[Vegan-commits] r1569 - in pkg/vegan: R man tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Apr 3 19:41:09 CEST 2011
Author: jarioksa
Date: 2011-04-03 19:41:09 +0200 (Sun, 03 Apr 2011)
New Revision: 1569
Added:
pkg/vegan/R/print.monoMDS.R
Modified:
pkg/vegan/man/monoMDS.Rd
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
basic methods for monoMDS: print, scores, plot
Added: pkg/vegan/R/print.monoMDS.R
===================================================================
--- pkg/vegan/R/print.monoMDS.R (rev 0)
+++ pkg/vegan/R/print.monoMDS.R 2011-04-03 17:41:09 UTC (rev 1569)
@@ -0,0 +1,39 @@
+### Method functions for monoMDS objects
+
+`print.monoMDS` <-
+ function(x, ...)
+{
+ cat("\nCall:\n")
+ cat(deparse(x$call), "\n\n")
+ modlab <- switch(x$model,
+ global = "Non-metric",
+ local = "Local non-metric",
+ linear = "Linear",
+ hybrid = "Hybrid")
+ cat(paste(modlab, "Multidimensional Scaling\n"))
+ cat("Dimensions:", x$ndim, "\n")
+ cat("Stress: ", x$stress)
+ if (x$isform == 2)
+ cat("(type 2)")
+ cat("\n")
+ stoplab <- switch(x$icause,
+ "Maximum number of iteration reached",
+ "Stress nearly zero",
+ "Stress nearly unchanged",
+ "Scale factor of gradient nearly zero")
+ cat("Stopped after ", x$iters, " iterations: ", stoplab, "\n", sep="")
+ invisible(x)
+}
+
+`scores.monoMDS` <-
+ function(x, ...)
+{
+ x$points
+}
+
+`plot.monoMDS` <-
+ function(x, choices = c(1,2), type = "t", ...)
+{
+ ordiplot(x, display = "sites", choices = choices, type = type, ...)
+}
+
Modified: pkg/vegan/man/monoMDS.Rd
===================================================================
--- pkg/vegan/man/monoMDS.Rd 2011-04-03 15:07:51 UTC (rev 1568)
+++ pkg/vegan/man/monoMDS.Rd 2011-04-03 17:41:09 UTC (rev 1569)
@@ -1,5 +1,8 @@
\name{monoMDS}
\alias{monoMDS}
+\alias{print.monoMDS}
+\alias{scores.monoMDS}
+\alias{plot.monoMDS}
\title{
Kruskal's Non-metric Multidimensional Scaling
@@ -12,6 +15,8 @@
monoMDS(dist, y, k = 2, model = c("global", "local", "linear", "hybrid"),
threshold = 0.8, maxit = 200, weakties = TRUE, stress = 1,
scaling = TRUE, smin = 0.00001, sfgrmin = 0.00001, sratmax=0.99999, ...)
+\method{scores}{monoMDS}(x, ...)
+\method{plot}{monoMDS}(x, choices = c(1,2), type = "t", ...)
}
\arguments{
@@ -45,7 +50,14 @@
drops below \code{sfgrmin}, or stress ratio goes over
\code{sratmax} (but is still \eqn{< 1}).}
- \item{\dots}{Other parameters to the functions (ignored).}
+ \item{x}{A \code{monoMDS} result.}
+ \item{choices}{Dimensions plotted.}
+
+ \item{type}{The type of the plot: \code{"t"} for text, \code{"p"}
+ for points, and \code{"n"} for none.}
+
+ \item{\dots}{Other parameters to the functions (ignored in
+ \code{monoMDS}, passed to graphical functions in \code{plot}.).}
}
\details{
@@ -77,7 +89,11 @@
\code{\link[smacof]{smacofSym}}, \code{\link[ecodist]{nmds}}. }
\examples{
-##
+data(dune)
+dis <- vegdist(dune)
+m <- monoMDS(dis, model = "loc")
+m
+plot(m)
}
\keyword{ multivariate }
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-04-03 15:07:51 UTC (rev 1568)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-04-03 17:41:09 UTC (rev 1569)
@@ -1,8 +1,8 @@
-R version 2.13.0 alpha (2011-03-28 r55109)
+R version 2.13.0 beta (2011-04-03 r55279)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
-Platform: x86_64-unknown-linux-gnu (64-bit)
+Platform: x86_64-apple-darwin10.7.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -22,7 +22,7 @@
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> library('vegan')
-This is vegan 1.18-26
+This is vegan 1.18-28
>
> assign(".oldSearch", search(), pos = 'CheckExEnv')
> cleanEx()
@@ -2934,22 +2934,22 @@
Coefficients:
Estimate Std. Error
-hump 5.3766e+02 3.3528e+01
-scale 1.8394e+01 1.7472e+00
-alpha 2.4233e+06 7.7206e+06
+hump 5.3767e+02 3.3533e+01
+scale 1.8393e+01 1.7634e+00
+alpha 9.2294e+06 3.4044e+07
Dispersion parameter for poisson family taken to be 1
-Deviance 41.44826 with 11 residual degrees of freedom
-AIC: 96.3778 BIC: 98.29497
+Deviance 41.44821 with 11 residual degrees of freedom
+AIC: 96.37774 BIC: 98.29492
Correlation of Coefficients:
hump scale
-scale -0.21
-alpha -0.02 0.01
+scale -0.20
+alpha -0.05 -0.14
Diagnostics from nlm:
-Number of iterations: 79, code: 2
+Number of iterations: 87, code: 5
> plot(sol)
> # confint is in MASS, and impicitly calls profile.humpfit.
> # Parameter 3 (alpha) is too extreme for profile and confint, and we
@@ -2959,8 +2959,8 @@
> confint(sol, parm=c(1,2))
Waiting for profiling to be done...
2.5 % 97.5 %
-hump 494.14179 607.25654
-scale 15.17642 22.02868
+hump 494.14239 607.25824
+scale 15.17635 22.02856
>
>
>
@@ -3560,6 +3560,35 @@
>
>
> cleanEx()
+> nameEx("monoMDS")
+> ### * monoMDS
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: monoMDS
+> ### Title: Kruskal's Non-metric Multidimensional Scaling
+> ### Aliases: monoMDS print.monoMDS scores.monoMDS plot.monoMDS
+> ### Keywords: multivariate
+>
+> ### ** Examples
+>
+> data(dune)
+> dis <- vegdist(dune)
+> m <- monoMDS(dis, model = "loc")
+> m
+
+Call:
+monoMDS(dist = dis, model = "loc")
+
+Local non-metric Multidimensional Scaling
+Dimensions: 2
+Stress: 0.07596768
+Stopped after 72 iterations: Stress nearly unchanged
+> plot(m)
+>
+>
+>
+> cleanEx()
> nameEx("mrpp")
> ### * mrpp
>
@@ -4668,7 +4697,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x467ea80>
+<environment: 0x102895988>
Estimated degrees of freedom:
6.2955 total = 7.295494
@@ -4684,7 +4713,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x66d7a58>
+<environment: 0x105c32108>
Estimated degrees of freedom:
4.9207 total = 5.920718
@@ -4840,7 +4869,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x47d8f80>
+<environment: 0x1060b2ae8>
Estimated degrees of freedom:
8.9275 total = 9.927492
@@ -4853,7 +4882,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x6d9e7f8>
+<environment: 0x1068ae078>
Estimated degrees of freedom:
7.7529 total = 8.75294
@@ -4866,7 +4895,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x711dbb8>
+<environment: 0x1068a9778>
Estimated degrees of freedom:
8.8962 total = 9.89616
@@ -6902,7 +6931,7 @@
Salrep 0.7118892 8.654457e-02
Achmil 1.5948052 8.449914e-01
Poatri 0.7367577 7.099165e-01
-Chealb 1.9479718 6.661338e-16
+Chealb 1.9479718 2.220446e-16
Elyrep 0.5160932 5.135604e-01
Sagpro 1.3031750 1.019154e+00
Plalan 1.7013794 6.393173e-01
@@ -7583,7 +7612,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x816faf0>
+<environment: 0x1073cfd80>
Estimated degrees of freedom:
2 total = 3
@@ -8027,13 +8056,13 @@
> ## Eigevalues are numerically similar
> ca$CA$eig - ord$eig
CA1 CA2 CA3 CA4 CA5
--7.771561e-16 -2.220446e-16 6.106227e-16 -3.608225e-16 -1.110223e-16
+ 9.992007e-16 -6.106227e-16 8.881784e-16 -2.775558e-17 2.220446e-16
CA6 CA7 CA8 CA9 CA10
- 1.387779e-17 9.714451e-17 1.387779e-17 2.775558e-17 1.318390e-16
+ 9.714451e-17 9.714451e-17 4.163336e-17 -1.387779e-17 8.326673e-17
CA11 CA12 CA13 CA14 CA15
- 9.714451e-17 6.938894e-18 -6.938894e-18 3.122502e-17 0.000000e+00
+ 7.632783e-17 1.040834e-16 -2.081668e-17 4.510281e-17 1.908196e-17
CA16 CA17 CA18 CA19
--3.295975e-17 2.428613e-17 2.862294e-17 5.637851e-18
+-1.908196e-17 0.000000e+00 7.025630e-17 2.125036e-17
> ## Configurations are similar when site scores are scaled by
> ## eigenvalues in CA
> procrustes(ord, ca, choices=1:19, scaling = 1)
@@ -8042,7 +8071,7 @@
procrustes(X = ord, Y = ca, choices = 1:19, scaling = 1)
Procrustes sum of squares:
- 0
+-4.263e-14
> plot(procrustes(ord, ca, choices=1:2, scaling=1))
> ## Reconstruction of non-Euclidean distances with negative eigenvalues
@@ -8060,7 +8089,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 55.898 0.306 56.327 0 0
+Time elapsed: 112.988 1.253 114.876 0 0
> grDevices::dev.off()
null device
1
More information about the Vegan-commits
mailing list