[R] Questions about bwplot
Dear R-experts,
I have some questions about boxplots with lattice.
My data is similar as in the example below, I have two factors
(Goodness of Fit and Algorithms) and data values but in each panels the scales
are quite different, therefore the normal boxplots produced by
set.seed(1)
GOF - factor(rep(c(GOF1,GOF2,GOF3),each=40))
Alg - rep(factor(rep(c(A1,A2,A3,R1),each=10)),3)
Value - c(runif(40),rnorm(40),rnorm(30,10,3),rnorm(10,20,3))
test.data - data.frame(Alg=Alg,GOF=GOF,Value=Value)
library(lattice)
bwplot(Value ~ Alg | GOF, data = test.data, as.table=T, layout=c(1,3))
are not very informative.
Then I used
bwplot(Value ~ Alg | GOF, data = test.data, scale=list(relation=free),
as.table=T, layout=c(1,3))
from which my first question arises:
Is it possible to have no vertical space between the panels though they have
different y-scales when using the
argument scale=list(relation=free)?
Then I would like to modify the boxplot - actually I'm not interested so much
in the boxes of factor R1 (=random guess)
but would rather have a horizontal line in each panel at the median of R1 for
the given panel, and only the boxes for levels
A1, A2 and A3 - and the horizontal line I would like only if it would fall in
the plotting area when only plotting the boxes
for the levels A1, A2 and A3 (this means in the third panel the line should not
be there).
My attempt
test.data$ind - ifelse(Alg==R1,1,0)
my.boxpanel - function(x, y, subscripts, groups, ...) {
orig - groups[subscripts] == 0
panel.bwplot(x[orig], y[orig], ...)
panel.abline(h=median(y[!orig]))
}
bwplot(Value ~ Alg | GOF, data = test.data, scale=list(relation=free),
as.table=T, groups=ind, layout=c(1,3),panel=my.boxpanel,
drop.unused.levels=T,
xlim=c(A1,A2,A3),
ylim=list(c(0,1),c(-2,2),c(0,17)))
requires that I know the range of the yaxis and at the xaxis leaves space for
the box of R1. Can that be avoided?
Then my last question - I would like to emphasise the best factor=algorithm in
each panel by coloring its box.
However best means in the first two panels lowest median and in the last
panel highest median. Can this be done?
I managed it only when in all panels the lowest median box should be filled
with color.
trellis.device(color = FALSE)
my.boxpanel2 - function(x, y, subscripts, groups, ...) {
orig - groups[subscripts] == 0
medians-tapply(y[orig],x[orig],median)
medians2-medians[!is.na(medians)]
cols-grey((1-as.numeric(medians2==min(medians2))/3))
z-x[orig]
levels(z)-c(A1,A2,A3,NA)
w-y[orig]
panel.bwplot(z, w, fill=cols, ...)
panel.abline(h=median(y[!orig]))
}
bwplot(Value ~ Alg | GOF, data = test.data, scale=list(relation=free),
as.table=T, groups=ind, layout=c(1,3),panel=my.boxpanel2,
drop.unused.levels=T, xlim=c(A1,A2,A3),
ylim=list(c(0,1),c(-2,2),c(0,17)))
It would be great if you could help me with this plot!
Thanks in advance,
Klaus
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[R] [R-pkgs] new packages 'ICS' and 'ICSNP'
Dear R useRs, The new contributed packages 'ICS' and 'ICSNP' are available on CRAN. Descriptions: The 'ICS' package implements the 2 scatter matrix transformation to obtain an invariant coordinate system or independent components, depending on the underlying assumptions. The result of the transformation is an object of the S4 class ics which is provided by this package. Besides generic functions to create and work with ics objects the package contains also some scatter matrices and two tests for multinormality. The 'ICSNP' package contains tools for nonparametric multivariate analysis, including the estimation of location and shape as well as some tests for location and independence. Shape matrices from this package can be used as one of the scatter matrices needed in the package ICS whereas the tests of this package can be used for testing in the framework of invariant coordinates or independent components obtained from the package ICS. The parametric Hotelling’s T test serves as a reference for the nonparametric location tests. Suggestions, bug reports and other comments are very welcome. Best wishes, Klaus, Seija, Hannu and Dave -- Klaus Nordhausen Researcher Tampere School of Public Health FIN-33014 University of Tampere phone: +358 3 3551 7086 fax:+358 3 3551 6057 e-mail: [EMAIL PROTECTED] ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Tail area of sum of Chi-square variables
Hi,
thanks everyone!
pchisqsum() in the survey package does exactly what I was looking for!
Best wishes,
Klaus
Original-Nachricht
Datum: Thu, 29 Mar 2007 07:45:15 -0700 (PDT)
Von: Thomas Lumley [EMAIL PROTECTED]
An: S Ellison [EMAIL PROTECTED]
CC: [EMAIL PROTECTED], [EMAIL PROTECTED], r-help@stat.math.ethz.ch, [EMAIL
PROTECTED]
Betreff: Re: [R] Tail area of sum of Chi-square variables
The Satterthwaite approximation is surprisingly good, especially in the
most interesting range in the right tail (say 0.9 to 0.999). There is also
another, better, approximation with a power of a chi-squared distribution
that has been used in the survey literature.
However, since it is easy to write down the characteristic function and
perfectly feasible to invert it by numerical integration, we might as well
use the right answer.
-thomas
On Thu, 29 Mar 2007, S Ellison wrote:
I was wondering if there are any R functions that give the tail area
of a sum of chisquare distributions of the type:
a_1 X_1 + a_2 X_2
where a_1 and a_2 are constants and X_1 and X_2 are independent
chi-square variables with different degrees of freedom.
You might also check out Welch and Satterthwaite's (separate) papers on
effective degrees of freedom for compound estimates of variance, which led
to a thing called the welch-satterthwaite equation by one (more or less
notorious, but widely used) document called the ISO Guide to Expression of
Uncertainty in Measurement (ISO, 1995). The original papers are
B. L. Welch, J. Royal Stat. Soc. Suppl.(1936) 3 29-48
B. L. Welch, Biometrika, (1938) 29 350-362
B. L. Welch, Biometrika, (1947) 34 28-35
F. E. Satterthwaite, Psychometrika (1941) 6 309-316
F. E. Satterthwaite, Biometrics Bulletin, (1946) 2 part 6 110-114
The W-S equation - which I believe is a special case of Welch's somewhat
more general treatment - says that if you have multiple independent
estimated variances v[i] (could be more or less equivalent to your a_i X_i?)
with
degrees of freedom nu[i], the distribution of their sum is approximately a
scaled chi-squared distribution with effective degrees of freedom
nu.effective given by
nu.effective = sum(v[i])^2 / sum((v[i]^2)/nu[i] )
If I recall correctly, with an observed variance s^2 (corresponding to
the sum(v[i] above if those are observed varianes), nu*(s^2 /sigma^2) is
distributed as chi-squared with degrees of freedom nu, so the scaling factor
for quantiles would come out of there (depending whether you're after the
tail areas for s^2 given sigma^2 or for a confidence interval for sigma^2
given s^2)
However, I will be most interested to see what a more exact calculation
provides!
Steve Ellison
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[R] Tail area of sum of Chi-square variables
Dear R experts, I was wondering if there are any R functions that give the tail area of a sum of chisquare distributions of the type: a_1 X_1 + a_2 X_2 where a_1 and a_2 are constants and X_1 and X_2 are independent chi-square variables with different degrees of freedom. Thanks, Klaus -- Feel free - 5 GB Mailbox, 50 FreeSMS/Monat ... __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] wireplot margins and additional z-axis
Dear Deepayan, sorry for not being clear - but my problem has nothing to do with the aspect. If I create the eps the following way library(lattice) plot.vol- wireframe(volcano, aspect = c(1,1.5), scales=list(arrows=F),zlab=list(Z-axis,rot=90)) postscript(example_plot_3.eps, width = 14.0/2.54, height = 19.0/2.54, horizontal = FALSE, onefile = FALSE,paper=special) trellis.par.set(axis.line,list(alpha=1,col=1,lty=1,lwd=1)) print(plot.vol) dev.off() The plot is still not in the left bottom corner of the file. There is a lot of space below the outer box line. If I include this eps in latex it will also include this space and if I put for example the figure caption below it I have this huge gap between actual graph and caption. And for comparison, if I create with xyplot an eps like postscript(example_plot_4.eps, width = 14.0/2.54, height = 19.0/2.54, horizontal = FALSE, onefile = FALSE,paper=special) Depth - equal.count(quakes$depth, number=8, overlap=.1) plot.depth-xyplot(lat ~ long | Depth, data = quakes) update(trellis.last.object(), strip = strip.custom(strip.names = TRUE, strip.levels = TRUE), par.strip.text = list(cex = 0.75), aspect = iso) print(plot.depth) dev.off() the figure is really in the left bottom corner and included in latex has not that gap between caption and actual figure. I hope this describes my problem better. Klaus On 9/12/06, Klaus Nordhausen [EMAIL PROTECTED] wrote: Dear Deepayan, thanks for your reply, the change of the aspect does however not solve my problem with the space below the graph on the .eps I attached the .eps (still with the old aspect) so that it is maybe clearer what my problem is. No, it's not clearer; this is basically the same EPS that I got, so it gives me no new information. What do you get with the new aspect? If it's not what you want, you'll have to explain what you want more clearly. Also, don't make the panel borders transparent, as it makes it difficult to understand what's going on. Deepayan Any other suggestions? Klaus Dear R experts, it would be very kind if you could help me with two wireplot problems. First, when I make a wireplot and transform it into an .eps using the postscript function the eps-file leaves always a lot of space below the plot, as if it would leave space for a legend or something like that. How can i get the plot into the bottom corner without the space below? The space is not there when I just display the plot in R on my screen (I use R.2.3.1 on Windows XP). Or in general, how can I get the margins on all sides as small as possible since I wnat to include the eps into a report and do not need the space around. The following code has the space on the eps: library(lattice) plot.vol - wireframe(volcano, aspect = 1, scales=list(arrows=F) ,zlab=list(Z-axis,rot=90)) Perhaps you want something like aspect = c(1, 1.5) instead. postscript(example_plot.eps, width = 14.0/2.54, height = 19.0/2.54, horizontal = FALSE, onefile = FALSE,paper=special) trellis.par.set(axis.line,list(alpha=1,col=1,lty=0,lwd=1)) print(plot.vol) dev.off() Secondly, is it possible to add to the wireplot a further z-axis. I found only how to choose at which veritcal line I want the tickmarks and label, but is it also possible to have it at two vertical lines? No (but it shouldn't be too hard to add that feature; I'll have to check). Deepayan -- Echte DSL-Flatrate ab 0,- Euro* http://www.gmx.net/de/go/dsl __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] wireplot margins and additional z-axis
Dear R experts, it would be very kind if you could help me with two wireplot problems. First, when I make a wireplot and transform it into an .eps using the postscript function the eps-file leaves always a lot of space below the plot, as if it would leave space for a legend or something like that. How can i get the plot into the bottom corner without the space below? The space is not there when I just display the plot in R on my screen (I use R.2.3.1 on Windows XP). Or in general, how can I get the margins on all sides as small as possible since I wnat to include the eps into a report and do not need the space around. The following code has the space on the eps: library(lattice) plot.vol - wireframe(volcano, aspect = 1, scales=list(arrows=F) ,zlab=list(Z-axis,rot=90)) postscript(example_plot.eps, width = 14.0/2.54, height = 19.0/2.54, horizontal = FALSE, onefile = FALSE,paper=special) trellis.par.set(axis.line,list(alpha=1,col=1,lty=0,lwd=1)) print(plot.vol) dev.off() Secondly, is it possible to add to the wireplot a further z-axis. I found only how to choose at which veritcal line I want the tickmarks and label, but is it also possible to have it at two vertical lines? Thank you very much for your help! Klaus -- Echte DSL-Flatrate ab 0,- Euro* http://www.gmx.net/de/go/dsl __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
