[Vegan-commits] r2135 - in pkg/vegan: R tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Apr 17 14:10:45 CEST 2012
Author: jarioksa
Date: 2012-04-17 14:10:45 +0200 (Tue, 17 Apr 2012)
New Revision: 2135
Modified:
pkg/vegan/R/print.adipart.R
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
Merge branch 'master' into HEAD
Modified: pkg/vegan/R/print.adipart.R
===================================================================
--- pkg/vegan/R/print.adipart.R 2012-04-17 10:57:33 UTC (rev 2134)
+++ pkg/vegan/R/print.adipart.R 2012-04-17 12:10:45 UTC (rev 2135)
@@ -3,7 +3,11 @@
{
n <- if (is.null(x$oecosimu$simulated))
0 else ncol(x$oecosimu$simulated)
- cat("adipart with", n, "simulations\n")
+ if (n > 0)
+ cat("adipart with", n, "simulations using method",
+ dQuote(x$oecosimu$method), "\n")
+ else
+ cat("adipart ")
att <- attributes(x)
att$names <- att$call <- att$class <- att$n.levels <- att$terms <- att$model <- NULL
cat("with", paste(names(att), att, collapse=", "))
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2012-04-17 10:57:33 UTC (rev 2134)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2012-04-17 12:10:45 UTC (rev 2135)
@@ -1,5 +1,5 @@
-R Under development (unstable) (2012-02-21 r58440)
+R Under development (unstable) (2012-04-16 r59057) -- "Unsuffered Consequences"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -23,7 +23,7 @@
> options(warn = 1)
> library('vegan')
Loading required package: permute
-This is vegan 2.1-12
+This is vegan 2.1-14
>
> assign(".oldSearch", search(), pos = 'CheckExEnv')
> cleanEx()
@@ -161,7 +161,7 @@
Formula:
y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x2cbf5f8>
+<environment: 0x336a260>
Total model degrees of freedom 3
GCV score: 0.0427924
@@ -522,7 +522,7 @@
> par(mfrow=c(1,1))
> ## Additive diversity partitioning
> adipart(mite ~., levsm, index="richness", nsimul=19)
-adipart with 19 simulations
+adipart with 19 simulations using method “r2dtable”
with index richness, weights unif
statistic z 2.5% 50% 97.5% Pr(sim.)
@@ -4730,7 +4730,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x95688d0>
+<environment: 0x9905320>
Estimated degrees of freedom:
6.4351 total = 7.43507
@@ -4746,7 +4746,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x8ced6a8>
+<environment: 0x8caa2e0>
Estimated degrees of freedom:
6.1039 total = 7.103853
@@ -4902,7 +4902,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x7c82a40>
+<environment: 0x9b50e30>
Estimated degrees of freedom:
8.9275 total = 9.927492
@@ -4915,7 +4915,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x9fbbb60>
+<environment: 0xa64ecc8>
Estimated degrees of freedom:
7.7529 total = 8.75294
@@ -4928,7 +4928,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x7f79688>
+<environment: 0x961bac8>
Estimated degrees of freedom:
8.8962 total = 9.89616
@@ -5998,34 +5998,40 @@
cumulative contributions of most influential species:
$BF_SF
- Agrsto Alogen Lolper Trirep Poatri Leoaut Brohor Achmil Plalan Elyrep Brarut
-0.09824271 0.18254830 0.25956958 0.33367870 0.40734444 0.47729205 0.53120026 0.57946526 0.62522255 0.67016196 0.71098133
+ Agrsto Alogen Lolper Trirep Poatri Leoaut Brohor
+0.09824271 0.18254830 0.25956958 0.33367870 0.40734444 0.47729205 0.53120026
+ Achmil Plalan Elyrep Brarut
+0.57946526 0.62522255 0.67016196 0.71098133
$BF_HF
- Rumace Poatri Plalan Brohor Lolper Elyrep Trirep Antodo Achmil Brarut Alogen Tripra
-0.08163219 0.15193797 0.21918333 0.27967181 0.33969561 0.39843338 0.45298204 0.50276849 0.55222648 0.60021994 0.64584333 0.69126471
- Junart
-0.73366621
+ Rumace Poatri Plalan Brohor Lolper Elyrep Trirep
+0.08163219 0.15193797 0.21918333 0.27967181 0.33969561 0.39843338 0.45298204
+ Antodo Achmil Brarut Alogen Tripra Junart
+0.50276849 0.55222648 0.60021994 0.64584333 0.69126471 0.73366621
$BF_NM
- Lolper Poatri Poapra Trirep Brohor Brarut Elepal Agrsto Achmil Leoaut Antodo Plalan
-0.1242718 0.1992126 0.2711756 0.3414609 0.3958520 0.4448077 0.4910724 0.5369083 0.5823926 0.6253645 0.6638182 0.7012577
+ Lolper Poatri Poapra Trirep Brohor Brarut Elepal Agrsto
+0.1242718 0.1992126 0.2711756 0.3414609 0.3958520 0.4448077 0.4910724 0.5369083
+ Achmil Leoaut Antodo Plalan
+0.5823926 0.6253645 0.6638182 0.7012577
$SF_HF
- Agrsto Alogen Lolper Plalan Rumace Elyrep Poatri Brarut Elepal Poapra Antodo Sagpro
-0.08350879 0.16534834 0.23934930 0.30843624 0.37716139 0.43334492 0.48351753 0.52804045 0.57205850 0.61423981 0.65549838 0.69628951
- Tripra
-0.73696831
+ Agrsto Alogen Lolper Plalan Rumace Elyrep Poatri
+0.08350879 0.16534834 0.23934930 0.30843624 0.37716139 0.43334492 0.48351753
+ Brarut Elepal Poapra Antodo Sagpro Tripra
+0.52804045 0.57205850 0.61423981 0.65549838 0.69628951 0.73696831
$SF_NM
- Poatri Alogen Agrsto Lolper Elepal Poapra Brarut Elyrep Leoaut Trirep Sagpro Salrep
-0.1013601 0.1935731 0.2667383 0.3377578 0.3999419 0.4526707 0.5044725 0.5505643 0.5926117 0.6320111 0.6712478 0.7091528
+ Poatri Alogen Agrsto Lolper Elepal Poapra Brarut Elyrep
+0.1013601 0.1935731 0.2667383 0.3377578 0.3999419 0.4526707 0.5044725 0.5505643
+ Leoaut Trirep Sagpro Salrep
+0.5926117 0.6320111 0.6712478 0.7091528
$HF_NM
- Poatri Lolper Rumace Poapra Plalan Brarut Elepal Agrsto Trirep Elyrep Antodo Junart
-0.09913221 0.17468460 0.23917190 0.29701331 0.35469313 0.40365488 0.44804851 0.49226546 0.53434466 0.57564661 0.61543243 0.65341300
- Tripra Salrep
-0.68921695 0.72432408
+ Poatri Lolper Rumace Poapra Plalan Brarut Elepal
+0.09913221 0.17468460 0.23917190 0.29701331 0.35469313 0.40365488 0.44804851
+ Agrsto Trirep Elyrep Antodo Junart Tripra Salrep
+0.49226546 0.53434466 0.57564661 0.61543243 0.65341300 0.68921695 0.72432408
> summary(sim)
@@ -7461,7 +7467,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x9a3e668>
+<environment: 0xa026f68>
Estimated degrees of freedom:
2 total = 3
@@ -7941,7 +7947,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 25.013 0.088 25.186 0 0
+Time elapsed: 24.949 0.148 25.187 0 0
> grDevices::dev.off()
null device
1
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