[Vegan-commits] r2833 - pkg/vegan/man

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

Author: jarioksa
Date: 2014-01-12 17:33:52 +0100 (Sun, 12 Jan 2014)
New Revision: 2833

Modified:
   pkg/vegan/man/prc.Rd
Log:
prc uses permute capabilities in anova example

Modified: pkg/vegan/man/prc.Rd
===================================================================
--- pkg/vegan/man/prc.Rd	2014-01-12 15:56:57 UTC (rev 2832)
+++ pkg/vegan/man/prc.Rd	2014-01-12 16:33:52 UTC (rev 2833)
@@ -109,19 +109,24 @@
 
 \seealso{\code{\link{rda}}, \code{\link{anova.cca}}.}
 \examples{
-# Chlorpyrifos experiment and experimental design
+## Chlorpyrifos experiment and experimental design: Pesticide
+## treatment in ditches (replicated) and followed over from 4 weeks
+## before to 24 weeks after exposure 
 data(pyrifos)
 week <- gl(11, 12, labels=c(-4, -1, 0.1, 1, 2, 4, 8, 12, 15, 19, 24))
 dose <- factor(rep(c(0.1, 0, 0, 0.9, 0, 44, 6, 0.1, 44, 0.9, 0, 6), 11))
+ditch <- gl(12, 1, length=132)
 # PRC
 mod <- prc(pyrifos, dose, week)
 mod            # RDA
 summary(mod)   # PRC
 logabu <- colSums(pyrifos)
 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, perm.max = 100)
+## Ditches are randomized, we have a time series, and are only
+## interested in the first axis
+ctrl <- how(plots = Plots(strata = ditch,type = "free"),
+    within = Within(type = "series"), nperm = 99)
+anova(mod, permutations = ctrl, first=TRUE)
 }
 \keyword{ multivariate }