[Vegan-commits] r2161 - pkg/vegan/tests/Examples

[noreply at r-forge.r-project.org]

Author: jarioksa
Date: 2012-05-10 10:26:06 +0200 (Thu, 10 May 2012)
New Revision: 2161

Modified:
   pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
update tests for r2160

Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save	2012-05-10 08:21:51 UTC (rev 2160)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save	2012-05-10 08:26:06 UTC (rev 2161)
@@ -1,5 +1,5 @@
 
-R version 2.15.0 Patched (2012-04-14 r59019) -- "Easter Beagle"
+R Under development (unstable) (2012-05-08 r59331) -- "Unsuffered Consequences"
 Copyright (C) 2012 The R Foundation for Statistical Computing
 ISBN 3-900051-07-0
 Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -154,14 +154,14 @@
 > plot(ef)
 > ordisurf(mod ~ pH, varechem, knots = 1, add = TRUE)
 Loading required package: mgcv
-This is mgcv 1.7-13. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-16. For overview type 'help("mgcv-package")'.
 
 Family: gaussian 
 Link function: identity 
 
 Formula:
 y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x3b58c00>
+<environment: 0x19711b8>
 Total model degrees of freedom 3 
 
 GCV score: 0.0427924
@@ -4425,6 +4425,14 @@
 > ##D ### Add species using xyz.convert function returned by ordiplot3d
 > ##D sp <- scores(ord, choices=1:3, display="species", scaling=3)
 > ##D text(pl$xyz.convert(sp), rownames(sp), cex=0.7, xpd=TRUE)
+> ##D ### Two ways of adding fitted variables to ordination plots
+> ##D ord <- cca(dune)
+> ##D ef <- envfit(ord ~ Moisture + A1, dune.env, choices = 1:3)
+> ##D ### 1. use argument 'envfit'
+> ##D ordiplot3d(ord, envfit = ef)
+> ##D ### 2. use returned envfit.convert function for better user control
+> ##D pl3 <- ordiplot3d(ord)
+> ##D plot(pl3$envfit.convert(ef), at = pl3$origin)
 > ##D ### ordirgl
 > ##D ordirgl(ord, size=2)
 > ##D ordirgl(ord, display = "species", type = "t")
@@ -4764,14 +4772,14 @@
 > vare.mds <- monoMDS(vare.dist)
 > with(varechem, ordisurf(vare.mds, Baresoil, bubble = 5))
 Loading required package: mgcv
-This is mgcv 1.7-13. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-16. For overview type 'help("mgcv-package")'.
 
 Family: gaussian 
 Link function: identity 
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x8d98370>
+<environment: 0x9012e08>
 
 Estimated degrees of freedom:
 6.4351  total = 7.43507 
@@ -4787,7 +4795,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x86d04d0>
+<environment: 0x88d2170>
 
 Estimated degrees of freedom:
 6.1039  total = 7.103853 
@@ -4936,14 +4944,14 @@
 > ## 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 1.7-13. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-16. For overview type 'help("mgcv-package")'.
 
 Family: gaussian 
 Link function: identity 
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x6b56e38>
+<environment: 0x8445ce8>
 
 Estimated degrees of freedom:
 8.9275  total = 9.927492 
@@ -4956,7 +4964,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x9397088>
+<environment: 0x940a710>
 
 Estimated degrees of freedom:
 7.7529  total = 8.75294 
@@ -4969,7 +4977,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x953fb68>
+<environment: 0x7eed968>
 
 Estimated degrees of freedom:
 8.8962  total = 9.89616 
@@ -7501,14 +7509,14 @@
 > ## add fitted surface of diversity to the model
 > ordisurf(mod, diversity(dune), add = TRUE)
 Loading required package: mgcv
-This is mgcv 1.7-13. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-16. For overview type 'help("mgcv-package")'.
 
 Family: gaussian 
 Link function: identity 
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x8825e30>
+<environment: 0x9eec7f0>
 
 Estimated degrees of freedom:
 2  total = 3 
@@ -7988,7 +7996,7 @@
 > ### * <FOOTER>
 > ###
 > cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  52.033 0.299 53.846 0 0 
+Time elapsed:  25.813 0.164 26.07 0 0 
 > grDevices::dev.off()
 null device 
           1