[Vegan-commits] r1612 - pkg/vegan/tests/Examples

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

Author: jarioksa
Date: 2011-05-28 16:21:28 +0200 (Sat, 28 May 2011)
New Revision: 1612

Modified:
   pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
update tests for r1609

Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save	2011-05-28 13:32:34 UTC (rev 1611)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save	2011-05-28 14:21:28 UTC (rev 1612)
@@ -22,7 +22,7 @@
 > source(file.path(R.home("share"), "R", "examples-header.R"))
 > options(warn = 1)
 > library('vegan')
-This is vegan 1.18-29
+This is vegan 1.18-31
 > 
 > assign(".oldSearch", search(), pos = 'CheckExEnv')
 > cleanEx()
@@ -2303,15 +2303,24 @@
 > invsimp <- diversity(BCI, "inv")
 > ## Unbiased Simpson of Hurlbert 1971 (eq. 5):
 > unbias.simp <- rarefy(BCI, 2) - 1
+> ## Fisher alpha
 > alpha <- fisher.alpha(BCI)
+> ## Plot all
 > pairs(cbind(H, simp, invsimp, unbias.simp, alpha), pch="+", col="blue")
 > ## Species richness (S) and Pielou's evenness (J):
 > S <- specnumber(BCI) ## rowSums(BCI > 0) does the same...
 > J <- H/log(S)
+> ## beta diversity defined as gamma/alpha - 1:
+> data(dune)
+> data(dune.env)
+> alpha <- with(dune.env, tapply(specnumber(dune), Management, mean))
+> gamma <- with(dune.env, specnumber(dune, Management))
+> gamma/alpha - 1
+       BF        HF        NM        SF 
+0.5483871 0.6666667 1.6250000 1.2909091 
 > 
 > 
 > 
-> 
 > cleanEx()
 > nameEx("dune")
 > ### * dune
@@ -4615,7 +4624,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x1034ff030>
+<environment: 0x103842ff0>
 
 Estimated degrees of freedom:
 6.2955  total = 7.295494 
@@ -4631,7 +4640,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x10486ac98>
+<environment: 0x1064d7840>
 
 Estimated degrees of freedom:
 4.9207  total = 5.920718 
@@ -4787,7 +4796,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x105dda708>
+<environment: 0x1065bb200>
 
 Estimated degrees of freedom:
 8.9275  total = 9.927492 
@@ -4800,7 +4809,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x1070190e8>
+<environment: 0x106934d90>
 
 Estimated degrees of freedom:
 7.7529  total = 8.75294 
@@ -4813,7 +4822,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x10695daa0>
+<environment: 0x106aabad0>
 
 Estimated degrees of freedom:
 8.8962  total = 9.89616 
@@ -6926,18 +6935,18 @@
 
    statistic         z      2.5%       50%  97.5% Pr(sim.)   
 2  411.98157  -2.99423 478.34101 575.57604 673.73     0.01 **
-13 548.84793  -0.51412 473.54839 574.19355 678.29     0.53   
+13 548.84793  -0.51412 473.54839 574.19355 678.29     0.57   
 4  606.91244  -1.28888 569.12442 694.00922 791.24     0.23   
 16 479.26267  -0.15414 364.51613 491.70507 591.24     0.93   
 6  572.35023  -0.84373 502.18894 619.81567 711.45     0.51   
 1  249.30876  -2.28880 267.74194 367.28111 444.70     0.05 * 
 8  692.16590   0.95083 552.53456 642.39631 744.19     0.33   
 5  640.09217  -1.68020 627.14286 724.88479 798.69     0.09 . 
-17 341.93548  -2.06383 362.67281 441.47465 544.19     0.01 **
+17 341.93548  -2.06383 362.67281 441.47465 544.19     0.03 * 
 15 599.53917   2.12165 384.23963 493.08756 575.07     0.03 * 
-10 563.59447  -1.61592 545.27650 650.69124 739.63     0.13   
-11 564.05530   0.54226 436.86636 535.02304 647.42     0.67   
-9  625.80645  -1.24238 596.26728 693.08756 795.81     0.23   
+10 563.59447  -1.61592 545.27650 650.69124 739.63     0.15   
+11 564.05530   0.54226 436.86636 535.02304 647.42     0.77   
+9  625.80645  -1.24238 596.26728 693.08756 795.81     0.27   
 18 543.31797   0.16005 431.29032 543.31797 622.12     1.00   
 3  489.40092  -1.54810 488.47926 565.89862 649.26     0.11   
 20 578.80184   1.71999 393.54839 493.08756 575.07     0.07 . 
@@ -7511,7 +7520,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x1080db7c0>
+<environment: 0x107b2d8d8>
 
 Estimated degrees of freedom:
 2  total = 3 
@@ -7988,7 +7997,7 @@
 > ### * <FOOTER>
 > ###
 > cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  106.217 1.196 108.951 0 0 
+Time elapsed:  134.739 1.544 138.186 0 0 
 > grDevices::dev.off()
 null device 
           1