[Vegan-commits] r1204 - pkg/vegan/man

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

Author: psolymos
Date: 2010-05-31 17:12:22 +0200 (Mon, 31 May 2010)
New Revision: 1204

Modified:
   pkg/vegan/man/adipart.Rd
   pkg/vegan/man/multipart.Rd
   pkg/vegan/man/permatfull.Rd
Log:
decreasing example timing with lowering # simuls

Modified: pkg/vegan/man/adipart.Rd
===================================================================
--- pkg/vegan/man/adipart.Rd	2010-05-30 10:49:44 UTC (rev 1203)
+++ pkg/vegan/man/adipart.Rd	2010-05-31 15:12:22 UTC (rev 1204)
@@ -103,6 +103,9 @@
 \author{\enc{P\'eter S\'olymos}{Peter Solymos}, \email{solymos at ualberta.ca}}
 \seealso{See \code{\link{oecosimu}} for permutation settings and calculating \eqn{p}-values.}
 \examples{
+## NOTE: 'nsimul' argument usually needs to be >= 99
+## here much lower value is used for demonstration
+
 data(mite)
 data(mite.xy)
 data(mite.env)
@@ -125,12 +128,12 @@
 plot(mite.xy, main="l3", col=as.numeric(levsm$l3)+1)
 par(mfrow=c(1,1))
 ## Additive diversity partitioning
-adipart(mite ~., levsm, index="richness", nsimul=20)
+adipart(mite ~., levsm, index="richness", nsimul=9)
 ## Hierarchical null model testing
 ## diversity analysis (similar to adipart)
-hiersimu(mite ~., levsm, diversity, relative=TRUE, nsimul=25)
+hiersimu(mite ~., levsm, diversity, relative=TRUE, nsimul=9)
 ## Hierarchical testing with the Morisita index
 morfun <- function(x) dispindmorisita(x)$imst
-hiersimu(mite ~., levsm, morfun, drop.highest=TRUE, nsimul=25)
+hiersimu(mite ~., levsm, morfun, drop.highest=TRUE, nsimul=9)
 }
 \keyword{multivariate}

Modified: pkg/vegan/man/multipart.Rd
===================================================================
--- pkg/vegan/man/multipart.Rd	2010-05-30 10:49:44 UTC (rev 1203)
+++ pkg/vegan/man/multipart.Rd	2010-05-31 15:12:22 UTC (rev 1204)
@@ -84,6 +84,9 @@
   \code{\link{hiersimu}} for hierarchical null model testing
   and \code{\link{oecosimu}} for permutation settings and calculating \eqn{p}-values.}
 \examples{
+## NOTE: 'nsimul' argument usually needs to be >= 99
+## here much lower value is used for demonstration
+
 data(mite)
 data(mite.xy)
 data(mite.env)
@@ -100,8 +103,8 @@
     l3=cutter(mite.xy$y, cut = seq(0, 10, by = 5)),
     l4=cutter(mite.xy$y, cut = seq(0, 10, by = 10)))
 ## Multiplicative diversity partitioning
-multipart(mite ~ ., levsm, index="renyi", scales=1, nsimul=25)
-multipart(mite ~ ., levsm, index="renyi", scales=1, nsimul=25, relative=TRUE)
-multipart(mite ~ ., levsm, index="renyi", scales=1, nsimul=25, global=TRUE)
+multipart(mite ~ ., levsm, index="renyi", scales=1, nsimul=9)
+multipart(mite ~ ., levsm, index="renyi", scales=1, nsimul=9, relative=TRUE)
+multipart(mite ~ ., levsm, index="renyi", scales=1, nsimul=9, global=TRUE)
 }
 \keyword{multivariate}

Modified: pkg/vegan/man/permatfull.Rd
===================================================================
--- pkg/vegan/man/permatfull.Rd	2010-05-30 10:49:44 UTC (rev 1203)
+++ pkg/vegan/man/permatfull.Rd	2010-05-31 15:12:22 UTC (rev 1204)
@@ -248,12 +248,16 @@
 ## check sums within strata:
 x4 <- permatfull(m, strata=c(1,1,2,2))
 summary(x4)
+
+## NOTE: 'times' argument usually needs to be >= 99
+## here much lower value is used for demonstration
+
 ## Not sequential algorithm
 data(BCI)
-a <- permatswap(BCI, "quasiswap")
+a <- permatswap(BCI, "quasiswap", times=19)
 ## Sequential algorithm
 b <- permatswap(BCI, "abuswap", fixedmar="col",
-    burnin=0, thin=100, times=50)
+    burnin=0, thin=100, times=19)
 opar <- par(mfrow=c(2,2))
 plot(a, main="Not sequential")
 plot(b, main="Sequential")