[Vegan-commits] r1296 - in pkg/vegan: . inst man

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

Author: jarioksa
Date: 2010-08-31 15:26:24 +0200 (Tue, 31 Aug 2010)
New Revision: 1296

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/diversity.Rd
Log:
tell that rarefy(x,2)-1 is the unbiased Simpson diversity

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2010-08-30 13:21:25 UTC (rev 1295)
+++ pkg/vegan/DESCRIPTION	2010-08-31 13:26:24 UTC (rev 1296)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 1.18-10
-Date: August 12, 2010
+Version: 1.18-11
+Date: August 31, 2010
 Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, 
    R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, 
    Helene Wagner  

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2010-08-30 13:21:25 UTC (rev 1295)
+++ pkg/vegan/inst/ChangeLog	2010-08-31 13:26:24 UTC (rev 1296)
@@ -2,11 +2,20 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 1.18-10 (opened August 20, 2010)
+Version 1.18-11 (opened August 31, 2010)
 
+	* diversity: example says that rarefy(x, 2) - 1 is the same as
+	unbiased Simpson of a true random sample of Hurlbert (1971,
+	eq. 5). Added after several wishes to have this function.
+	
+Version 1.18-10 (closed August 31, 2010)
+
 	* New version opened with the release of vegan_1.17-4 on August
 	20, 2010.
 
+	* rankindex: can take a list of dissimlarity functions as an
+	argument. 
+
 	* deviance.cca/rda: return 0 (instead of NULL) if there is no
 	residual variation.
 
@@ -17,7 +26,8 @@
 
 	* ordiR2step: can go to the end and include all variables of the
 	scope (and checks there is a scope).  Additional stopping
-	criterion of exceeding P-value.
+	criterion of exceeding P-value. Looks like being up to specs and
+	left for approval.
 
 	* permutest.cca: defaults to 99 permutations instead of 100 (to
 	be consistent). Item 'call' now stores the call to permutest()

Modified: pkg/vegan/man/diversity.Rd
===================================================================
--- pkg/vegan/man/diversity.Rd	2010-08-30 13:21:25 UTC (rev 1295)
+++ pkg/vegan/man/diversity.Rd	2010-08-31 13:26:24 UTC (rev 1296)
@@ -133,9 +133,10 @@
 H <- diversity(BCI)
 simp <- diversity(BCI, "simpson")
 invsimp <- diversity(BCI, "inv")
-r.2 <- rarefy(BCI, 2)
+## Unbiased Simpson of Hurlbert 1971 (eq. 5):
+unbias.simp <- rarefy(BCI, 2) - 1
 alpha <- fisher.alpha(BCI)
-pairs(cbind(H, simp, invsimp, r.2, alpha), pch="+", col="blue")
+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)