[Vegan-commits] r1587 - branches/1.17/inst branches/1.17/man pkg/vegan/inst pkg/vegan/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Apr 11 17:55:48 CEST 2011
Author: jarioksa
Date: 2011-04-11 17:55:48 +0200 (Mon, 11 Apr 2011)
New Revision: 1587
Modified:
branches/1.17/inst/ChangeLog
branches/1.17/man/adipart.Rd
branches/1.17/man/kendall.global.Rd
branches/1.17/man/mantel.correlog.Rd
branches/1.17/man/multipart.Rd
branches/1.17/man/permatfull.Rd
branches/1.17/man/radfit.Rd
pkg/vegan/inst/ChangeLog
pkg/vegan/man/kendall.global.Rd
Log:
merge example speed-ups to branches/1.17
Modified: branches/1.17/inst/ChangeLog
===================================================================
--- branches/1.17/inst/ChangeLog 2011-04-11 15:26:19 UTC (rev 1586)
+++ branches/1.17/inst/ChangeLog 2011-04-11 15:55:48 UTC (rev 1587)
@@ -4,6 +4,9 @@
Version 1.17-10 (opened April 10, 2011)
+ * merged r1204, 1206, 1209, 1568: speed-up of examples in Rd
+ files.
+
* merged 1555: #include's in vegdist.c.
* merged 1564: missing definitionin ordering.f.
Modified: branches/1.17/man/adipart.Rd
===================================================================
--- branches/1.17/man/adipart.Rd 2011-04-11 15:26:19 UTC (rev 1586)
+++ branches/1.17/man/adipart.Rd 2011-04-11 15:55:48 UTC (rev 1587)
@@ -103,6 +103,9 @@
\author{\enc{Péter Sólymos}{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$l3)+1)
par(mfrow=c(1,1))
## Additive diversity partitioning
-adipart(mite ~., levsm, index="richness", nsimul=20)
+adipart(mite ~., levsm, index="richness", nsimul=19)
## Hierarchical null model testing
## diversity analysis (similar to adipart)
-hiersimu(mite ~., levsm, diversity, relative=TRUE, nsimul=25)
+hiersimu(mite ~., levsm, diversity, relative=TRUE, nsimul=19)
## Hierarchical testing with the Morisita index
morfun <- function(x) dispindmorisita(x)$imst
-hiersimu(mite ~., levsm, morfun, drop.highest=TRUE, nsimul=25)
+hiersimu(mite ~., levsm, morfun, drop.highest=TRUE, nsimul=19)
}
\keyword{multivariate}
Modified: branches/1.17/man/kendall.global.Rd
===================================================================
--- branches/1.17/man/kendall.global.Rd 2011-04-11 15:26:19 UTC (rev 1586)
+++ branches/1.17/man/kendall.global.Rd 2011-04-11 15:55:48 UTC (rev 1587)
@@ -156,15 +156,15 @@
# 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, nperm=99)
-kendall.post(mite.small, mult="holm", nperm=99)
+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, nperm=99)
-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 99.
+# NOTE: 'nperm' argument usually needs to be larger than 49.
# It was set to this low value for demonstration purposes.
}
Modified: branches/1.17/man/mantel.correlog.Rd
===================================================================
--- branches/1.17/man/mantel.correlog.Rd 2011-04-11 15:26:19 UTC (rev 1586)
+++ branches/1.17/man/mantel.correlog.Rd 2011-04-11 15:55:48 UTC (rev 1587)
@@ -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
Modified: branches/1.17/man/multipart.Rd
===================================================================
--- branches/1.17/man/multipart.Rd 2011-04-11 15:26:19 UTC (rev 1586)
+++ branches/1.17/man/multipart.Rd 2011-04-11 15:55:48 UTC (rev 1587)
@@ -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=19)
+multipart(mite ~ ., levsm, index="renyi", scales=1, nsimul=19, relative=TRUE)
+multipart(mite ~ ., levsm, index="renyi", scales=1, nsimul=19, global=TRUE)
}
\keyword{multivariate}
Modified: branches/1.17/man/permatfull.Rd
===================================================================
--- branches/1.17/man/permatfull.Rd 2011-04-11 15:26:19 UTC (rev 1586)
+++ branches/1.17/man/permatfull.Rd 2011-04-11 15:55:48 UTC (rev 1587)
@@ -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")
Modified: branches/1.17/man/radfit.Rd
===================================================================
--- branches/1.17/man/radfit.Rd 2011-04-11 15:26:19 UTC (rev 1586)
+++ branches/1.17/man/radfit.Rd 2011-04-11 15:55:48 UTC (rev 1587)
@@ -225,7 +225,7 @@
\code{\link[lattice]{xyplot}}, \code{\link[lattice]{lset}}. }
\examples{
data(BCI)
-mod <- rad.lognormal(BCI[1,])
+mod <- rad.lognormal(BCI[5,])
mod
plot(mod)
mod <- radfit(BCI[1,])
@@ -237,7 +237,7 @@
## Lattice graphics separately for each model
radlattice(mod)
# Take a subset of BCI to save time and nerves
-mod <- radfit(BCI[2:5,])
+mod <- radfit(BCI[3:5,])
mod
plot(mod, pch=".")
}
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2011-04-11 15:26:19 UTC (rev 1586)
+++ pkg/vegan/inst/ChangeLog 2011-04-11 15:55:48 UTC (rev 1587)
@@ -6,13 +6,15 @@
* adipart.Rd, multipart.Rd: cancelled some excessive speed-ups in
example code made in r1204. Some of these speed-ups never made to
- the release version, but were only made in the devel branch. Now
- it seems that sped-up examples could be merged to the release
- (adipart.Rd, multipart.Rd, mantel.correlog.Rd, pertmatfull.Rd)
- radfit.Rd). Probably we should speed up some other examples. The
- five worst cases (timing in MacBook Air) are: ordistep (19.0 sec),
+ the release version, but were only made in the devel branch. The
+ sped-up examples were also merged to the release (adipart.Rd,
+ kendall.global.Rd, multipart.Rd, mantel.correlog.Rd,
+ pertmatfull.Rd, radfit.Rd). Also reverted r1224 so that
+ Guillaume's original r1206 (49 permutations instead of 99) is used
+ again. Probably we should speed up some other examples. The five
+ worst cases (timing in MacBook Air) are: ordistep (19.0 sec),
add1.cca (7.2 sec), tsallis (7.0 sec), prc (5.6 sec),
- vegan-package (5.2 sec).
+ vegan-package (5.2 sec).
Version 1.18-28 (closed April 11, 2011)
Modified: pkg/vegan/man/kendall.global.Rd
===================================================================
--- pkg/vegan/man/kendall.global.Rd 2011-04-11 15:26:19 UTC (rev 1586)
+++ pkg/vegan/man/kendall.global.Rd 2011-04-11 15:55:48 UTC (rev 1587)
@@ -156,15 +156,15 @@
# 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, nperm=99)
-kendall.post(mite.small, mult="holm", nperm=99)
+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, nperm=99)
-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 99.
+# NOTE: 'nperm' argument usually needs to be larger than 49.
# It was set to this low value for demonstration purposes.
}
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