[Vegan-commits] r2208 - in pkg/vegan: man tests/Examples

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sat Jun 2 07:39:42 CEST 2012 

Author: jarioksa
Date: 2012-06-02 07:39:41 +0200 (Sat, 02 Jun 2012)
New Revision: 2208

Modified:
   pkg/vegan/man/ordiplot3d.Rd
   pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
one new example on oridplot3d().convert()

Modified: pkg/vegan/man/ordiplot3d.Rd
===================================================================
--- pkg/vegan/man/ordiplot3d.Rd	2012-06-01 08:14:05 UTC (rev 2207)
+++ pkg/vegan/man/ordiplot3d.Rd	2012-06-02 05:39:41 UTC (rev 2208)
@@ -216,6 +216,9 @@
 ### 2. use returned envfit.convert function for better user control
 pl3 <- ordiplot3d(ord)
 plot(pl3$envfit.convert(ef), at = pl3$origin)
+### envfit.convert() also handles different 'choices' of axes
+pl3 <- ordiplot3d(ord, choices = c(1,3,2))
+plot(pl3$envfit.convert(ef), at = pl3$origin)
 ### ordirgl
 ordirgl(ord, size=2)
 ordirgl(ord, display = "species", type = "t")

Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save	2012-06-01 08:14:05 UTC (rev 2207)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save	2012-06-02 05:39:41 UTC (rev 2208)
@@ -1,8 +1,8 @@
 
-R Under development (unstable) (2012-05-28 r59461) -- "Unsuffered Consequences"
+R version 2.15.0 (2012-03-30)
 Copyright (C) 2012 The R Foundation for Statistical Computing
 ISBN 3-900051-07-0
-Platform: x86_64-unknown-linux-gnu (64-bit)
+Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.
@@ -154,14 +154,14 @@
 > plot(ef)
 > ordisurf(mod ~ pH, varechem, knots = 1, add = TRUE)
 Loading required package: mgcv
-This is mgcv 1.7-16. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-13. For overview type 'help("mgcv-package")'.
 
 Family: gaussian 
 Link function: identity 
 
 Formula:
 y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x2692be8>
+<environment: 0x1023eddf0>
 Total model degrees of freedom 3 
 
 GCV score: 0.0427924
@@ -2552,7 +2552,7 @@
 Run 17 stress 0.1825664 
 ... New best solution
 ... procrustes: rmse 0.0421789  max resid 0.1544029 
-Run 18 stress 0.1843201 
+Run 18 stress 0.1843199 
 Run 19 stress 0.2570123 
 Run 20 stress 0.3760596 
 > (fit <- envfit(ord, varechem, perm = 999))
@@ -3018,7 +3018,7 @@
 Run 17 stress 0.1825664 
 ... New best solution
 ... procrustes: rmse 0.0421789  max resid 0.1544029 
-Run 18 stress 0.1843201 
+Run 18 stress 0.1843199 
 Run 19 stress 0.2570123 
 Run 20 stress 0.3760596 
 > stressplot(mod)
@@ -4460,6 +4460,9 @@
 > ##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 ### envfit.convert() also handles different 'choices' of axes
+> ##D pl3 <- ordiplot3d(ord, choices = c(1,3,2))
+> ##D plot(pl3$envfit.convert(ef), at = pl3$origin)
 > ##D ### ordirgl
 > ##D ordirgl(ord, size=2)
 > ##D ordirgl(ord, display = "species", type = "t")
@@ -4799,17 +4802,17 @@
 > vare.mds <- monoMDS(vare.dist)
 > with(varechem, ordisurf(vare.mds, Baresoil, bubble = 5))
 Loading required package: mgcv
-This is mgcv 1.7-16. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-13. For overview type 'help("mgcv-package")'.
 
 Family: gaussian 
 Link function: identity 
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x95bf158>
+<environment: 0x1096c3750>
 
 Estimated degrees of freedom:
-6.4351  total = 7.43507 
+6.4351  total = 7.435071 
 
 GCV score: 144.1236
 > 
@@ -4822,7 +4825,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x7763580>
+<environment: 0x109733fc8>
 
 Estimated degrees of freedom:
 6.1039  total = 7.103853 
@@ -4834,13 +4837,13 @@
 > ## Get fitted values
 > calibrate(fit)
          1          2          3          4          5          6          7 
-22.0644615  6.0132250  3.6350484  4.1019743  9.0030990  5.9202602  8.6399182 
+22.0644614  6.0132251  3.6350483  4.1019742  9.0030989  5.9202601  8.6399184 
          8          9         10         11         12         13         14 
-11.0719302  0.6561783 35.2282116 10.4346331  7.2900019  5.5710617 24.6503109 
+11.0719303  0.6561781 35.2282118 10.4346331  7.2900018  5.5710617 24.6503110 
         15         16         17         18         19         20         21 
-18.8754520 29.7286540  5.6158934  9.5869715  3.2876268  2.7111723 10.7832857 
+18.8754521 29.7286543  5.6158934  9.5869716  3.2876267  2.7111721 10.7832857 
         22         23         24 
- 3.0020415  9.8128952  7.3656934 
+ 3.0020413  9.8128952  7.3656932 
 > 
 > ## Plot method
 > plot(fit, what = "contour")
@@ -4971,14 +4974,14 @@
 > ## 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 1.7-16. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-13. For overview type 'help("mgcv-package")'.
 
 Family: gaussian 
 Link function: identity 
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x97f77f0>
+<environment: 0x106156f78>
 
 Estimated degrees of freedom:
 8.9275  total = 9.927492 
@@ -4991,7 +4994,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x6ed8420>
+<environment: 0x109eccca0>
 
 Estimated degrees of freedom:
 7.7529  total = 8.75294 
@@ -5004,7 +5007,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x95b6798>
+<environment: 0x10a8d12e0>
 
 Estimated degrees of freedom:
 8.8962  total = 9.89616 
@@ -5770,8 +5773,8 @@
 [2,] 0.1169579  0.9931369
 
 Translation of averages:
-            [,1]         [,2]
-[1,] 1.79048e-17 9.246476e-19
+             [,1]          [,2]
+[1,] 3.893131e-18 -9.725997e-18
 
 Scaling of target:
 [1] 0.6736868
@@ -7366,7 +7369,7 @@
 Run 17 stress 0.1825664 
 ... New best solution
 ... procrustes: rmse 0.0421789  max resid 0.1544029 
-Run 18 stress 0.1843201 
+Run 18 stress 0.1843199 
 Run 19 stress 0.2570123 
 Run 20 stress 0.3760596 
 > plot(ord, type = "t")
@@ -7536,14 +7539,14 @@
 > ## add fitted surface of diversity to the model
 > ordisurf(mod, diversity(dune), add = TRUE)
 Loading required package: mgcv
-This is mgcv 1.7-16. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-13. For overview type 'help("mgcv-package")'.
 
 Family: gaussian 
 Link function: identity 
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x9488ef8>
+<environment: 0x10b48ca98>
 
 Estimated degrees of freedom:
 2  total = 3 
@@ -8023,7 +8026,7 @@
 > ### * <FOOTER>
 > ###
 > cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  25.313 0.132 25.532 0 0 
+Time elapsed:  82.41 1.676 85.548 0 0 
 > grDevices::dev.off()
 null device 
           1

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