[Vegan-commits] r1586 - in pkg/vegan: . inst man

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

Author: jarioksa
Date: 2011-04-11 17:26:19 +0200 (Mon, 11 Apr 2011)
New Revision: 1586

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/adipart.Rd
   pkg/vegan/man/multipart.Rd
Log:
cancel some excessive speed-up in examples (made in r1204)

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2011-04-10 08:48:20 UTC (rev 1585)
+++ pkg/vegan/DESCRIPTION	2011-04-11 15:26:19 UTC (rev 1586)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 1.18-28
-Date: April 1, 2011
+Version: 1.18-29
+Date: April 11, 2011
 Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, 
    Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, 
    M. Henry H. Stevens, Helene Wagner  

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-04-10 08:48:20 UTC (rev 1585)
+++ pkg/vegan/inst/ChangeLog	2011-04-11 15:26:19 UTC (rev 1586)
@@ -2,8 +2,20 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 1.18-28 (opened April 1, 2011)
+Version 1.18-29 (opened April 11, 2011)
 
+	* adipart.Rd, multipart.Rd: cancelled some excessive speed-ups in
+	example code made in r1204. Some of these speed-ups never made to
+	the release version, but were only made in the devel branch. Now
+	it seems that sped-up examples could be merged to the release
+	(adipart.Rd, multipart.Rd, mantel.correlog.Rd, pertmatfull.Rd)
+	radfit.Rd). Probably we should speed up some other examples. The
+	five worst cases (timing in MacBook Air) are: ordistep (19.0 sec),
+	add1.cca (7.2 sec), tsallis (7.0 sec), prc (5.6 sec),
+	vegan-package (5.2 sec). 
+	
+Version 1.18-28 (closed April 11, 2011)
+
 	* Peter Minchin joined the vegan team.
 
 	* monoMDS: a new function with Peter Minchin's Fortran90 code for

Modified: pkg/vegan/man/adipart.Rd
===================================================================
--- pkg/vegan/man/adipart.Rd	2011-04-10 08:48:20 UTC (rev 1585)
+++ pkg/vegan/man/adipart.Rd	2011-04-11 15:26:19 UTC (rev 1586)
@@ -128,12 +128,12 @@
 plot(mite.xy, main="l3", col=as.numeric(levsm$l3)+1)
 par(mfrow=c(1,1))
 ## Additive diversity partitioning
-adipart(mite ~., levsm, index="richness", nsimul=9)
+adipart(mite ~., levsm, index="richness", nsimul=19)
 ## Hierarchical null model testing
 ## diversity analysis (similar to adipart)
-hiersimu(mite ~., levsm, diversity, relative=TRUE, nsimul=9)
+hiersimu(mite ~., levsm, diversity, relative=TRUE, nsimul=19)
 ## Hierarchical testing with the Morisita index
 morfun <- function(x) dispindmorisita(x)$imst
-hiersimu(mite ~., levsm, morfun, drop.highest=TRUE, nsimul=9)
+hiersimu(mite ~., levsm, morfun, drop.highest=TRUE, nsimul=19)
 }
 \keyword{multivariate}

Modified: pkg/vegan/man/multipart.Rd
===================================================================
--- pkg/vegan/man/multipart.Rd	2011-04-10 08:48:20 UTC (rev 1585)
+++ pkg/vegan/man/multipart.Rd	2011-04-11 15:26:19 UTC (rev 1586)
@@ -103,8 +103,8 @@
     l3=cutter(mite.xy$y, cut = seq(0, 10, by = 5)),
     l4=cutter(mite.xy$y, cut = seq(0, 10, by = 10)))
 ## Multiplicative diversity partitioning
-multipart(mite ~ ., levsm, index="renyi", scales=1, nsimul=9)
-multipart(mite ~ ., levsm, index="renyi", scales=1, nsimul=9, relative=TRUE)
-multipart(mite ~ ., levsm, index="renyi", scales=1, nsimul=9, global=TRUE)
+multipart(mite ~ ., levsm, index="renyi", scales=1, nsimul=19)
+multipart(mite ~ ., levsm, index="renyi", scales=1, nsimul=19, relative=TRUE)
+multipart(mite ~ ., levsm, index="renyi", scales=1, nsimul=19, global=TRUE)
 }
 \keyword{multivariate}