[Vegan-commits] r1225 - branches/1.17/man

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

Author: jarioksa
Date: 2010-06-10 08:17:32 +0200 (Thu, 10 Jun 2010)
New Revision: 1225

Modified:
   branches/1.17/man/add1.cca.Rd
   branches/1.17/man/kendall.global.Rd
   branches/1.17/man/ordipointlabel.Rd
   branches/1.17/man/prc.Rd
Log:
merge some (but not all) check time speed-up

Modified: branches/1.17/man/add1.cca.Rd
===================================================================
--- branches/1.17/man/add1.cca.Rd	2010-06-10 06:16:38 UTC (rev 1224)
+++ branches/1.17/man/add1.cca.Rd	2010-06-10 06:17:32 UTC (rev 1225)
@@ -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: branches/1.17/man/kendall.global.Rd
===================================================================
--- branches/1.17/man/kendall.global.Rd	2010-06-10 06:16:38 UTC (rev 1224)
+++ branches/1.17/man/kendall.global.Rd	2010-06-10 06:17:32 UTC (rev 1225)
@@ -156,13 +156,16 @@
 
 # Reproduce the results shown in Table 2 of Legendre (2005), a single group
 mite.small <- mite.hel[c(4,9,14,22,31,34,45,53,61,69),c(13:15,23)]
-kendall.global(mite.small)
-kendall.post(mite.small, mult="holm")
+kendall.global(mite.small, nperm=99)
+kendall.post(mite.small, mult="holm", nperm=99)
 
 # Reproduce the results shown in Tables 3 and 4 of Legendre (2005), 2 groups
 group <-c(1,1,2,1,1,1,1,1,2,1,1,1,1,1,1,2,1,2,1,1,1,1,2,1,2,1,1,1,1,1,2,2,2,2,2)
-kendall.global(mite.hel, group=group)
+kendall.global(mite.hel, group=group, nperm=99)
 kendall.post(mite.hel, group=group, mult="holm", nperm=99)
+
+# NOTE: 'nperm' argument usually needs to be larger than 99.
+# It was set to this low value for demonstration purposes.
 }
 
 \keyword{ multivariate }

Modified: branches/1.17/man/ordipointlabel.Rd
===================================================================
--- branches/1.17/man/ordipointlabel.Rd	2010-06-10 06:16:38 UTC (rev 1224)
+++ branches/1.17/man/ordipointlabel.Rd	2010-06-10 06:17:32 UTC (rev 1225)
@@ -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: branches/1.17/man/prc.Rd
===================================================================
--- branches/1.17/man/prc.Rd	2010-06-10 06:16:38 UTC (rev 1224)
+++ branches/1.17/man/prc.Rd	2010-06-10 06:17:32 UTC (rev 1225)
@@ -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 }