[Vegan-commits] r1963 - pkg/vegan/tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Oct 28 18:50:04 CEST 2011
Author: jarioksa
Date: 2011-10-28 18:50:04 +0200 (Fri, 28 Oct 2011)
New Revision: 1963
Modified:
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
update for r1954: add column 'double' to the ?commsim table
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-10-28 16:28:40 UTC (rev 1962)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-10-28 16:50:04 UTC (rev 1963)
@@ -1,8 +1,8 @@
-R version 2.13.1 (2011-07-08)
+R version 2.14.0 RC (2011-10-27 r57452)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
-Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
+Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -23,7 +23,7 @@
> options(warn = 1)
> library('vegan')
Loading required package: permute
-This is vegan 2.1-3
+This is vegan 2.1-5
>
> assign(".oldSearch", search(), pos = 'CheckExEnv')
> cleanEx()
@@ -161,7 +161,7 @@
Formula:
y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x1019a69f8>
+<environment: 0x101fadcd0>
Total model degrees of freedom 3
GCV score: 0.0427924
@@ -1819,45 +1819,46 @@
+ y <- simulate(m, nsim=n)
+ out <- rowMeans(sapply(1:dim(y)[3],
+ function(i) diagfun(attr(y, "data"), y[,,i])))
-+ z <- as.numeric(c(attr(y, "binary"), attr(y, "isSeq")))
-+ names(z) <- c("binary", "isSeq")
++ z <- as.numeric(c(attr(y, "binary"), attr(y, "isSeq"),
++ attr(y, "mode") == "double"))
++ names(z) <- c("binary", "isSeq", "double")
+ c(z, out)
+ }
> x <- matrix(rbinom(10*12, 1, 0.5)*rpois(10*12, 3), 12, 10)
> algos <- make.commsim()
> a <- t(sapply(algos, evalfun, x=x, n=10))
> print(as.table(ifelse(a==1,1,0)), zero.print = ".")
- binary isSeq sum fill rowSums colSums rowFreq colFreq
-r00 1 . 1 1 . . . .
-c0 1 . 1 1 . 1 . 1
-r0 1 . 1 1 1 . 1 .
-r0_old 1 . 1 1 1 . 1 .
-r1 1 . 1 1 1 . 1 .
-r2 1 . 1 1 1 . 1 .
-quasiswap 1 . 1 1 1 1 1 1
-swap 1 1 1 1 1 1 1 1
-tswap 1 1 1 1 1 1 1 1
-backtrack 1 . 1 1 1 1 1 1
-r2dtable . . 1 . 1 1 . .
-swap_count . 1 1 1 1 1 . .
-quasiswap_count . . 1 1 1 1 . .
-swsh_samp . . 1 1 . . 1 1
-swsh_both . . 1 1 . . 1 1
-swsh_samp_r . . 1 1 1 . 1 1
-swsh_samp_c . . 1 1 . 1 1 1
-swsh_both_r . . 1 1 1 . 1 1
-swsh_both_c . . 1 1 . 1 1 1
-abuswap_r . 1 1 1 1 . 1 1
-abuswap_c . 1 1 1 . 1 1 1
-r00_samp . . 1 1 . . . .
-c0_samp . . 1 1 . 1 . 1
-r0_samp . . 1 1 1 . 1 .
-r00_ind . . 1 . . . . .
-c0_ind . . 1 . . 1 . .
-r0_ind . . 1 . 1 . . .
-r00_both . . 1 1 . . . .
-c0_both . . 1 1 . 1 . 1
-r0_both . . 1 1 1 . 1 .
+ binary isSeq double sum fill rowSums colSums rowFreq colFreq
+r00 1 . . 1 1 . . . .
+c0 1 . . 1 1 . 1 . 1
+r0 1 . . 1 1 1 . 1 .
+r0_old 1 . . 1 1 1 . 1 .
+r1 1 . . 1 1 1 . 1 .
+r2 1 . . 1 1 1 . 1 .
+quasiswap 1 . . 1 1 1 1 1 1
+swap 1 1 . 1 1 1 1 1 1
+tswap 1 1 . 1 1 1 1 1 1
+backtrack 1 . . 1 1 1 1 1 1
+r2dtable . . . 1 . 1 1 . .
+swap_count . 1 . 1 1 1 1 . .
+quasiswap_count . . . 1 1 1 1 . .
+swsh_samp . . . 1 1 . . 1 1
+swsh_both . . . 1 1 . . 1 1
+swsh_samp_r . . . 1 1 1 . 1 1
+swsh_samp_c . . . 1 1 . 1 1 1
+swsh_both_r . . . 1 1 1 . 1 1
+swsh_both_c . . . 1 1 . 1 1 1
+abuswap_r . 1 1 1 1 1 . 1 1
+abuswap_c . 1 1 1 1 . 1 1 1
+r00_samp . . 1 1 1 . . . .
+c0_samp . . 1 1 1 . 1 . 1
+r0_samp . . 1 1 1 1 . 1 .
+r00_ind . . . 1 . . . . .
+c0_ind . . . 1 . . 1 . .
+r0_ind . . . 1 . 1 . . .
+r00_both . . . 1 1 . . . .
+c0_both . . . 1 1 . 1 . 1
+r0_both . . . 1 1 1 . 1 .
>
>
>
@@ -3990,7 +3991,7 @@
>
> ### ** Examples
>
-> x <- matrix(rbinom(10*12, 1, 0.5)*rpois(10*12, 3), 12, 10)
+> x <- matrix(rbinom(12*10, 1, 0.5)*rpois(12*10, 3), 12, 10)
>
> ## non-sequential nullmodel
> (nm <- nullmodel(x, "r00"))
@@ -4691,7 +4692,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x1077de908>
+<environment: 0x109cec958>
Estimated degrees of freedom:
6.4351 total = 7.435071
@@ -4707,7 +4708,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10595d098>
+<environment: 0x1098eef40>
Estimated degrees of freedom:
6.1039 total = 7.103853
@@ -4863,7 +4864,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x106e48ed0>
+<environment: 0x108f78578>
Estimated degrees of freedom:
8.9275 total = 9.927492
@@ -4876,7 +4877,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x107c88140>
+<environment: 0x107654278>
Estimated degrees of freedom:
7.7529 total = 8.75294
@@ -4889,7 +4890,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10779bcd8>
+<environment: 0x109e1a758>
Estimated degrees of freedom:
8.8962 total = 9.89616
@@ -5656,7 +5657,7 @@
Translation of averages:
[,1] [,2]
-[1,] 3.893131e-18 -9.725997e-18
+[1,] 1.047183e-17 -1.381645e-17
Scaling of target:
[1] 0.6736868
@@ -6497,7 +6498,7 @@
Salrep 0.7118892 8.654457e-02
Achmil 1.5948052 8.449914e-01
Poatri 0.7367577 7.099165e-01
-Chealb 1.9479718 6.661338e-16
+Chealb 1.9479718 2.220446e-16
Elyrep 0.5160932 5.135604e-01
Sagpro 1.3031750 1.019154e+00
Plalan 1.7013794 6.393173e-01
@@ -7158,7 +7159,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10711bab0>
+<environment: 0x10a9c72a8>
Estimated degrees of freedom:
2 total = 3
@@ -7601,13 +7602,13 @@
> ## Eigevalues are numerically similar
> ca$CA$eig - ord$eig
CA1 CA2 CA3 CA4 CA5
--7.771561e-16 -2.220446e-16 6.106227e-16 -3.608225e-16 -1.110223e-16
+ 9.992007e-16 -6.106227e-16 8.881784e-16 -2.775558e-17 2.220446e-16
CA6 CA7 CA8 CA9 CA10
- 1.387779e-17 9.714451e-17 1.387779e-17 2.775558e-17 1.318390e-16
+ 9.714451e-17 9.714451e-17 4.163336e-17 -1.387779e-17 8.326673e-17
CA11 CA12 CA13 CA14 CA15
- 9.714451e-17 6.938894e-18 -6.938894e-18 3.122502e-17 0.000000e+00
+ 7.632783e-17 1.040834e-16 -2.081668e-17 4.510281e-17 1.908196e-17
CA16 CA17 CA18 CA19
--3.295975e-17 2.428613e-17 2.862294e-17 5.637851e-18
+-1.908196e-17 0.000000e+00 7.025630e-17 2.125036e-17
> ## Configurations are similar when site scores are scaled by
> ## eigenvalues in CA
> procrustes(ord, ca, choices=1:19, scaling = 1)
@@ -7616,7 +7617,7 @@
procrustes(X = ord, Y = ca, choices = 1:19, scaling = 1)
Procrustes sum of squares:
- 0
+-4.263e-14
> plot(procrustes(ord, ca, choices=1:2, scaling=1))
> ## Reconstruction of non-Euclidean distances with negative eigenvalues
@@ -7634,7 +7635,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 101.859 1.444 104.809 0 0
+Time elapsed: 90.316 1.908 92.398 0 0
> grDevices::dev.off()
null device
1
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