[Vegan-commits] r1667 - in pkg/vegan: inst man tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jul 1 14:11:19 CEST 2011
Author: jarioksa
Date: 2011-07-01 14:11:19 +0200 (Fri, 01 Jul 2011)
New Revision: 1667
Modified:
pkg/vegan/inst/ChangeLog
pkg/vegan/man/anosim.Rd
pkg/vegan/man/bioenv.Rd
pkg/vegan/man/cca.Rd
pkg/vegan/man/decorana.Rd
pkg/vegan/man/ordiplot.Rd
pkg/vegan/man/ordisurf.Rd
pkg/vegan/man/procrustes.Rd
pkg/vegan/man/rankindex.Rd
pkg/vegan/man/wascores.Rd
pkg/vegan/man/wcmdscale.Rd
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
update cross refs to monoMDS in man files
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2011-06-30 15:13:09 UTC (rev 1666)
+++ pkg/vegan/inst/ChangeLog 2011-07-01 12:11:19 UTC (rev 1667)
@@ -17,7 +17,8 @@
the update() in 1.18-31 -- problems were anticipated in ChangeLog,
and they were realized.
- * monoMDS: text for a proper help (Rd file).
+ * monoMDS: text for a proper help (Rd file). Other help files
+ updated for monoMDS.
Version 1.18-33 (closed June 21, 2011)
Modified: pkg/vegan/man/anosim.Rd
===================================================================
--- pkg/vegan/man/anosim.Rd 2011-06-30 15:13:09 UTC (rev 1666)
+++ pkg/vegan/man/anosim.Rd 2011-07-01 12:11:19 UTC (rev 1667)
@@ -36,7 +36,7 @@
dissimilarity matrix. A suitable dissimilarity matrix is produced by
functions \code{\link{dist}} or \code{\link{vegdist}}. The
method is philosophically allied with NMDS ordination
- (\code{\link[MASS]{isoMDS}}), in that it uses only the rank order of
+ (\code{\link{monoMDS}}), in that it uses only the rank order of
dissimilarity values.
If two groups of sampling units are really different in their species
Modified: pkg/vegan/man/bioenv.Rd
===================================================================
--- pkg/vegan/man/bioenv.Rd 2011-06-30 15:13:09 UTC (rev 1666)
+++ pkg/vegan/man/bioenv.Rd 2011-07-01 12:11:19 UTC (rev 1667)
@@ -92,10 +92,10 @@
tests based on \emph{a priori} selection of variables are biased.
}
-\seealso{\code{\link{vegdist}},
- \code{\link{dist}}, \code{\link{cor}} for underlying routines,
- \code{\link[MASS]{isoMDS}} for ordination, \code{\link{procrustes}}
- for Procrustes analysis, \code{\link{protest}} for an alternative, and
+\seealso{\code{\link{vegdist}}, \code{\link{dist}}, \code{\link{cor}}
+ for underlying routines, \code{\link{monoMDS}} and
+ \code{\link{metaMDS}} for ordination, \code{\link{procrustes}} for
+ Procrustes analysis, \code{\link{protest}} for an alternative, and
\code{\link{rankindex}} for studying alternatives to the default
Bray-Curtis index.}
Modified: pkg/vegan/man/cca.Rd
===================================================================
--- pkg/vegan/man/cca.Rd 2011-06-30 15:13:09 UTC (rev 1666)
+++ pkg/vegan/man/cca.Rd 2011-07-01 12:11:19 UTC (rev 1667)
@@ -118,7 +118,7 @@
analysed with
unconstrained methods such as correspondence analysis
(\code{\link{decorana}}, \code{\link[MASS]{corresp}}) or non-metric
- multidimensional scaling (\code{\link[MASS]{isoMDS}}) and
+ multidimensional scaling (\code{\link{metaMDS}}) and
environmental interpretation after analysis
(\code{\link{envfit}}, \code{\link{ordisurf}}).
CCA is a good choice if the user has
Modified: pkg/vegan/man/decorana.Rd
===================================================================
--- pkg/vegan/man/decorana.Rd 2011-06-30 15:13:09 UTC (rev 1666)
+++ pkg/vegan/man/decorana.Rd 2011-07-01 12:11:19 UTC (rev 1667)
@@ -167,7 +167,7 @@
\seealso{
For unconstrained ordination, non-metric multidimensional scaling in
- \code{\link[MASS]{isoMDS}} may be more robust (see also
+ \code{\link{monoMDS}} may be more robust (see also
\code{\link{metaMDS}}). Constrained (or
\sQuote{canonical}) correspondence analysis can be made with
\code{\link{cca}}. Orthogonal correspondence analysis can be
Modified: pkg/vegan/man/ordiplot.Rd
===================================================================
--- pkg/vegan/man/ordiplot.Rd 2011-06-30 15:13:09 UTC (rev 1666)
+++ pkg/vegan/man/ordiplot.Rd 2011-07-01 12:11:19 UTC (rev 1667)
@@ -96,13 +96,10 @@
}
\examples{
-# Draw a cute NMDS plot from a non-vegan ordination (isoMDS).
-# Function metaMDS would be an easier alternative.
+# Draw a plot for a non-vegan ordination (cmdscale).
data(dune)
dune.dis <- vegdist(wisconsin(dune))
-library(MASS)
-dune.mds <- isoMDS(dune.dis)
-dune.mds <- postMDS(dune.mds, dune.dis)
+dune.mds <- cmdscale(dune.dis, eig = TRUE)
dune.mds$species <- wascores(dune.mds$points, dune, expand = TRUE)
fig <- ordiplot(dune.mds, type = "none")
points(fig, "sites", pch=21, col="red", bg="yellow")
Modified: pkg/vegan/man/ordisurf.Rd
===================================================================
--- pkg/vegan/man/ordisurf.Rd 2011-06-30 15:13:09 UTC (rev 1666)
+++ pkg/vegan/man/ordisurf.Rd 2011-07-01 12:11:19 UTC (rev 1667)
@@ -183,9 +183,8 @@
\examples{
data(varespec)
data(varechem)
-library(MASS)
vare.dist <- vegdist(varespec)
-vare.mds <- isoMDS(vare.dist)
+vare.mds <- monoMDS(vare.dist)
with(varechem, ordisurf(vare.mds, Baresoil, bubble = 5))
## as above but with extra penalties on smooth terms:
Modified: pkg/vegan/man/procrustes.Rd
===================================================================
--- pkg/vegan/man/procrustes.Rd 2011-06-30 15:13:09 UTC (rev 1666)
+++ pkg/vegan/man/procrustes.Rd 2011-07-01 12:11:19 UTC (rev 1667)
@@ -184,16 +184,15 @@
but the implementation is still after Mardia \emph{et al.}
(1979).}
-\seealso{\code{\link[MASS]{isoMDS}}, \code{\link{initMDS}} for obtaining
+\seealso{\code{\link{monoMDS}}, for obtaining
objects for \code{procrustes}, and \code{\link{mantel}} for an
alternative to \code{protest} without need of dimension reduction.}
\examples{
data(varespec)
vare.dist <- vegdist(wisconsin(varespec))
-library(MASS) ## isoMDS
-mds.null <- isoMDS(vare.dist, tol=1e-7)
-mds.alt <- isoMDS(vare.dist, initMDS(vare.dist), maxit=200, tol=1e-7)
+mds.null <- monoMDS(vare.dist, y = cmdscale(vare.dist))
+mds.alt <- monoMDS(vare.dist)
vare.proc <- procrustes(mds.alt, mds.null)
vare.proc
summary(vare.proc)
Modified: pkg/vegan/man/rankindex.Rd
===================================================================
--- pkg/vegan/man/rankindex.Rd 2011-06-30 15:13:09 UTC (rev 1666)
+++ pkg/vegan/man/rankindex.Rd 2011-07-01 12:11:19 UTC (rev 1667)
@@ -77,7 +77,7 @@
}
\seealso{\code{\link{vegdist}}, \code{\link{stepacross}},
- \code{\link{no.shared}}, \code{\link[MASS]{isoMDS}},
+ \code{\link{no.shared}}, \code{\link{monoMDS}},
\code{\link{cor}}, \code{\link{Machine}}, and for
alternatives \code{\link{anosim}}, \code{\link{mantel}} and
\code{\link{protest}}. }
Modified: pkg/vegan/man/wascores.Rd
===================================================================
--- pkg/vegan/man/wascores.Rd 2011-06-30 15:13:09 UTC (rev 1666)
+++ pkg/vegan/man/wascores.Rd 2011-07-01 12:11:19 UTC (rev 1667)
@@ -42,14 +42,13 @@
\author{ Jari Oksanen }
-\seealso{ \code{\link[MASS]{isoMDS}}, \code{\link{cca}}. }
+\seealso{ \code{\link{monoMDS}}, \code{\link{cca}}. }
\examples{
data(varespec)
data(varechem)
-library(MASS) ## isoMDS
vare.dist <- vegdist(wisconsin(varespec))
-vare.mds <- isoMDS(vare.dist)
+vare.mds <- monoMDS(vare.dist)
vare.points <- postMDS(vare.mds$points, vare.dist)
vare.wa <- wascores(vare.points, varespec)
plot(scores(vare.points), pch="+", asp=1)
Modified: pkg/vegan/man/wcmdscale.Rd
===================================================================
--- pkg/vegan/man/wcmdscale.Rd 2011-06-30 15:13:09 UTC (rev 1666)
+++ pkg/vegan/man/wcmdscale.Rd 2011-07-01 12:11:19 UTC (rev 1667)
@@ -68,11 +68,12 @@
Mardia, K. V., Kent, J. T. and Bibby, J. M. (1979). Chapter 14 of
\emph{Multivariate Analysis}, London: Academic Press.
}
-\seealso{
- \code{\link{cmdscale}}.
- Also \code{\link[MASS]{isoMDS}} and \code{\link[MASS]{sammon}}
- in package \pkg{MASS}.
+
+\seealso{ \code{\link{cmdscale}}. Also \code{\link{monoMDS}}, and
+ \code{\link[MASS]{isoMDS}} and \code{\link[MASS]{sammon}} in package
+ \pkg{MASS}.
}
+
\examples{
## Correspondence analysis as a weighted principal coordinates
## analysis of Euclidean distances of Chi-square transformed data
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-06-30 15:13:09 UTC (rev 1666)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-07-01 12:11:19 UTC (rev 1667)
@@ -4093,19 +4093,10 @@
>
> ### ** Examples
>
-> # Draw a cute NMDS plot from a non-vegan ordination (isoMDS).
-> # Function metaMDS would be an easier alternative.
+> # Draw a plot for a non-vegan ordination (cmdscale).
> data(dune)
> dune.dis <- vegdist(wisconsin(dune))
-> library(MASS)
-> dune.mds <- isoMDS(dune.dis)
-initial value 17.440604
-iter 5 value 11.776556
-iter 10 value 11.603233
-iter 10 value 11.596516
-final value 11.562320
-converged
-> dune.mds <- postMDS(dune.mds, dune.dis)
+> dune.mds <- cmdscale(dune.dis, eig = TRUE)
> dune.mds$species <- wascores(dune.mds$points, dune, expand = TRUE)
> fig <- ordiplot(dune.mds, type = "none")
> points(fig, "sites", pch=21, col="red", bg="yellow")
@@ -4120,9 +4111,6 @@
>
>
> cleanEx()
-
-detaching ‘package:MASS’
-
> nameEx("ordiplot3d")
> ### * ordiplot3d
>
@@ -4618,13 +4606,8 @@
>
> data(varespec)
> data(varechem)
-> library(MASS)
> vare.dist <- vegdist(varespec)
-> vare.mds <- isoMDS(vare.dist)
-initial value 18.026495
-iter 5 value 10.095483
-final value 10.020469
-converged
+> vare.mds <- monoMDS(vare.dist)
> with(varechem, ordisurf(vare.mds, Baresoil, bubble = 5))
Loading required package: mgcv
This is mgcv 1.7-5. For overview type 'help("mgcv-package")'.
@@ -4634,12 +4617,12 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x103cf98d8>
+<environment: 0x103b07b90>
Estimated degrees of freedom:
-6.2955 total = 7.295494
+6.4351 total = 7.435071
-GCV score: 177.6966
+GCV score: 144.1236
>
> ## as above but with extra penalties on smooth terms:
> with(varechem, ordisurf(vare.mds, Baresoil, bubble = 5, col = "blue",
@@ -4650,25 +4633,25 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10187dad0>
+<environment: 0x1049a7298>
Estimated degrees of freedom:
-4.9207 total = 5.920718
+6.0761 total = 7.076141
-GCV score: 166.6991
+GCV score: 140.2187
>
> ## Cover of Cladina arbuscula
> fit <- with(varespec, ordisurf(vare.mds, Cla.arb, family=quasipoisson))
> ## Get fitted values
> calibrate(fit)
1 2 3 4 5 6 7
-21.7718381 8.0217184 3.7389252 2.3141513 6.4228083 5.4870157 6.7890109
+22.0644704 6.0132156 3.6350565 4.1019775 9.0031309 5.9203047 8.6398803
8 9 10 11 12 13 14
-11.4240724 0.6785602 31.1495927 16.5936957 9.5810013 5.5200242 29.3414323
+11.0718916 0.6562064 35.2281050 10.4346237 7.2900391 5.5710523 24.6503175
15 16 17 18 19 20 21
-23.4774998 29.9710379 7.0213117 15.7428646 2.7320035 0.8380256 3.4990451
+18.8754108 29.7285810 5.6159070 9.5869408 3.2876591 2.7112108 10.7832711
22 23 24
- 1.2362978 10.9537267 0.7443408
+ 3.0020769 9.8129184 7.3657528
>
> ## Plot method
> plot(fit, what = "contour")
@@ -4683,7 +4666,7 @@
>
> cleanEx()
-detaching ‘package:mgcv’, ‘package:MASS’
+detaching ‘package:mgcv’
> nameEx("orditkplot")
> ### * orditkplot
@@ -4806,7 +4789,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x106523200>
+<environment: 0x104aa7200>
Estimated degrees of freedom:
8.9275 total = 9.927492
@@ -4819,7 +4802,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x105decb18>
+<environment: 0x1069545c8>
Estimated degrees of freedom:
7.7529 total = 8.75294
@@ -4832,7 +4815,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10665fd78>
+<environment: 0x106aff948>
Estimated degrees of freedom:
8.8962 total = 9.89616
@@ -5563,44 +5546,8 @@
>
> data(varespec)
> vare.dist <- vegdist(wisconsin(varespec))
-> library(MASS) ## isoMDS
-> mds.null <- isoMDS(vare.dist, tol=1e-7)
-initial value 27.004018
-iter 5 value 19.627798
-iter 10 value 19.080657
-iter 15 value 18.587495
-iter 20 value 18.075166
-iter 25 value 17.922314
-iter 30 value 17.858977
-iter 35 value 17.823041
-iter 40 value 17.816456
-iter 45 value 17.812079
-iter 50 value 17.811040
-final value 17.811040
-stopped after 50 iterations
-> mds.alt <- isoMDS(vare.dist, initMDS(vare.dist), maxit=200, tol=1e-7)
-initial value 40.946864
-iter 5 value 35.233817
-iter 10 value 29.213576
-iter 15 value 27.267129
-iter 20 value 26.789268
-iter 25 value 26.326361
-iter 30 value 26.022929
-iter 35 value 25.583087
-iter 40 value 24.798014
-iter 45 value 24.186366
-iter 50 value 22.970805
-iter 55 value 22.791064
-iter 60 value 22.650504
-iter 65 value 22.192285
-iter 70 value 22.042446
-iter 75 value 22.016123
-iter 80 value 22.006493
-iter 85 value 22.003260
-iter 90 value 22.002696
-iter 95 value 22.002568
-final value 22.002559
-converged
+> mds.null <- monoMDS(vare.dist, y = cmdscale(vare.dist))
+> mds.alt <- monoMDS(vare.dist)
> vare.proc <- procrustes(mds.alt, mds.null)
> vare.proc
@@ -5608,7 +5555,7 @@
procrustes(X = mds.alt, Y = mds.null)
Procrustes sum of squares:
-476.9
+13.11
> summary(vare.proc)
@@ -5618,43 +5565,40 @@
Number of objects: 24 Number of dimensions: 2
Procrustes sum of squares:
- 476.8696
+ 13.10751
Procrustes root mean squared error:
- 4.457529
+ 0.739017
Quantiles of Procrustes errors:
Min 1Q Median 3Q Max
- 0.4414805 1.4921114 2.0623186 4.1475454 13.2852587
+0.02322413 0.27259237 0.34146895 0.64121655 2.23350654
Rotation matrix:
- [,1] [,2]
-[1,] 0.2217232 -0.9751096
-[2,] 0.9751096 0.2217232
+ [,1] [,2]
+[1,] -0.2427790 -0.9700816
+[2,] 0.9700816 -0.2427790
Translation of averages:
- [,1] [,2]
-[1,] 0.5428091 0.5073825
+ [,1] [,2]
+[1,] -9.65583e-18 7.915471e-19
Scaling of target:
-[1] 9.01332
+[1] 0.6736868
> plot(vare.proc)
> plot(vare.proc, kind=2)
> residuals(vare.proc)
18 15 24 27 23 19 22
- 1.9188822 0.7545389 7.8149973 3.8711767 2.3330069 0.8367255 1.9704564
+0.27803992 0.12847298 1.72993477 0.63690082 0.37244204 0.11829836 0.38555390
16 28 13 14 20 25 7
- 1.3378486 7.4734078 1.9821648 1.2580153 0.4414805 2.3028258 3.4903312
+0.27735743 1.22675827 0.65416375 0.25829720 0.02322413 0.35904126 0.28489676
5 6 3 4 2 9 12
- 5.6982274 1.5244639 1.9559438 4.9766513 13.2852587 1.8906924 1.3950539
+0.69505200 0.19983445 0.29397151 0.50089415 2.23350654 0.31836035 0.21622926
10 11 21
- 2.1424725 3.4187558 6.6343849
+0.32389663 0.56349530 0.77939208
>
>
>
> cleanEx()
-
-detaching ‘package:MASS’
-
> nameEx("pyrifos")
> ### * pyrifos
>
@@ -7064,7 +7008,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x1081c2098>
+<environment: 0x107a4b918>
Estimated degrees of freedom:
2 total = 3
@@ -7361,17 +7305,8 @@
>
> data(varespec)
> data(varechem)
-> library(MASS) ## isoMDS
> vare.dist <- vegdist(wisconsin(varespec))
-> vare.mds <- isoMDS(vare.dist)
-initial value 27.004018
-iter 5 value 19.627798
-iter 10 value 19.080657
-iter 15 value 18.587495
-iter 20 value 18.075166
-iter 20 value 18.064314
-final value 17.850149
-converged
+> vare.mds <- monoMDS(vare.dist)
> vare.points <- postMDS(vare.mds$points, vare.dist)
> vare.wa <- wascores(vare.points, varespec)
> plot(scores(vare.points), pch="+", asp=1)
@@ -7482,9 +7417,6 @@
>
>
> cleanEx()
-
-detaching ‘package:MASS’
-
> nameEx("wcmdscale")
> ### * wcmdscale
>
@@ -7541,7 +7473,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 101.713 1.044 103.58 0 0
+Time elapsed: 109.042 1.175 111.06 0 0
> grDevices::dev.off()
null device
1
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