[Vegan-commits] r1206 - pkg/vegan/man

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

Author: gblanchet
Date: 2010-05-31 19:09:56 +0200 (Mon, 31 May 2010)
New Revision: 1206

Modified:
   pkg/vegan/man/kendall.global.Rd
   pkg/vegan/man/mantel.correlog.Rd
Log:
decreasing example time by lowering number of permutations

Modified: pkg/vegan/man/kendall.global.Rd
===================================================================
--- pkg/vegan/man/kendall.global.Rd	2010-05-31 16:54:24 UTC (rev 1205)
+++ pkg/vegan/man/kendall.global.Rd	2010-05-31 17:09:56 UTC (rev 1206)
@@ -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=49)
+kendall.post(mite.small, mult="holm", nperm=49)
 
 # 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.post(mite.hel, group=group, mult="holm", nperm=99)
+kendall.global(mite.hel, group=group, nperm=49)
+kendall.post(mite.hel, group=group, mult="holm", nperm=49)
+
+# NOTE: 'nperm' argument usually needs to be larger than 49.
+# It was set to this low value for demonstration purposes.
 }
 
 \keyword{ multivariate }

Modified: pkg/vegan/man/mantel.correlog.Rd
===================================================================
--- pkg/vegan/man/mantel.correlog.Rd	2010-05-31 16:54:24 UTC (rev 1205)
+++ pkg/vegan/man/mantel.correlog.Rd	2010-05-31 17:09:56 UTC (rev 1206)
@@ -116,7 +116,7 @@
   \item{call }{The function call. }  
 }
 
-\author{ Pierre Legendre, Universite de Montreal }
+\author{ Pierre Legendre, Université de Montréal }
 
 \references{
 
@@ -150,7 +150,7 @@
 mite.hel.D = dist(mite.hel.resid)
 
 # Compute Mantel correlogram with cutoff, Pearson statistic
-mite.correlog = mantel.correlog(mite.hel.D, XY=mite.xy, nperm=99)
+mite.correlog = mantel.correlog(mite.hel.D, XY=mite.xy, nperm=49)
 summary(mite.correlog)
 mite.correlog   
 # or: print(mite.correlog)
@@ -159,11 +159,14 @@
 
 # Compute Mantel correlogram without cutoff, Spearman statistic
 mite.correlog2 = mantel.correlog(mite.hel.D, XY=mite.xy, cutoff=FALSE, 
-r.type="spearman", nperm=99)
+r.type="spearman", nperm=49)
 summary(mite.correlog2)
 mite.correlog2
 plot(mite.correlog2)
 
+# NOTE: 'nperm' argument usually needs to be larger than 49.
+# It was set to this low value for demonstration purposes.
+
 }
 
 \keyword{ multivariate }
\ No newline at end of file