[Vegan-commits] r1791 - pkg/vegan/tests/Examples

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

Author: jarioksa
Date: 2011-09-04 22:02:19 +0200 (Sun, 04 Sep 2011)
New Revision: 1791

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

Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save	2011-09-04 18:02:30 UTC (rev 1790)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save	2011-09-04 20:02:19 UTC (rev 1791)
@@ -23,7 +23,7 @@
 > options(warn = 1)
 > library('vegan')
 Loading required package: permute
-This is vegan 1.92-2
+This is vegan 2.0-0
 > 
 > assign(".oldSearch", search(), pos = 'CheckExEnv')
 > cleanEx()
@@ -161,7 +161,7 @@
 
 Formula:
 y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x100e8aa00>
+<environment: 0x100c0cb08>
 Total model degrees of freedom 3 
 
 GCV score: 0.0427924
@@ -2559,6 +2559,48 @@
 
 detaching ‘dune.env’, ‘package:MASS’
 
+> nameEx("eventstar")
+> ### * eventstar
+> 
+> flush(stderr()); flush(stdout())
+> 
+> ### Name: eventstar
+> ### Title: Scale Parameter at the Minimum of the Tsallis Evenness Profile
+> ### Aliases: eventstar
+> ### Keywords: optimize multivariate utilities
+> 
+> ### ** Examples
+> 
+> data(BCI)
+> (x <- eventstar(BCI[1:5,]))
+      qstar     Estar     Hstar    Dstar
+1 0.6146389 0.4263687 10.524584 67.03551
+2 0.6249249 0.4080263  9.534034 57.66840
+3 0.6380858 0.4062032  9.225458 57.69174
+4 0.6245808 0.4062213 10.140189 65.50247
+5 0.6404825 0.4219957  9.828138 66.96440
+> ## profiling
+> y <- as.numeric(BCI[10,])
+> (z <- eventstar(y))
+      qstar     Estar    Hstar    Dstar
+1 0.6372529 0.4117557 9.546332 61.77715
+> q <- seq(0, 2, 0.05)
+> Eprof <- tsallis(y, scales=q, norm=TRUE)
+> Hprof <- tsallis(y, scales=q)
+> Dprof <- tsallis(y, scales=q, hill=TRUE)
+> opar <- par(mfrow=c(3,1))
+> plot(q, Eprof, type="l", main="Evenness")
+> abline(v=z$qstar, h=tsallis(y, scales=z$qstar, norm=TRUE), col=2)
+> plot(q, Hprof, type="l", main="Diversity")
+> abline(v=z$qstar, h=tsallis(y, scales=z$qstar), col=2)
+> plot(q, Dprof, type="l", main="Effective number of species")
+> abline(v=z$qstar, h=tsallis(y, scales=z$qstar, hill=TRUE), col=2)
+> par(opar)
+> 
+> 
+> 
+> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
+> cleanEx()
 > nameEx("fisherfit")
 > ### * fisherfit
 > 
@@ -4730,7 +4772,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x106b19a60>
+<environment: 0x106a22f10>
 
 Estimated degrees of freedom:
 6.4351  total = 7.435071 
@@ -4746,7 +4788,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x106c8a578>
+<environment: 0x107df0520>
 
 Estimated degrees of freedom:
 6.1039  total = 7.103853 
@@ -4902,7 +4944,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x10834f1c0>
+<environment: 0x107a64f10>
 
 Estimated degrees of freedom:
 8.9275  total = 9.927492 
@@ -4915,7 +4957,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x107c08f88>
+<environment: 0x106b59208>
 
 Estimated degrees of freedom:
 7.7529  total = 8.75294 
@@ -4928,7 +4970,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x106822948>
+<environment: 0x106060608>
 
 Estimated degrees of freedom:
 8.8962  total = 9.89616 
@@ -7151,7 +7193,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x107e89588>
+<environment: 0x1061a7c40>
 
 Estimated degrees of freedom:
 2  total = 3 
@@ -7627,7 +7669,7 @@
 > ### * <FOOTER>
 > ###
 > cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  104.698 1.034 106.772 0 0 
+Time elapsed:  106.235 1.184 109.603 0 0 
 > grDevices::dev.off()
 null device 
           1