[Vegan-commits] r1208 - pkg/vegan/man

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

Author: jarioksa
Date: 2010-06-01 08:25:01 +0200 (Tue, 01 Jun 2010)
New Revision: 1208

Modified:
   pkg/vegan/man/add1.cca.Rd
   pkg/vegan/man/ordipointlabel.Rd
   pkg/vegan/man/ordistep.Rd
   pkg/vegan/man/prc.Rd
   pkg/vegan/man/treedive.Rd
Log:
speed up of some examples (more needed)

Modified: pkg/vegan/man/add1.cca.Rd
===================================================================
--- pkg/vegan/man/add1.cca.Rd	2010-06-01 05:55:57 UTC (rev 1207)
+++ pkg/vegan/man/add1.cca.Rd	2010-06-01 06:25:01 UTC (rev 1208)
@@ -73,7 +73,7 @@
 ## Automatic model building based on AIC but with permutation tests
 step(cca(dune ~  1, dune.env), reformulate(names(dune.env)), test="perm")
 ## The same, but based on permutation P-values
-ordistep(cca(dune ~  1, dune.env), reformulate(names(dune.env)), perm.max=500)
+ordistep(cca(dune ~  1, dune.env), reformulate(names(dune.env)), perm.max=200)
 ## Manual model building
 ## -- define the maximal model for scope
 mbig <- rda(dune ~  ., dune.env)

Modified: pkg/vegan/man/ordipointlabel.Rd
===================================================================
--- pkg/vegan/man/ordipointlabel.Rd	2010-06-01 05:55:57 UTC (rev 1207)
+++ pkg/vegan/man/ordipointlabel.Rd	2010-06-01 06:25:01 UTC (rev 1208)
@@ -66,8 +66,8 @@
 \seealso{ \code{\link[maptools]{pointLabel}} for the model
   implementation, and \code{\link{optim}} for the optimization. }
 \examples{
-data(varespec)
-ord <- cca(varespec)
+data(dune)
+ord <- cca(dune)
 ordipointlabel(ord)
 }
 \keyword{ hplot }

Modified: pkg/vegan/man/ordistep.Rd
===================================================================
--- pkg/vegan/man/ordistep.Rd	2010-06-01 05:55:57 UTC (rev 1207)
+++ pkg/vegan/man/ordistep.Rd	2010-06-01 06:25:01 UTC (rev 1208)
@@ -130,7 +130,7 @@
 data(dune.env)
 mod1 <- rda(dune ~ ., dune.env)
 ordistep(mod1)
-ordistep(rda(dune ~ 1, dune.env), scope = formula(mod1))
+ordistep(rda(dune ~ 1, dune.env), scope = formula(mod1), perm.max = 200)
 ordiR2step(rda(dune ~ 1, dune.env), mod1)
 }
 

Modified: pkg/vegan/man/prc.Rd
===================================================================
--- pkg/vegan/man/prc.Rd	2010-06-01 05:55:57 UTC (rev 1207)
+++ pkg/vegan/man/prc.Rd	2010-06-01 06:25:01 UTC (rev 1208)
@@ -119,7 +119,7 @@
 plot(mod, select = logabu > 100)
 # Permutations should be done only within one week, and we only
 # are interested on the first axis
-anova(mod, strata = week, first=TRUE)
+anova(mod, strata = week, first=TRUE, perm.max = 100)
 }
 \keyword{ multivariate }
 

Modified: pkg/vegan/man/treedive.Rd
===================================================================
--- pkg/vegan/man/treedive.Rd	2010-06-01 05:55:57 UTC (rev 1207)
+++ pkg/vegan/man/treedive.Rd	2010-06-01 06:25:01 UTC (rev 1208)
@@ -101,8 +101,8 @@
 cl <- hclust(d, "aver")
 treedive(dune, cl)
 ## Significance test using Null model communities.
-## The current choice fixes both species and site totals.
-oecosimu(dune, treedive, "quasiswap", tree = cl)
+## The current choice fixes only site totals.
+oecosimu(dune, treedive, "r0", tree = cl)
 ## Clustering of tree distances
 dtree <- treedist(dune, cl)
 plot(hclust(dtree, "aver"))