[Vegan-commits] r804 - in branches/1.15: R inst man

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

Author: jarioksa
Date: 2009-04-14 21:21:18 +0200 (Tue, 14 Apr 2009)
New Revision: 804

Modified:
   branches/1.15/R/adonis.R
   branches/1.15/inst/ChangeLog
   branches/1.15/inst/NEWS
   branches/1.15/man/adonis.Rd
Log:
merged r800 (adonis uses less memory) and r802 (enhanced example in adonis.Rd)

Modified: branches/1.15/R/adonis.R
===================================================================
--- branches/1.15/R/adonis.R	2009-04-14 18:56:20 UTC (rev 803)
+++ branches/1.15/R/adonis.R	2009-04-14 19:21:18 UTC (rev 804)
@@ -80,15 +80,13 @@
     ## Permutations
     if (missing(strata)) 
         strata <- NULL
-    G.p <- lapply(1:permutations, function(x) {
-        permutes <- permuted.index(n, strata = strata)
-        G[permutes, permutes]
-    } )
+    p <- sapply(1:permutations,
+                function(x) permuted.index(n, strata=strata))
     
-    ## SS.s <- sapply(G.p, function(Gs) { SS.perms(H, Gs, I) } )
+    ## Apply permutations for each term
     f.perms <- sapply(1:nterms, function(i) {
         sapply(1:permutations, function(j) {
-            f.test(H.s[[i]], G.p[[j]], I, df.Exp[i], df.Res, H.snterm)
+            f.test(H.s[[i]], G[p[,j],p[,j]], I, df.Exp[i], df.Res, H.snterm)
         } )
     })
   

Modified: branches/1.15/inst/ChangeLog
===================================================================
--- branches/1.15/inst/ChangeLog	2009-04-14 18:56:20 UTC (rev 803)
+++ branches/1.15/inst/ChangeLog	2009-04-14 19:21:18 UTC (rev 804)
@@ -5,6 +5,9 @@
 
 Version 1.15-2 (opened January 14, 2009)
 
+	* merged r800 (adonis uses less memory in permutation tests) and
+	r802 (example enhanced in adonis.Rd, with formatting).
+
 	* merged r600: Oribatid mites (dataset 'mite') got taxon names. 
 
 	* copied nestednodf.R and print.nestednodf.R from pkg/vegan at

Modified: branches/1.15/inst/NEWS
===================================================================
--- branches/1.15/inst/NEWS	2009-04-14 18:56:20 UTC (rev 803)
+++ branches/1.15/inst/NEWS	2009-04-14 19:21:18 UTC (rev 804)
@@ -7,7 +7,8 @@
     
     - adonis: adds one to numerator and denominator of permutation
       tests, the default number of iterations was raised from 5 to
-      999, and the result object got a 'terms' component.
+      999, and the result object got a 'terms' component. Uses much 
+      less memory  allowing analysis of larger problems.
 
     - anova.cca: anova(..., by = "axis") gained new keyword 'cutoff'
       to stop permutation tests after exceeding the given cut-off

Modified: branches/1.15/man/adonis.Rd
===================================================================
--- branches/1.15/man/adonis.Rd	2009-04-14 18:56:20 UTC (rev 803)
+++ branches/1.15/man/adonis.Rd	2009-04-14 19:21:18 UTC (rev 804)
@@ -60,6 +60,15 @@
 \code{\link[ade4]{amova}} in the \pkg{ade4} package) for both crossed
 and nested factors.
 
+If the experimental design has nestedness, then use \code{strata} to
+test hypotheses. For instance, imagine we are testing the whether a
+plant community is influenced by nitrate amendments, and we have two
+replicate plots at each of two levels of nitrate (0, 10 ppm). We have
+replicated the experiment in three fields with (perhaps) different
+average productivity. In this design, we would need to specify
+\code{strata = field} so that randomizations occur only \emph{within
+each field} and not across all fields . See example below.
+
 Like AMOVA (Excoffier et al. 1992), \code{adonis} relies on a
 long-understood phenomenon that allows one to partition sums of squared
 deviations from a centroid in two different ways (McArdle and Anderson
@@ -162,6 +171,33 @@
 data(dune)
 data(dune.env)
 adonis(dune ~ Management*A1, data=dune.env, permutations=99)
+
+
+### Example of use with strata, for nested (e.g., block) designs.
+
+dat <- expand.grid(rep=gl(2,1), NO3=factor(c(0,10)),field=gl(3,1) )
+dat
+Agropyron <- with(dat, as.numeric(field) + as.numeric(NO3)+2) +rnorm(12)/2
+Schizachyrium <- with(dat, as.numeric(field) - as.numeric(NO3)+2) +rnorm(12)/2
+total <- Agropyron + Schizachyrium
+library(lattice)
+dotplot(total ~ NO3, dat, jitter.x=TRUE, groups=field,
+        type=c('p','a'), xlab="NO3", auto.key=list(columns=3, lines=TRUE) )
+
+Y <- data.frame(Agropyron, Schizachyrium)
+mod <- metaMDS(Y)
+plot(mod)
+### Hulls show treatment
+ordihull(mod, group=dat$NO3, show="0")
+ordihull(mod, group=dat$NO3, show="10", col=3)
+### Spider shows fields
+ordispider(mod, group=dat$field, lty=3, col="red")
+
+### Correct hypothesis test (with strata)
+adonis(Y ~ NO3, data=dat, strata=dat$field, perm=1e3)
+
+### Incorrect (no strata)
+adonis(Y ~ NO3, data=dat, perm=1e3)
 }
 
 \keyword{multivariate }