03 %
Sums within strata retained: 100 %
Bray-Curtis dissimilarities among original and permuted matrices:
Min. 1st Qu. Median Mean 3rd Qu. Max.
-0.06667 0.20000 0.20000 0.22560 0.26670 0.40000
+0.06667 0.20000 0.20000 0.21950 0.26670 0.40000
Chi-squared for original matrix: 18.55)
Chi-squared values among expected and permuted matrices:
Min. 1st Qu. Median Mean 3rd Qu. Max.
- 14.21 18.47 21.32 21.63 23.47 37.14
+ 14.21 18.28 19.84 20.85 23.01 32.63
>
> ## NOTE: 'times' argument usually needs to be >= 99
> ## here much lower value is used for demonstration
@@ -5189,17 +5189,17 @@
Coefficients:
ar1 intercept
- 0.9920 0.0976
-s.e. 0.0114 0.0744
+ 0.9914 0.1847
+s.e. 0.0122 0.1343
-sigma^2 estimated as 9.522e-05: log likelihood = 58.94, aic = -111.88
+sigma^2 estimated as 0.0003348: log likelihood = 47.03, aic = -88.06
> ## Ljung-Box test of residuals
> Box.test(mar$residuals)
Box-Pierce test
data: mar$residuals
-X-squared = 0.0142, df = 1, p-value = 0.9051
+X-squared = 0.0011, df = 1, p-value = 0.9739
> ## Graphical diagnostics
> tsdiag(mar)
@@ -7193,7 +7193,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x1061a7c40>
+<environment: 0x107dd7428>
Estimated degrees of freedom:
2 total = 3
@@ -7669,7 +7669,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 106.235 1.184 109.603 0 0
+Time elapsed: 106.67 1.059 108.278 0 0
> grDevices::dev.off()
null device
1
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