[Vegan-commits] r2204 - in pkg/vegan: man tests/Examples

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

Author: jarioksa
Date: 2012-05-28 08:53:14 +0200 (Mon, 28 May 2012)
New Revision: 2204

Modified:
   pkg/vegan/man/betadisper.Rd
   pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
fix mark-up and update tests

Modified: pkg/vegan/man/betadisper.Rd
===================================================================
--- pkg/vegan/man/betadisper.Rd	2012-05-27 15:15:38 UTC (rev 2203)
+++ pkg/vegan/man/betadisper.Rd	2012-05-28 06:53:14 UTC (rev 2204)
@@ -1,3 +1,4 @@
+\encoding{UTF-8}
 \name{betadisper}
 \alias{betadisper}
 \alias{scores.betadisper}
@@ -38,7 +39,7 @@
 \method{boxplot}{betadisper}(x, ylab = "Distance to centroid", ...)
 
 \method{TukeyHSD}{betadisper}(x, which = "group", ordered = FALSE,
-         conf.level = 0.95, \ldots)
+         conf.level = 0.95, \dots)
 }
 
 \arguments{
@@ -205,7 +206,7 @@
 
   O'Neill, M.E. (2000) A Weighted Least Squares Approach to Levene's 
   Test of Homogeneity of Variance. \emph{Australian & New Zealand Journal of 
-  Statistics \strong{42}, 81-–100.
+  Statistics} \strong{42}, 81-–100.
 
   Stier, A.C., Geange, S.W., Hanson, K.M., & Bolker, B.M. (2012) Predator 
   density and timing of arrival affect reef fish community assembly. Ms.

Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save	2012-05-27 15:15:38 UTC (rev 2203)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save	2012-05-28 06:53:14 UTC (rev 2204)
@@ -1,5 +1,5 @@
 
-R Under development (unstable) (2012-05-22 r59410) -- "Unsuffered Consequences"
+R Under development (unstable) (2012-05-28 r59461) -- "Unsuffered Consequences"
 Copyright (C) 2012 The R Foundation for Statistical Computing
 ISBN 3-900051-07-0
 Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -161,7 +161,7 @@
 
 Formula:
 y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x38567e8>
+<environment: 0x2692be8>
 Total model degrees of freedom 3 
 
 GCV score: 0.0427924
@@ -1268,8 +1268,34 @@
 > boxplot(mod3)
 > plot(TukeyHSD(mod3))
 > 
+> ## try out bias correction; compare with mod3
+> (mod3B <- betadisper(dis, groups, type = "median", bias.adjust=TRUE))
+Warning in betadisper(dis, groups, type = "median", bias.adjust = TRUE) :
+  Missing observations due to 'group' removed.
+Warning in betadisper(dis, groups, type = "median", bias.adjust = TRUE) :
+  Missing observations due to 'd' removed.
+
+	Homogeneity of multivariate dispersions
+
+Call: betadisper(d = dis, group = groups, type = "median", bias.adjust
+= TRUE)
+
+No. of Positive Eigenvalues: 14
+No. of Negative Eigenvalues: 5
+
+Average distance to centroid:
+  grazed ungrazed 
+  0.4134   0.3295 
+
+Eigenvalues for PCoA axes:
+  PCoA1   PCoA2   PCoA3   PCoA4   PCoA5   PCoA6   PCoA7   PCoA8   PCoA9  PCoA10 
+ 1.4755  0.8245  0.4218  0.3456  0.2159  0.1688  0.1150  0.1060  0.0912  0.0639 
+ PCoA11  PCoA12  PCoA13  PCoA14  PCoA15  PCoA16  PCoA17  PCoA18  PCoA19 
+ 0.0420  0.0267  0.0157  0.0020 -0.0025 -0.0215 -0.0221 -0.0486 -0.0592 
 > 
 > 
+> 
+> 
 > cleanEx()
 > nameEx("betadiver")
 > ### * betadiver
@@ -4780,7 +4806,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0xa720c90>
+<environment: 0x95bf158>
 
 Estimated degrees of freedom:
 6.4351  total = 7.43507 
@@ -4796,7 +4822,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0xa0b8058>
+<environment: 0x7763580>
 
 Estimated degrees of freedom:
 6.1039  total = 7.103853 
@@ -4952,7 +4978,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x9bbcd00>
+<environment: 0x97f77f0>
 
 Estimated degrees of freedom:
 8.9275  total = 9.927492 
@@ -4965,7 +4991,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0xa7920a8>
+<environment: 0x6ed8420>
 
 Estimated degrees of freedom:
 7.7529  total = 8.75294 
@@ -4978,7 +5004,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0xb12a2c0>
+<environment: 0x95b6798>
 
 Estimated degrees of freedom:
 8.8962  total = 9.89616 
@@ -7517,7 +7543,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0xb1c9470>
+<environment: 0x9488ef8>
 
 Estimated degrees of freedom:
 2  total = 3 
@@ -7997,7 +8023,7 @@
 > ### * <FOOTER>
 > ###
 > cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  26.445 0.216 26.972 0 0 
+Time elapsed:  25.313 0.132 25.532 0 0 
 > grDevices::dev.off()
 null device 
           1