RE: [R] statistical significance test for cluster agreement
Like you said, such kind of test will not give me anything that Rand index does not, except for p-value. The null hypothesis, in my case, is that clustering results does not match a different clustering, that someone alse did on the same data. And I do believe that this hypothesis is valid. Basicly, it's not that different from chi-squared goodness of fit test which check whether or not my data comes from particular distribution. With an exception that I don't know how to do chi-squared test in this case :) --- Liaw, Andy [EMAIL PROTECTED] wrote: But what would such a test do that the rand index does not? Would you interpret the p-value from such a test, if exists, to have the meaning that a real test of hypothesis has? AFAIK you basically need to have the hypotheses pinned down even before you see any data, for the inference to be valid. Is that possible with clustering? Just my $0.02... Andy From: Alexander Sirotkin [at Yahoo] I was wondering, whether there is a way to have statistical significance test for cluster agreement. I know that I can use classAgreement() function to get Rand index, which will give me some indication whether the clusters agree or not, but it would be interesting to have a formal test. Thanks. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan as Banyu) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Scaling of font sizes in layout()
Hi all,
In the following example,
#--EXAMPLE--
test - function(subfigure)
{
plot(c(1:10),c(1:10),cex=4)
text(1,9,subfigure,cex=10)
}
m - matrix(c(1,2,5,5,3,4,5,5),4,2)
layout(m)
test(a)
test(b)
test(c)
test(d)
test(e)
#---
Is it possible to have the font (a,b,...,e) and pch sizes (including the
axis-label, tick and tick-label sizes) scaled proportionally with the
size of each plot when I put multiple plots on the same page?
Thanks in advance!!
Regards
Tempo
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[R] Job Vacancy
www.kssg.com a pricing consulatancy based in Manchester (UK) are seeking an
experienced statistical analyst.
Candidates must be eligible to work in the EU. If you are interested please
send an updated CV to [EMAIL PROTECTED] .
Company Overview
KSS is a leading provider of pricing and revenue management systems for the
Retail and Petroleum sectors. Our business applications help our clients get
more out of their existing pricing strategies, as well as improve the
efficiency and productivity of their pricing processes, enabling them to
achieve sustainable net profit improvements and increased market share.
KSS' solutions are the result of many years of research into price
management and optimisation techniques, and can quantify the impact of
pricing and promotional activities on consumer demand, revenues and profit.
Using a deep understanding of consumer behaviour, clients can apply their
pricing policy and determine pricing and promotional campaigns that maximize
profit for given revenue goals - all within a carefully managed pricing
image.
KSS' solutions have proven to deliver immediate and sustainable profit
improvements, and are implemented within a number of successful retail
companies throughout the world.
With over 50% of the company engaged in research and development, we are
continually enhancing our products to meet the requirements of our
customers. Combined with our solid understanding of marketing and
merchandizing we deliver business solutions to enable our customers to meet
their strategic goals more profitably.
Job Description
We require an experienced statistician to join our existing research team of
statisticians and mathematical programmers.
The work done by the research team is very varied and covers the entire
product life cycle from initial design through to deployment and customer
support. In addition to supporting product development we sometimes
undertake specific consultancy projects for retail clients. There is
considerable scope for tailoring the job description to suit a candidates
particular interests and preferences. It is likely to involve some or all of
the following:
* Mathematical modelling for product development team. This
involves enhancing current techniques or researching new ones for our
current or future business applications.
* Provide statistical support to operations team during
product trials or deployment. Typically work includes analysing pricing
data sets (price elasticity modelling) for retail and petroleum sectors.
Analyse feasibility and risks of applying particular techniques to a given
data set.
* Lead, or assist with, statistical consultancy projects on
behalf of retail clients. Present results as a report or in person.
Desirable Skills and Experience
* Good degree in Statistics or other maths related subject.
* Postgraduate degree (MSc or PhD) would be an advantage.
* Commercial experience within the pricing industry (although
not essential)
* Previous experience within retail pricing would be very
valuable
* At least two years experience in applying statistics to
'real' data.
* Strong analytical skills
* Team player
* Experience in analysing and making inferences from complex
data sets.
* Excellent communication and interpersonal skills.
* Understanding of the issues involved in software
development.
* Good presentation skills
* Experience with SQL an advantage
Statistical Methods
The ideal candidate would have experience in the majority of the following
statistical methods:
* Statistical tools such as R, S-Plus or Matlab.
* Forecasting techniques
* Mixed effects models
* Clustering techniques
* Econometric models (price elasticity modelling)
* Time series analysis
* Regression analysis
* Multivariate methods
* Bayesian statistics/inference
Dr Wayne R. Jones
Senior Statistician / Research Analyst
KSS Limited
St James's Buildings
79 Oxford Street
Manchester M1 6SS
Tel: +44(0)161 609 4084
Mob: +44(0)7810 523 713
KSS Ltd
Seventh Floor St James's Buildings 79 Oxford Street Manchester M1 6SS England
Company Registration Number 2800886
Tel: +44 (0) 161 228 0040 Fax: +44 (0) 161 236 6305
mailto:[EMAIL PROTECTED]http://www.kssg.com
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[R] GLMM
Dear all, I'm working with count data following over-dispersed poisson distribution and have to work with mixed-models on them (like proc GENMOD on SAS sys.). I'm still not to sure about what function to use. It seems to me that a glmmPQL will do the job I want, but I'll be glad if people who worked on this type of data can share what they learned. Thanks for your time. simon [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Problems with postscript output
Hi all! I have a little problem with saving plots to file. I use the command postscript() followed by the plotting command and a dev.off(). When I then look at the resulting image saved to disk, some of the axis labels are missing (see attached image). Is there a way to fix this. Yours, -- Frank G. Zoellner AG Angewandte Informatik Technische Fakultat Universitat Bielefeld phone: +49(0)521-106-2951 fax: +49(0)521-106-2992 email: [EMAIL PROTECTED] distclassreschi2.eps Description: PostScript document __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] significance testing under sampling from small finite populations
Dear All, Are there recommended functions to test for (exact) significance when the samples are drawn from small finite populations (which sometimes are not much bigger than the sample)? I am looking for - differences in central tendency - differences of proportions - difference in distributions My current application would be on unpaired comparision of discrete (6-valued) questionaire data, but I would also appreciate pointers to functions for continuous data or paired comparisions. Thanks for any help Best regards Jens Oehlschlägel -- __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] colour scheme in: plot(survfit.model)
Dear All, I would like to ask a question on the colour scheme I can specify for a plot(survfit.model). I have four lines of Drosophila, kept at 3 different temperatures. About 100 individuals per line and temperature were scored, no censoring. the data looks like: linetempday status line1 18 23 1 . My model (quite trivial) is like: surv.model-survfit(Surv(day, status)~line+temp, mydata) My problem comes when I: plot(surv.model,col=1:4) The plot shows three main groupings, because temperature affects longevity in drosophila. The problem is that the colour used for line1 at temperature 18C is not the same for line1 at temperature 28C, which I find extremely confusing. How can I specify to keep the same colour for the same line across the plot? regards, Federico Calboli -- = Federico C. F. Calboli Dipartimento di Biologia Via Selmi 3 40126 Bologna Italy tel (+39) 051 209 4187 fax (+39) 051 251 4286 f.calboli at ucl.ac.uk __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problems with postscript output
This is not a PS problem. The barplot you made has its horizontl axis
suppressed by default. See argument axis.lty in ?barplot
Joris
Frank Gerrit Zoellner wrote:
Hi all!
I have a little problem with saving plots to file.
I use the command postscript() followed by the plotting command and a dev.off().
When I then look at the resulting image saved to disk, some of the axis labels are missing (see attached image). Is there a way to fix this.
Yours,
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--
==
Joris De Wolf
CropDesign N.V.
Plant Evaluation Group
Technologiepark 3
B-9052 Zwijnaarde
Belgium
Tel. : +32 9 242 91 55
Fax : +32 9 241 91 73
==
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[R] High/low level: Plot 2 time series with different axis (left and ri ght)
Sun, 14 Mar 2004, Jan Verbesselt wrote:
Dear R specialists,
I have two time series in a data.frame and want to plot them in the same
plot(), with the left axis scaled to time series 1 (-700,0) and the
right axis scaled to time series 2 (-0.2, 0.4).
plot(timeserie1)
lines(timeserie2, col=c(2)) = this one should be scaled differently
with a new axis on the right handside.
How can these be visualised such that the fit is optimal for
visualisation of the two time series? Which commands can I use?
I have composed a simple R function to do this. See usage example in the function
description.
##
## Description: A simple function which plots two time series on one plot where
##the series can have different value intervals over the same time interval.
## Usage: ts.plot.2Axis(xleft, xright)
## Arguments: xleft is the time series for the left vertical axis and xright
## is for the right axis. xleft and xright are defined as time series with
## the 'ts' function in package ts.
## ts.plot function must be available, do library(ts) to ensure this if
## necessary.
## In addition the usual 'ts.plot' and 'plot' parameters can be set
## directly (mar, main, xlab, ylab, lwd) or through gpars as in ts.plot.
## Also parameter digits is the preferred number of decimal digits on right
## axis and ticks is the preferred number of tick marks on right axis.
## Details: The time series for the right vertical axis is scaled with a simple
## rule of thumb scaling.
## The ts.plot function is used to plot the series.
## Value: None.
## Note: When scaling is not acceptable try switching the series parameters.
## If a ylabel is to be set it is here only possible for the left axis.
## See also: 'ts.plot', 'ts', 'legend'.
## Author and date: Hauksson, Bjorn Arnar. March 2004.
## Example:
## First paste this function into the R console or use 'source'.
#library(ts)
#data(UKLungDeaths)
#x - ldeaths
#y - fdeaths/mdeaths
#ts.plot.2Axis(x, y)
#legTxt - c(UK lung deaths, UK female/male deaths (rhs))
#legend(1976.5, 3950, legTxt, lty=c(1:2), col=c(1:2), lwd=2, bty=n)
##
ts.plot.2Axis - function(xleft, xright, digits=1, ticks=5,
mar=(c(4,4,4,4)+0.1), main=,
xlab=, ylab=, lwd=2, gpars=list()) {
# Settings for other parameters than those in the function parameter list
par(mar=mar)# Margins
k - ncol(as.matrix(xleft)) # Number of time series on left vertical scale
lty - c(1:(k+1)) # Line types
col - c(1:(k+1)) # Line colors
# Scale time series on right vertical axis
scale - (max(xleft)-min(xleft))/(max(xright)-min(xright))
xright2 - xright*scale
meanScale - mean(xleft) - mean(xright2)
xright2 - xright2 + meanScale
# Plot the series
ts.plot(xleft, xright2, lty=lty, col=col, main=main, ylab=ylab, xlab=xlab,
lwd=lwd, gpars=gpars)
# Add the right vertical axis labels
lab - seq(round(min(xright), digits), round(max(xright), digits),
length=ticks)
labAt - seq(min(xright2), max(xright2), length=ticks)
axis(side=4, labels=lab, at=labAt)
}
Comments and suggestions for this function would be helpful. A text file with the
function is available at my website,
http://www.bjornarnar.net/hugbunadur/R/ts.plot.2Axis.R
Best regards,
Bjorn Arnar Hauksson
bjorn.hauksson at sedlabanki.is
http://www.bjornarnar.net/english.php
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Re: [R] Problems with postscript output
Hi! I have a little problem with saving plots to file. I use the command postscript() followed by the plotting command and a dev.off(). When I then look at the resulting image saved to disk, some of the axis labels are missing (see attached image). Is there a way to fix this. R is trying to be smart about labels getting too close/overlap. Specify the graph to be a little wider and the labels will appear. cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/~pagel __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] combined random effects
Hi, I have the following linear mixed model: y(g,i,j,k,l)=u + L(g) + T(i) + D(j) + S(k) + (TS)(i,k) + error(g,i,j,k,l) where S(k) and the combined effect (TS)(i,k) are random effects whereas the rest are fixed effects. How do I specifiy the random part of the model formula in lme(), especially concerning the combined effect (TS)? Moreover, when I run the model as a fixed effect model I get the following error: lm(logMed ~ lenAA + TREAT + DYE + SLIDE + SLIDE:DYE,data=MA) Error in lm.fit(x, y, offset = offset, ...) : NA/NaN/Inf in foreign function call (arg 4) However, when I run the model with a reduced data set it works. In the first case I have 16512 data points whereas in the reduced case I use only have of it. Do I reach some internal threshold here? Thanks for help, joerg __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] statistical significance test for cluster agreement
[Apology to the list for the off-topic rant...] As it turned out, I also have a problem with LOF/GOL/etc. tests: I'd bet most of the time when such a test is carried out, it is _not_ the only test being done, but the p-values in the downstream analysis are almost never adjusted for this. How valid would the p-values be? IMHO, it's bad enough that users of statistical methods do things like this, but it's quite something else that statisticians do just the same, or even promote such tests. It's not a crime to do analysis like that, but to treat the p-values as if they actually are meaningful probably ought to be outlawed. OK, I better run for cover now... Andy From: Alexander Sirotkin [at Yahoo] [mailto:[EMAIL PROTECTED] Like you said, such kind of test will not give me anything that Rand index does not, except for p-value. The null hypothesis, in my case, is that clustering results does not match a different clustering, that someone alse did on the same data. And I do believe that this hypothesis is valid. Basicly, it's not that different from chi-squared goodness of fit test which check whether or not my data comes from particular distribution. With an exception that I don't know how to do chi-squared test in this case :) --- Liaw, Andy [EMAIL PROTECTED] wrote: But what would such a test do that the rand index does not? Would you interpret the p-value from such a test, if exists, to have the meaning that a real test of hypothesis has? AFAIK you basically need to have the hypotheses pinned down even before you see any data, for the inference to be valid. Is that possible with clustering? Just my $0.02... Andy From: Alexander Sirotkin [at Yahoo] I was wondering, whether there is a way to have statistical significance test for cluster agreement. I know that I can use classAgreement() function to get Rand index, which will give me some indication whether the clusters agree or not, but it would be interesting to have a formal test. Thanks. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan as Banyu) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. -- __ Do you Yahoo!? Yahoo! Finance Tax Center - File online. File on time. http://taxes.yahoo.com/filing.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] string problems ( grep and regepxr)
Recently working with strings and data I have found a small problem. Windows XP R 1.8.1 Reading data from a txt file with readLine. finding a specific line with grep command, all OK. but here comes the problem... After finding the correct line(s) i need to find a substring inside each string. In this case tabs I think it represented by \t in the grep command trying to use grep in each string it only returns 1 ... Afterwards I tried regexpr command it returns the correct position of the substring that I am looking for but it only reports the first one. does regexpr only returns the first one ? Partial example: d5 = load0004 node00140.050.01458 load0005 node00170.050.01458 load0006 node00190.050.01458 grep(\t,d5[1]) [1] 1 regexpr(\t,d5[1] [1] 9 attr(,match.length) [1] 1 any idea how to make regexpr return the several substrings ? or the grep and Am I missing anything obvious ? THanks in advance Marco Marques __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] wolfinger microarray normalization
Hi, concerning my earlier mail, maybe someone has noted from the variable names that I try to analyse mircoarrary experiments. Does anybody know of a R-implementation of the two-step mixed-model normalization procedure proposed by Wolfinger et al. (2001) J. Comput. Biol. 8:625-637? That would be great, best, joerg __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] string problems ( grep and regepxr)
On Wed, 24 Mar 2004, MMarques Power wrote: Recently working with strings and data I have found a small problem. Windows XP R 1.8.1 Reading data from a txt file with readLine. finding a specific line with grep command, all OK. but here comes the problem... After finding the correct line(s) i need to find a substring inside each string. In this case tabs I think it represented by \t in the grep command trying to use grep in each string it only returns 1 ... That says it is present in character element one. Do read the help page Value: For 'grep' a vector giving either the indices of the elements of 'x' that yielded a match or, if 'value' is 'TRUE', the matched elements. Afterwards I tried regexpr command it returns the correct position of the substring that I am looking for but it only reports the first one. does regexpr only returns the first one ? Yes. Partial example: d5 = load0004 node00140.050.01458 load0005 node00170.050.01458 load0006 node00190.050.01458 grep(\t,d5[1]) [1] 1 regexpr(\t,d5[1] [1] 9 attr(,match.length) [1] 1 any idea how to make regexpr return the several substrings ? or the grep and Am I missing anything obvious ? Telling us what you actually want to do! Would sapply(strsplit(d5, \t), length) be closer to what you have in mind? -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] loess parameters
Hi, I have been successfully using the loess function for normalisation of a 2D array set. We have recently improved the quality criteria for the data and the numbers of data points has been reduced to around from around 1000 to 700. Previously the following would return the loess normalised values for array$logratio but I am now getting an error: array - read.table(A1.txt, header=T, sep=\t) array$logratio-array$logs555-array$logs647 array$logav-(array$logs555+array$logs647)/2 library(modreg) loess2d-loess(logratio~x+y,data=array) array$logratio2DLoeNorm -array$logratio - predict(loess2d, array) Error in vector(double, length) : negative length vectors are not allowed I am assuming that this is due to a problem fitting the data at some locations and I have tried altering span without much success. Can anyone please advise ? With thanks Thomas __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] loess parameters
You are probably running out of memory address space. Can you 1) Try this in 1.9.0 beta which gives a more informative error message, and 2) Use traceback() and the debugging tools to locate the error more exactly. 3) Consider using the options to loess to reduce the load. Loess is not designed for smoothing a 2D grid and you appear only to want the fitted values at your grid. If so, try the fitted() extractor function. (Or the residual() extractor function if all you want are residuals.) On Wed, 24 Mar 2004, Thomas Jagoe wrote: Hi, I have been successfully using the loess function for normalisation of a 2D array set. We have recently improved the quality criteria for the data and the numbers of data points has been reduced to around from around 1000 to 700. Previously the following would return the loess normalised values for array$logratio but I am now getting an error: array - read.table(A1.txt, header=T, sep=\t) array$logratio-array$logs555-array$logs647 array$logav-(array$logs555+array$logs647)/2 library(modreg) loess2d-loess(logratio~x+y,data=array) array$logratio2DLoeNorm -array$logratio - predict(loess2d, array) Error in vector(double, length) : negative length vectors are not allowed I am assuming that this is due to a problem fitting the data at some locations and I have tried altering span without much success. Can anyone please advise ? With thanks Thomas __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] combined random effects
Joerg Schaber [EMAIL PROTECTED] writes: Hi, I have the following linear mixed model: y(g,i,j,k,l)=u + L(g) + T(i) + D(j) + S(k) + (TS)(i,k) + error(g,i,j,k,l) where S(k) and the combined effect (TS)(i,k) are random effects whereas the rest are fixed effects. How do I specifiy the random part of the model formula in lme(), especially concerning the combined effect (TS)? I think you should be able to specify this as random = ~ 1 | SLIDE/TREAT Moreover, when I run the model as a fixed effect model I get the following error: lm(logMed ~ lenAA + TREAT + DYE + SLIDE + SLIDE:DYE,data=MA) Error in lm.fit(x, y, offset = offset, ...) : NA/NaN/Inf in foreign function call (arg 4) However, when I run the model with a reduced data set it works. In the first case I have 16512 data points whereas in the reduced case I use only half of it. Do I reach some internal threshold here? You should get a different error message if you did reach a threshold. I'd offer to look at the problem in more detail except that I just learned that one of the main servers in the r-project.org domain (the one that serves as cran.us.r-project.org, among other things) has crashed and I need to get in to the office to check on it. -- Douglas Bates[EMAIL PROTECTED] Statistics Department608/262-2598 University of Wisconsin - Madisonhttp://www.stat.wisc.edu/~bates/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Rmpi and PBS
Please remove me from the mailing list -Original Message- From: [EMAIL PROTECTED] To: Shengqiao Li Cc: r-help Sent: 24/03/2004 10:10 AM Subject: Re: [R] Rmpi and PBS On Tue, 2003-12-30 at 08:39, Shengqiao Li wrote: Hello: Anybody knows how to run Rmpi through PBS (Portable Batch System) on a cluster computer. I'm using a supercomputer which require to submit jobs to PBS queue for dispatching. I tried use mpirun in my PBS script. But all my Rslaves are spawned to the same node. This is not desired. Any suggestions are welcome! Thanks in advance. This is a late reply, but perhaps still of interest to some. It looks as if this problem has been solved, though only integrated into LAM with release 7: http://www.lam-mpi.org/papers/hpcs2003/tm-implementation.pdf __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R][S] library question
Dear R and S+ People: Is it possible to take one of the R libraries and put it into S+ please? R Windows XP 1.8.1 S+ Version 6.2 Thanks in advance! Sincerely, Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R][S] library question
In some cases it is possible to port an R *package* to S-PLUS: people have done both that and the reverse. If you have some specific examples in mind we may be able to help you further. Since you are on Windows, it may not be easy unless you have the requisite tools (e.g. Visuall C++ and Fortran). On Wed, 24 Mar 2004, Erin Hodgess wrote: Is it possible to take one of the R libraries and put it into S+ please? R Windows XP 1.8.1 S+ Version 6.2 -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R][S] library question
Erin == Erin Hodgess [EMAIL PROTECTED]
on Wed, 24 Mar 2004 08:13:01 -0600 writes:
Erin Dear R and S+ People: Is it possible to take one of
Erin the R libraries and put it into S+ please?
libraries (i.e. a collection of compiled code): definitely not
as is.
However, I presume you mean packages.
There, it depends if the package only consists of S code (in the
R dialect). If yes, you often can use most, if not all of the
code in S+.
But do read the FAQ about S and R differences
and consider the fact that for graphics,
the step from R to S-plus is quite a bit of a downgrade,
and code usually will only work if it was written with back
portability in mind (back : to S+).
{read all of the above with a bit of humour ..}
Note that R is fully open source, so you can always port R
packages that contain compiled code and data sets, and doing so
can be easy -- but may be not at all:
The C API of R being quite rich nowadays,
you may have to work quite a bit on the source before you can
link the compiled code into S-Plus.
Regards,
Martin
Erin R Windows XP 1.8.1 S+ Version 6.2
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Re: [R] GLMM
At 11:17 2004-03-24, you wrote: I'm working with count data following over-dispersed poisson distribution and have to work with mixed-models on them (like proc GENMOD on SAS sys.). I'm still not to sure about what function to use. This is confusing: Proc GENMOD fits generalized linear models (GLM) and handles modelling of overdispersed Poisson data using quasi-likelihood (e.g. SCALE=P) or the negative binomial distribution (DIST=NEGBIN), but not generalized linear mixed models (GLMM). In R a GLM is fitted using the glm function, and specifying family=quasipoisson is the equivalent of SCALE=P in SAS. The negative binomial case is handled either by the negative.binomial family function (when the shape parameter is known) or the glm.nb function (if you want to estimate the shape by ML). Both negative.binomial and glm.nb are found in Venables and Ripley's MASS package. It seems to me that a glmmPQL will do the job I want, If GLMM is what you want, the functions glmmPQL (from MASS) or GLMM (from lme4, by Bates and co-workers) will most likely handle your needs. but I'll be glad if people who worked on this type of data can share what they learned. Thanks for your time. If you describe your data and what you'd like to do, someone may be able to help you. The MASS functions, and much more, are described in Venables and Ripley Modern Applied Statistics with S. GLMMs are described in e.g. Brown and Prescott Applied Mixed Models in Medicine, but it's very SAS oriented. //Henric __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] colors, lines, characters .... documentation
Hi, Very so often when i am plotting something, doing a histogram, or whatever i am struggling to find out which are the numbers for different colors, palette names, types of lines, symbols, etc. Is there any documentation on line with all these numbers / names and the associated symbol / color??? For example if i am using the command image it uses a palette from red to yellow, with red the lowest value, and yellow the highest value. What if i want a reverse palette, with green the lowest value and yellow middle values and red highest value??? Or much more simple, just yellow lowest value and red highest value??? Thank you for assistance, Monica __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] LM omitted variables test
Dear all, Does anybody know whether the (general) Lagrange Multiplier testing framework for restrictions on linear models has been implemented in some package? My goal is to test for omitted variables, i.e. restrictions of the kind beta_i=0, in the specification of an econometric model. There are some particular implementations in this fashion in the lmtest package (e,g, the bgtest() function, where the lagged residuals are taken as the omitted variable); before trying to adapt that code, I would like to check out if there are ready-to-use solutions available. Thanks in advance Giovanni Giovanni Millo Research Dept. Assicurazioni Generali SpA Ai sensi del D.Lgs.196/2003 si precisa che le informazioni contenute in questo messaggio sono riservate ed a uso esclusivo del destinatario. Qualora il messaggio in parola Le fosse pervenuto per errore, La invitiamo ad eliminarlo senza copiarlo e a non inoltrarlo a terzi, dandocene gentilmente comunicazione. Grazie.BRBRPursuant to Legislative Decree No. 196/2003, you are hereby informed that this message contains confidential information intended only for the use of the addressee. If you are not the addressee, and have received this message by mistake, please delete it and immediately notify us. You may not copy or disseminate this message to anyone. Thank you. [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] colors, lines, characters .... documentation
Hi, many questions at once there, but here some help regarding
*symbols*.
I've pasted a function plotSymbols() that shows all symbols available.
Note that the the symbols pch = 128 are system dependent so you
should not expect them to look the same on Windows, Mac and Unix. Try
also plotSymbols(TRUE). To turn of the click-bell do
'options(locatorBell=FALSE)' (see ?locator).
Cheers
Henrik
BEGIN code
plotSymbols - function(interactive=FALSE) {
ASCII - c(\000, sapply(1:255, function(i)
parse(text=paste(\\\,
structure(i,class=octmode), \,
sep=))[[1]]));
intToChar - function(i) {
ASCII[i %% 256 + 1];
}
interactive - interactive interactive();
i - 0:255;
ncol -16;
top - 3 + 2*interactive;
opar - par(cex.axis=0.7, mar=c(3,3,top,3)+0.1)
on.exit(par(opar))
plot(i%%ncol,1+i%/%ncol, pch=i, xlim=c(0,ncol-1), xlab=, ylab=,
axes=FALSE);
axis(1, at=0:15)
axis(2, at=1:16, labels=0:15*16, las=2)
axis(3, at=0:15)
axis(4, at=1:16, labels=0:15*16+15, las=2)
if (interactive) {
title(main=Click on a symbol to add it to the data frame. Click
in margin to quit!, cex.main=0.8, line=3.5);
}
if (interactive) {
df - list();
usr - par(usr);
ready - FALSE;
while (!ready) {
click - locator(n=1);
x - click$x;
y - click$y - 1;
ready - !(x 0.5 x 15.5 y 0.5 y 15.5);
if (!ready) {
x - round(x);
y - round(y);
z - 16*y + x;
ch - intToChar(z);
dec - as.character(z);
hex - intToHex(z);
oct - intToOct(z);
spc - paste(rep(0, 2-nchar(hex)), collapse=);
hex - paste(spc, hex, sep=);
spc - paste(rep(0, 3-nchar(oct)), collapse=);
oct - paste(spc, oct, sep=);
df$ch - c(df$ch , ch );
df$dec - c(df$dec, dec);
df$hex - c(df$hex, hex);
df$oct - c(df$oct, oct);
if (nchar(ch) == 0) ch - ;
spc - paste(rep( , 3-nchar(dec)), collapse=);
dec - paste(spc, dec, sep=);
cat(Selected ASCII character ', ch, ' , dec, 0x, hex,
\\, oct, \n,
sep=);
}
}
return(df);
}
invisible()
} # plotSymbols()
END code
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Monica
Palaseanu-Lovejoy
Sent: den 24 mars 2004 16:06
To: [EMAIL PROTECTED]
Subject: [R] colors, lines, characters documentation
Hi,
Very so often when i am plotting something, doing a histogram, or
whatever i am struggling to find out which are the numbers for
different colors, palette names, types of lines, symbols, etc. Is
there any documentation on line with all these numbers / names
and the associated symbol / color???
For example if i am using the command image it uses a palette
from red to yellow, with red the lowest value, and yellow the
highest
value. What if i want a reverse palette, with green the lowest value
and yellow middle values and red highest value??? Or much more
simple, just yellow lowest value and red highest value???
Thank you for assistance,
Monica
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do read the posting guide!
http://www.R-project.org/posting-guide.html
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[R] hierarchical clustering: stopping rule
I'm using 'agnes' from the 'cluster' package to cluster my data
hierarchically.
I need to find out the 'optimal' number of clusters.
In 'Finding Groups in Data: An Introduction to Cluster Analysis' Kaufman
and Rousseeuw refer to a strategy proposed by R. Mojena ('Hierarchical
grouping methods and stopping rules: An evaluation' (The Computer
Journal, 20(4), 1977).
Mojena describes group weighted average hierarchical clustering methods
with the following formula:
n_p n_q
d_is = d_ps + d_qs
n_i n_i
where i is the index for the new group to be formed out of groups p and q
and s represents a third group
d is the distance measure.
In every clustering step a_j = min_{im} (d_im)
My question now is:
are the values of agnes.object$heights identical to the a_j defined above?
(Despite of the fact that the heights are permutated for drawing)
I also read the publication of Lance and Williams who originally introduced the above notation but it didn't help ...
Thanks for any hint ...
Felix Salfner
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[R] line number of errors?
Is it possible to instruct R to output a line number when an error or warning is encountered in a source() file? sincerely, /iaw __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] First Variable in lm
Hi all,
I just cannot think of how to do it:
I want to take the first variable (column) of a data frame and regress
it against all other variables.
bla - function (dat) {
reg - lm(whateverthefirstofthevariablenamesis ~., data=dat)
return(reg)
}
What kind of function do I have to take instead of the
whateverthefirstofthevariablenamesis,
eval(), substitute(), get(), ...
to correctly compute this regression?
With lm(get(names(dat)[1] ~., data=dat) there are no errors, but the
first variable also shows up among the regressors.
Thanks for help.
Christian Hoffmann
--
Dr.sc.math.Christian W. Hoffmann,
http://www.wsl.ch/staff/christian.hoffmann
Mathematics + Statistical Computing e-mail: [EMAIL PROTECTED]
Swiss Federal Research Institute WSL Tel: ++41-44-73922- -77 (office)
CH-8903 Birmensdorf, Switzerland -11(exchange), -15 (fax)
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RE: [R] colors, lines, characters .... documentation
Hello,
-Original Message-
From: Monica Palaseanu-Lovejoy
[SMTP:[EMAIL PROTECTED]
Sent: Wednesday, March 24, 2004 4:06 PM
To: [EMAIL PROTECTED]
Subject: [R] colors, lines, characters documentation
Hi,
Very so often when i am plotting something, doing a histogram, or
whatever i am struggling to find out which are the numbers for
different colors, palette names, types of lines, symbols, etc. Is
there any documentation on line with all these numbers / names
and the associated symbol / color???
what I found to be quite useful is found in the library Hmisc.
(Thanks, Frank Harrell!)
library(Hmisc)
show.col()
show.pch()
And if you look at the definitions of these functions, it might be
quite easy to modify them for your exact needs.
Hope this helps,
Roland
+
This mail has been sent through the MPI for Demographic Rese...{{dropped}}
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Re: [R] snow documentation comments
On Tue, 23 Mar 2004, Ross Boylan wrote: There are a few points I found unclear or unmentioned in the snow documentation (mostly I looked at the cluster.html web page). I thought I'd mention them here. What is the start up environment for the children? -- My best guess at the answer is in parentheses Do they inherit shell variables? (no) Do they inherit variables set in R or other aspects of the R environment? (no) What directory does it start in? (the directory you are running in) What user are you? (same as original) I realize some of these answers might depend on the parallelization layer you are using, or whether you select the homogenous option. They do Number of nodes or number of children? -- I thought all the counts of nodes (e.g., in makeCluster(5)) were of the total nodes in the cluster, i.e., children + 1. However, I did a makeCluster(2) and I got 2 additional R processes running. Have I misunderstood the semantics, or is it essentially an implementation detail that the master node starts a new R process? makeCluster(2) creates a cluster of two processes that the master process uses. So there are a total of three processes. luke -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED] Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] line number of errors?
ivo == ivo welch [EMAIL PROTECTED] on Wed, 24 Mar 2004 10:49:55 -0500 writes: ivo Is it possible to instruct R to output a line number ivo Is it possible to instruct R to output a line number ivo when an error or warning is encountered in a source() ivo file? yes, it is possible, since R is a complete programming language, you can write a new version of source()... ;-) :-) Note that this feature is for free when using ESS (Emacs Speaks Statistics), and it's C-c C-l (or [Load Source File] entry from the 'iESS' or [Load File] from the 'ESS' menu) Regards, Martin __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] colors, lines, characters .... documentation
Stephane DRAY dray at biomserv.univ-lyon1.fr writes: [...] the colors used when you use number are those in palette: palette() [1] black red green3 bluecyanmagenta yellow gray plot(1:20,col=1:20) You can define your own palette with colors available in colors: palette(colors()[sample(1:657,20)]) palette() [...] plot(1:20,col=1:20) For the image function, you can enter your own vector of colors (by default, col = heat.colors(12)) and one way to define your colors is to use 'rgb' function with values for Red - Green - Blue. In conjunction with these sorts of manipulations you might also be interested in the color name -- hex code conversion functions previously posted on r-help and found at: http://maths.newcastle.edu.au/~rking/R/help/03a/7417.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] colors, lines, characters .... documentation
Here is a little function that will show available colors in groups
of 100 at a time.
I've only tested it in an X windows environment.
function (indx = 0:6)
{
for (ii in unique(indx)) {
is - 100 * ii + 1:100
if (min(is) length(colors())) {
cat(Maximum value of arg is, floor(length(colors())/100),
\n)
return(NULL)
}
foo - matrix(colors()[is], nrow = 10)
par(mar = c(3, 3, 0.25, 0.25))
plot(1:10, 1:10, type = n, yaxt = n, xlab = , ylab = )
axis(2, at = 1:10, lab = 10:1)
for (j in 1:10) {
for (i in 1:10) {
points(j, 11 - i, col = foo[i, j], pch = 16,
cex = 4)
text(j, 11 - i - 0.3, foo[i, j], cex = 0.8)
}
}
if (length(indx) 1 ii max(indx))
readline(paste(Currently showing group, ii, CR to continue ))
}
invisible(foo)
}
-Don
At 3:05 PM + 3/24/04, Monica Palaseanu-Lovejoy wrote:
Hi,
Very so often when i am plotting something, doing a histogram, or
whatever i am struggling to find out which are the numbers for
different colors, palette names, types of lines, symbols, etc. Is
there any documentation on line with all these numbers / names
and the associated symbol / color???
For example if i am using the command image it uses a palette
from red to yellow, with red the lowest value, and yellow the highest
value. What if i want a reverse palette, with green the lowest value
and yellow middle values and red highest value??? Or much more
simple, just yellow lowest value and red highest value???
Thank you for assistance,
Monica
__
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--
--
Don MacQueen
Environmental Protection Department
Lawrence Livermore National Laboratory
Livermore, CA, USA
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Re: [R] First Variable in lm
On Wed, 24 Mar 2004, Christian Hoffmann wrote:
Hi all,
I just cannot think of how to do it:
I want to take the first variable (column) of a data frame and regress
it against all other variables.
bla - function (dat) {
reg - lm(whateverthefirstofthevariablenamesis ~., data=dat)
return(reg)
}
What kind of function do I have to take instead of the
whateverthefirstofthevariablenamesis,
eval(), substitute(), get(), ...
to correctly compute this regression?
With lm(get(names(dat)[1] ~., data=dat) there are no errors, but the
first variable also shows up among the regressors.
Andy Liaw has pointed out that lm(dat) happens to work. But for a more
generalizable solution try
bla - function (dat)
eval(substitute(lm(foo ~., data=dat), list(foo=as.name(names(dat)[1]
which has the advantage of embedding a clean value of $call.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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RE: [R] statistical significance test for cluster agreement
Dear Alexander, On Wed, 24 Mar 2004, Alexander Sirotkin [at Yahoo] wrote: Like you said, such kind of test will not give me anything that Rand index does not, except for p-value. The null hypothesis, in my case, is that clustering results does not match a different clustering, that someone alse did on the same data. Usually, probability distributions (which you need to formulate null hypotheses) are over data, not over different methods applied to the same data. If you see two clusterings on the same data, they are identical, if they are 100% identical, and if not, then not. That's not a question of significance. What you seem to want is the assessment of stability of a clustering on given data by applying different cluster analyses, but this kind of problem is not treated in terms of significance. Different cluster analyses do different things, and there is no reason to expect that their results are the same apart from random variation (the only exception is random variation in running the same algorithm such as k-means from different random starting values - but that's not a problem to investigate if you *know* the cluster analysis method that produced your clustering). Christian *** Christian Hennig Fachbereich Mathematik-SPST/ZMS, Universitaet Hamburg [EMAIL PROTECTED], http://www.math.uni-hamburg.de/home/hennig/ ### ich empfehle www.boag-online.de __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] First Variable in lm
Christian Hoffmann christian.hoffmann at wsl.ch writes:
Hi all,
I just cannot think of how to do it:
I want to take the first variable (column) of a data frame and regress
it against all other variables.
bla - function (dat) {
reg - lm(whateverthefirstofthevariablenamesis ~., data=dat)
return(reg)
}
Andy has already given a particularly concise solution but if your
variable is not in first position then you could rearrange the
order of the variables to allow his solution or use this which works
for any specified position of the dependent variable:
data(longley)
lm( longley[,7] ~. , data = longley[,-7] )
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[R] how to customize .First.lib
Hi, I am looking for an elegant solution to the following problem. When I load a package, let's say ROracle, I want some custom actions to be done on top of what package's .First.lib does. In this specific example I want to open a connection to the only database I have around. And I don't see how this could be done: there seems to be no hooks in a couple of .First.lib functions I checked out, and there is no on.library.load() function to register a call-back too. It's just a nice to have, but I am curious to hear what people might suggest. Thanks, Vadim [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Ordered logit/probit
Hello everyone I am trying to fit an ordered probit/logit model for bank rating prediction. Besides polr() in MASS package which is not written especially for this as far as I know, do you know how else I can do this? I already found the modified polr () version on the Valentin STANESCU Enrst and Young Tel. 402 4000 -- The information contained in this communication is intended solely for the use of the individual or entity to whom it is addressed and others authorized to receive it. It may contain confidential or legally privileged information. If you are not the intended recipient you are hereby notified that any disclosure, copying, distribution or taking any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this communication in error, please notify us immediately by responding to this email and then delete it from your system. Ernst Young is neither liable for the proper and complete transmission of the information contained in this communication nor for any delay in its receipt. Note: If you have received a delivery failure report, it may be due to the change in the Ernst Young e-mail domain from eyi.com to ey.com. Could you please make the necessary amendment, if required, and resend the message. [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] First Variable in lm
First: Thanks to everyone who develops R, maintains r-help, and participates
in the list :)
This is a silly follow up question.
From Andy Liaw:
dat - data.frame(y=rnorm(10), x1=rnorm(10), x2=rnorm(10))
(Silly question - if the answer is on the lm or formula help page I didn't
get it:)
Why does lm | formula treat dat[,1] slightly differently than dat$y?
I see what it is doing - I am curious as to why:)
lm(dat$y ~ .,data = dat)
Call:
lm(formula = dat$y ~ ., data = dat)
Coefficients:
(Intercept) x1 x2
-0.08754 -0.04456 -0.16905
lm(dat[,1] ~ .,data = dat)
Call:
lm(formula = dat[, 1] ~ ., data = dat)
Coefficients:
(Intercept)y x1 x2
-5.266e-171.000e+004.121e-17 -3.274e-17
As Gabor Grothendieck pointed out:
lm(formula = dat[, 1] ~ ., data = dat[,-1])
works like
lm(formula = dat$y ~ ., data = dat)
Curious Minds Want to Know
Bob
-Original Message-
From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
Sent: Wednesday, March 24, 2004 12:51 PM
To: [EMAIL PROTECTED]
Subject: Re: [R] First Variable in lm
Christian Hoffmann christian.hoffmann at wsl.ch writes:
Hi all,
I just cannot think of how to do it:
I want to take the first variable (column) of a data frame and regress
it against all other variables.
bla - function (dat) {
reg - lm(whateverthefirstofthevariablenamesis ~., data=dat)
return(reg)
}
Andy has already given a particularly concise solution but if your
variable is not in first position then you could rearrange the
order of the variables to allow his solution or use this which works
for any specified position of the dependent variable:
data(longley)
lm( longley[,7] ~. , data = longley[,-7] )
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RE: [R] First Variable in lm
It isn't lm but terms.formula. Compare terms(dat$y ~ .,data = dat) terms(dat[, 1] ~ ., data = dat) Now as to why, exactly, see the C code in src/main/model.c. The short answer is that dat$y matches y, and dat[, 1] does not. (I am not at all sure the first is intentional.) On Wed, 24 Mar 2004, Baskin, Robert wrote: First: Thanks to everyone who develops R, maintains r-help, and participates in the list :) This is a silly follow up question. From Andy Liaw: dat - data.frame(y=rnorm(10), x1=rnorm(10), x2=rnorm(10)) (Silly question - if the answer is on the lm or formula help page I didn't get it:) Why does lm | formula treat dat[,1] slightly differently than dat$y? -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] binding vectors or matrix using their names
Hello list, I have two vectors x and x2: x=runif(10) x2=runif(10) and one vectors with their names : my.names=c(x,x2) I would like to cbind these two vectors using their names contained in the vector my.names. I can create a string with comma ncomma=paste(my.names,collapse=,) and now, I just need a function to transform this string into a adequate argument for cbind: cbind(afunction(ncomma)) Is there in R a function that can do the job ? If not, how can I do it ?? Thanks in advance, Sincerely. Stéphane DRAY -- Département des Sciences Biologiques Université de Montréal, C.P. 6128, succursale centre-ville Montréal, Québec H3C 3J7, Canada Tel : 514 343 6111 poste 1233 E-mail : [EMAIL PROTECTED] -- Web http://www.steph280.freesurf.fr/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] binding vectors or matrix using their names
?get to convert names into objects -Original Message- From: Stephane DRAY [mailto:[EMAIL PROTECTED] Sent: Wednesday, March 24, 2004 11:41 AM To: [EMAIL PROTECTED] Subject: [R] binding vectors or matrix using their names Hello list, I have two vectors x and x2: x=runif(10) x2=runif(10) and one vectors with their names : my.names=c(x,x2) I would like to cbind these two vectors using their names contained in the vector my.names. I can create a string with comma ncomma=paste(my.names,collapse=,) and now, I just need a function to transform this string into a adequate argument for cbind: cbind(afunction(ncomma)) Is there in R a function that can do the job ? If not, how can I do it ?? Thanks in advance, Sincerely. Stéphane DRAY -- Département des Sciences Biologiques Université de Montréal, C.P. 6128, succursale centre-ville Montréal, Québec H3C 3J7, Canada Tel : 514 343 6111 poste 1233 E-mail : [EMAIL PROTECTED] -- Web http://www.steph280.freesurf.fr/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo /r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] binding vectors or matrix using their names
I believe the syntax is result - do.call(cbind, as.list(my.names)) Haven't checked this on your example, though. - tom blackwell - u michigan medical school - ann arbor - On Wed, 24 Mar 2004, Stephane DRAY wrote: Hello list, I have two vectors x and x2: x=runif(10) x2=runif(10) and one vectors with their names : my.names=c(x,x2) I would like to cbind these two vectors using their names contained in the vector my.names. I can create a string with comma ncomma=paste(my.names,collapse=,) and now, I just need a function to transform this string into a adequate argument for cbind: cbind(afunction(ncomma)) Is there in R a function that can do the job ? If not, how can I do it ?? Thanks in advance, Sincerely. Stéphane DRAY -- Département des Sciences Biologiques Université de Montréal, C.P. 6128, succursale centre-ville Montréal, Québec H3C 3J7, Canada Tel : 514 343 6111 poste 1233 E-mail : [EMAIL PROTECTED] -- Web http://www.steph280.freesurf.fr/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] binding vectors or matrix using their names
Hi Tom, Your approach did not work, do.call(cbind, as.list(my.names)) [,1] [,2] [1,] x x2 but it helps me a lot to find the good one: do.call(cbind, as.list(parse(text=my.names))) Thanks, At 14:56 24/03/2004, Tom Blackwell wrote: I believe the syntax is result - do.call(cbind, as.list(my.names)) Haven't checked this on your example, though. - tom blackwell - u michigan medical school - ann arbor - On Wed, 24 Mar 2004, Stephane DRAY wrote: Hello list, I have two vectors x and x2: x=runif(10) x2=runif(10) and one vectors with their names : my.names=c(x,x2) I would like to cbind these two vectors using their names contained in the vector my.names. I can create a string with comma ncomma=paste(my.names,collapse=,) and now, I just need a function to transform this string into a adequate argument for cbind: cbind(afunction(ncomma)) Is there in R a function that can do the job ? If not, how can I do it ?? Thanks in advance, Sincerely. Stéphane DRAY -- Département des Sciences Biologiques Université de Montréal, C.P. 6128, succursale centre-ville Montréal, Québec H3C 3J7, Canada Tel : 514 343 6111 poste 1233 E-mail : [EMAIL PROTECTED] -- Web http://www.steph280.freesurf.fr/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Stéphane DRAY -- Département des Sciences Biologiques Université de Montréal, C.P. 6128, succursale centre-ville Montréal, Québec H3C 3J7, Canada Tel : 514 343 6111 poste 1233 E-mail : [EMAIL PROTECTED] -- Web http://www.steph280.freesurf.fr/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] snow documentation comments
On Wed, 2004-03-24 at 08:03, Luke Tierney wrote: On Tue, 23 Mar 2004, Ross Boylan wrote: There are a few points I found unclear or unmentioned in the snow documentation (mostly I looked at the cluster.html web page). I thought I'd mention them here. What is the start up environment for the children? -- My best guess at the answer is in parentheses Do they inherit shell variables? (no) Do they inherit variables set in R or other aspects of the R environment? (no) What directory does it start in? (the directory you are running in) What user are you? (same as original) I realize some of these answers might depend on the parallelization layer you are using, or whether you select the homogenous option. They do I've since realized they may also depend on the exact version of the package used (e.g., newer lams apparently have the ability to export environment variables) and the way it is invoked. Personally, I'd even find a single sentence saying explicitly that it depends clarifying. It would probably also be good to discuss the behavior of the socket-based communication, since that it supplied by the snow package. Information on the other interfaces would be nice too, but probably hazardous to provide accurately. I'll not for the record that my answers above are using Rmpi with lam/mpi 6.5.8-2 on Debian, running just on my local computer. And some of the answers are speculative! Number of nodes or number of children? -- I thought all the counts of nodes (e.g., in makeCluster(5)) were of the total nodes in the cluster, i.e., children + 1. However, I did a makeCluster(2) and I got 2 additional R processes running. Have I misunderstood the semantics, or is it essentially an implementation detail that the master node starts a new R process? makeCluster(2) creates a cluster of two processes that the master process uses. So there are a total of three processes. So work that is distributed via snow goes to the two processes only? __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] binding vectors or matrix using their names
Perhaps simler: x1 - 1:5 x2 - 2:7 xname - c(x1, x2) sapply(xname, get) x1 x2 [1,] 1 2 [2,] 2 3 [3,] 3 4 [4,] 4 5 [5,] 5 6 HTH, Andy From: Stephane DRAY Hi Tom, Your approach did not work, do.call(cbind, as.list(my.names)) [,1] [,2] [1,] x x2 but it helps me a lot to find the good one: do.call(cbind, as.list(parse(text=my.names))) Thanks, At 14:56 24/03/2004, Tom Blackwell wrote: I believe the syntax is result - do.call(cbind, as.list(my.names)) Haven't checked this on your example, though. - tom blackwell - u michigan medical school - ann arbor - On Wed, 24 Mar 2004, Stephane DRAY wrote: Hello list, I have two vectors x and x2: x=runif(10) x2=runif(10) and one vectors with their names : my.names=c(x,x2) I would like to cbind these two vectors using their names contained in the vector my.names. I can create a string with comma ncomma=paste(my.names,collapse=,) and now, I just need a function to transform this string into a adequate argument for cbind: cbind(afunction(ncomma)) Is there in R a function that can do the job ? If not, how can I do it ?? Thanks in advance, Sincerely. Stéphane DRAY -- Département des Sciences Biologiques Université de Montréal, C.P. 6128, succursale centre-ville Montréal, Québec H3C 3J7, Canada Tel : 514 343 6111 poste 1233 E-mail : [EMAIL PROTECTED] -- Web http://www.steph280.freesurf.fr/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Stéphane DRAY -- Département des Sciences Biologiques Université de Montréal, C.P. 6128, succursale centre-ville Montréal, Québec H3C 3J7, Canada Tel : 514 343 6111 poste 1233 E-mail : [EMAIL PROTECTED] -- Web http://www.steph280.freesurf.fr/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] binding vectors or matrix using their names
I think you are looking for the eval-parse-text idiom: eval(parse(text=paste(cbind(, paste(my.names, collapse=, ), Patrick Burns Burns Statistics [EMAIL PROTECTED] +44 (0)20 8525 0696 http://www.burns-stat.com (home of S Poetry and A Guide for the Unwilling S User) Stephane DRAY wrote: Hi Tom, Your approach did not work, do.call(cbind, as.list(my.names)) [,1] [,2] [1,] x x2 but it helps me a lot to find the good one: do.call(cbind, as.list(parse(text=my.names))) Thanks, At 14:56 24/03/2004, Tom Blackwell wrote: I believe the syntax is result - do.call(cbind, as.list(my.names)) Haven't checked this on your example, though. - tom blackwell - u michigan medical school - ann arbor - On Wed, 24 Mar 2004, Stephane DRAY wrote: Hello list, I have two vectors x and x2: x=runif(10) x2=runif(10) and one vectors with their names : my.names=c(x,x2) I would like to cbind these two vectors using their names contained in the vector my.names. I can create a string with comma ncomma=paste(my.names,collapse=,) and now, I just need a function to transform this string into a adequate argument for cbind: cbind(afunction(ncomma)) Is there in R a function that can do the job ? If not, how can I do it ?? Thanks in advance, Sincerely. Stéphane DRAY -- Département des Sciences Biologiques Université de Montréal, C.P. 6128, succursale centre-ville Montréal, Québec H3C 3J7, Canada Tel : 514 343 6111 poste 1233 E-mail : [EMAIL PROTECTED] -- Web http://www.steph280.freesurf.fr/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Stéphane DRAY -- Département des Sciences Biologiques Université de Montréal, C.P. 6128, succursale centre-ville Montréal, Québec H3C 3J7, Canada Tel : 514 343 6111 poste 1233 E-mail : [EMAIL PROTECTED] -- Web http://www.steph280.freesurf.fr/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] binding vectors or matrix using their names
Gefore anyone jumps on me, I fibbed: From: Liaw, Andy Perhaps simler: x1 - 1:5 x2 - 2:7 That should've been x2 - 2:6. (I mistyped the first time, but cut-and-pasted the wrong line...) xname - c(x1, x2) sapply(xname, get) x1 x2 [1,] 1 2 [2,] 2 3 [3,] 3 4 [4,] 4 5 [5,] 5 6 HTH, Andy From: Stephane DRAY Hi Tom, Your approach did not work, do.call(cbind, as.list(my.names)) [,1] [,2] [1,] x x2 but it helps me a lot to find the good one: do.call(cbind, as.list(parse(text=my.names))) Thanks, At 14:56 24/03/2004, Tom Blackwell wrote: I believe the syntax is result - do.call(cbind, as.list(my.names)) Haven't checked this on your example, though. - tom blackwell - u michigan medical school - ann arbor - On Wed, 24 Mar 2004, Stephane DRAY wrote: Hello list, I have two vectors x and x2: x=runif(10) x2=runif(10) and one vectors with their names : my.names=c(x,x2) I would like to cbind these two vectors using their names contained in the vector my.names. I can create a string with comma ncomma=paste(my.names,collapse=,) and now, I just need a function to transform this string into a adequate argument for cbind: cbind(afunction(ncomma)) Is there in R a function that can do the job ? If not, how can I do it ?? Thanks in advance, Sincerely. Stéphane DRAY -- Département des Sciences Biologiques Université de Montréal, C.P. 6128, succursale centre-ville Montréal, Québec H3C 3J7, Canada Tel : 514 343 6111 poste 1233 E-mail : [EMAIL PROTECTED] -- Web http://www.steph280.freesurf.fr/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Stéphane DRAY -- Département des Sciences Biologiques Université de Montréal, C.P. 6128, succursale centre-ville Montréal, Québec H3C 3J7, Canada Tel : 514 343 6111 poste 1233 E-mail : [EMAIL PROTECTED] -- Web http://www.steph280.freesurf.fr/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. -- __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problems with postscript output
On Wed, 24-Mar-2004 at 12:23PM +0100, Philipp Pagel wrote: | Hi! | | I have a little problem with saving plots to file. I use the command | postscript() followed by the plotting command and a dev.off(). | | When I then look at the resulting image saved to disk, some of the | axis labels are missing (see attached image). Is there a way to fix | this. | | R is trying to be smart about labels getting too close/overlap. Specify the | graph to be a little wider and the labels will appear. Looks as though that one's already taking up a whole page. Might be simpler to reduce the axis.cex a tad (assuming the missing ones are not more than 3 letters). HTH -- Patrick Connolly HortResearch Mt Albert Auckland New Zealand Ph: +64-9 815 4200 x 7188 ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~ I have the world`s largest collection of seashells. I keep it on all the beaches of the world ... Perhaps you`ve seen it. ---Steven Wright ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Status of Rmpi--Good with tweaks
I have some more good news and some questions. On Tue, 2004-03-23 at 20:50, Hao Yu wrote: Sorry. I have not been able to update Rmpi since the version 0.4-4 on R site. I don't think any version of Rmpi is on the R site at the moment. Minor aside: Also, it would be nice if the packages starting with R were consistent about whether it's R or r. Rmpi but rpvm is a little dissonant. Unfortunately, there seems to be no agreement. However, I have been using and testing Rmpi internally since 0.4-4. Now it is version 0.4-7. See the attached package. It requires R 1.8.1 (no more serialize package requirement) and works with the newest MPI-LAM versions 7. It will configure automatically if a rpm package from www.lam-mpi.org is used. I tested it on both Redhat 9 and Debian. At least it passed the package check without any warning on Redhat 9. Now the problem is that it may have some problems with the default lam coming with Debian system. This is the reason why I hesitate to release it to R. I'm happy to report the Rmpi 0.4-7 installs and works without a problem (or any necessary modification) on my Debian mostly testing system (it does have some unstable stuff, but in particular it has the older lam/mpi 6.5.8-2. version 7 has been held in unstable for 60 days because of some problems on alpha hardware). Note this is not quite the lam in the current stable Debian distro, which is at 6.5.6-6. I am also working on it to see if #ifdef can be used to work MPI 1.2 specs other than LAM-MPI. Hopefully in a couple of months, I am able to submit a stable version to R. Great. Thanks. I think it would be well worth making 0.4-7 available at http://www.stats.uwo.ca/faculty/yu/Rmpi/. I'll send you, off list, the hacks I made to get the thing (starting with 0.4-6) to compile with the MPI 1.2ish mpich. It didn't run, but at least it did compile and load at the end. By the way, I'm in the dark about (r)sprng. From some of the snow docs, I thought that was really snow's business. But your site notes that the Rmpi packages are withough SPRNG support. And Tony Rossini's pages (I think) had a slightly cryptic remark that SPRNG under MPI was a bit dicey. Regards, Hao PS: Rmpi should still work without serializing as long as native MPI calls are used. The serializing is mainly used to help moving an arbitrarily R object around. I don't completely follow that, since I don't control whether or not native MPI calls are used, as far as I know. Do you mean that Rmpi can be used alone OK, but if you use snow (or, I guess Rmpi calls oriented toward snow and the transmission of R objects) it will need the serialize facility (prior to R 1.8)? __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Status of Rmpi--Good with tweaks
Ross Boylan [EMAIL PROTECTED] writes:
By the way, I'm in the dark about (r)sprng. From some of the snow docs,
I thought that was really snow's business. But your site notes that the
Rmpi packages are withough SPRNG support. And Tony Rossini's pages (I
think) had a slightly cryptic remark that SPRNG under MPI was a bit
dicey.
SPRNG doesn't need to be invoked via MPI, but can be configured to use
it as the invocation/transport layer.
It shouldn't matter to SNOW in the least, or rpvm. I think it
shouldn't matter to Rmpi, but we won't have a cluster to play with for
a month or so.
Luke -- I've seen the gentle hints.
best,
-tony
--
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Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
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Re: [R] debugging a code
You also have carriage return as a debug command. I think
you are looking for:
?recover
Fred J. phddas at yahoo.com writes:
:
: Hello
: just learned HowTo but R, reminded me with the way
: Perl does it but with much less on-line commands, R
: AFAIK has n, c, Q and where and cann't debug outside
: the {}.
:
: 1) is there a more versatile/flexable debugging method
: for R?
:
: I have saved 2 functions in an ASCII file digfun.
: getdata function calls squash function and both
: use loops. In another file.R I have
:
: source(digfun)
: debug(getdata)
: data - getdata(c:/data/)
:
: Browse[1] c
: Error in if (d[i, V3] == d[i + 1, V3] d[i,
: V4] == d[i + 1, V4] :
: missing value where TRUE/FALSE needed
: : traceback()
: 2: squash(dt1)
: 1: getdata(c:/data/)
: :
: to dubug this I need to know the value of some
: variable at this particular loop/sub-fun loop case,
: and since the dubuger terminated by showing
: prompt, how then I am going to debug this error?
:
: thanks for helping
:
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Re: [R] Scaling of font sizes in layout()
Hi
Pisut Tempatarachoke wrote:
Hi all,
In the following example,
#--EXAMPLE--
test - function(subfigure)
{
plot(c(1:10),c(1:10),cex=4)
text(1,9,subfigure,cex=10)
}
m - matrix(c(1,2,5,5,3,4,5,5),4,2)
layout(m)
test(a)
test(b)
test(c)
test(d)
test(e)
#---
Is it possible to have the font (a,b,...,e) and pch sizes (including the
axis-label, tick and tick-label sizes) scaled proportionally with the
size of each plot when I put multiple plots on the same page?
When you have multiple figures, R tries to think for you and reduces the
base size of text. You can explicitly control this base size through
par(). Does the following slight modification of your example do what
you want?
test - function(subfigure)
{
plot(c(1:10),c(1:10),cex=4)
text(1,9,subfigure,cex=10)
}
m - matrix(c(1,2,5,5,3,4,5,5),4,2)
layout(m)
test(a)
test(b)
test(c)
test(d)
par(cex=1)
test(e)
Paul
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[R] http://cran.us.r-project.org/ inaccessible
For the last couple of days when I go to http://cran.us.r-project.org/ I see only the left-hand margin logo and table of contents. If I click on one of the links there, I get a timeout. Other sites (e.g., http://cran.stat.ucla.edu/) work fine for me. Lacking complete confidence this is a bug*, as well as any better notion of where to report this, I'm reporting it here. *I have had problems accessing one other site, http://www.oasis-open.org/, that is generally accessible. It has been suggested the problem is that oasis does not cope with congestion notifications (ECN) properly, so it's not clear whether this is my problem or the sites. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] if block and brackets
Hello
the maunal states When the if statement is not in a
block the else, if present, must appear on the same
line as statement1. Otherwise the new line at the end
of statement1 yields a syntactically complete
statement that is evaluated.
well, what is wrong with this if structure? I am
getting an error on the line where else is
thanks
if (exists(f)){
dt - read.csv(file.path(d,f),header=F)#data frame
builddl(dt,f)
else
for (i in dir(d)){
dt -
read.csv(file.path(c:/data,i),header=F)#data frame
an - sub(([^.]+)(\\..+),\\1, i))
builddl(dt,an)
}
}
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RE: [R] statistical significance test for cluster agreement
Christian, I think I understand your point, but I do not completely agree with you. I also did not describe my problem clear enough. If you see two clusterings on the same data, they are identical, if they are 100% identical, and if not, then not. What you are actually saying is that all values of Rand index for cluster agreement other then 1 inidicate that clusters do not agree. I believe that many people would disagree with this statement. Let me explain my problem in a little bit more detail. I have some classified data set. These classes were ontained using non-statistical methods. What I'm trying to do is run some clustering algorithm and compare it's results to this known classification. I think that this is not very different from calculating mean and comparing it to some known value. I think that is should be theoretically possible to use Rand index as a test statistic. Or maybe I'm missing something... __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] http://cran.us.r-project.org/ inaccessible
Ross Boylan [EMAIL PROTECTED] writes: For the last couple of days when I go to http://cran.us.r-project.org/ I see only the left-hand margin logo and table of contents. If I click on one of the links there, I get a timeout. Other sites (e.g., http://cran.stat.ucla.edu/) work fine for me. Lacking complete confidence this is a bug*, as well as any better notion of where to report this, I'm reporting it here. *I have had problems accessing one other site, http://www.oasis-open.org/, that is generally accessible. It has been suggested the problem is that oasis does not cope with congestion notifications (ECN) properly, so it's not clear whether this is my problem or the sites. cran.us.r-project.org is down temporarily. We're not sure exactly what happened but it looks like it was compromised. Please use another CRAN mirror for the next few days. That machine is also rsync.r-project.org and cvs.r-project.org. The latter isn't very important to those not on the core development team but it is very important to us and I have been working all afternoon to bring the archive back up on another machine. I think I have that now. Rsync and CRAN mirror will follow tomorrow. -- Douglas Bates[EMAIL PROTECTED] Statistics Department608/262-2598 University of Wisconsin - Madisonhttp://www.stat.wisc.edu/~bates/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] if block and brackets
what is wrong with this if structure? I am
getting an error on the line where else is
thanks
if (exists(f)){
dt - read.csv(file.path(d,f),header=F)#data frame
builddl(dt,f)
else
The block started by if(...){ isn't complete - it needs a matching }
before it is. As such, the else is just hanging by itself. An else
with no corresponding if is a syntax error. This would be correct
(UNTESTED)
if (exists(f)){
dt - read.csv(file.path(d,f),header=F)#data frame
builddl(dt,f)
}
else
Cheers
Jason
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Re: [R] colors, lines, characters .... documentation
On 24 Mar 2004 at 15:05, Monica Palaseanu-Lovejoy wrote:
Hi,
Very so often when i am plotting something, doing a histogram, or
whatever i am struggling to find out which are the numbers for
different colors, palette names, types of lines, symbols, etc. Is
there any documentation on line with all these numbers / names and the
associated symbol / color???
I do usually something like:
plot(1:20, rep(1,20), pch=1:20, col=1:20)
plot(1:20, 1:20, type=n)
for (i in 1:20) {
+lines( c(1,20), c(i,i), lty=i) }
For example if i am using the command image it uses a palette
from red to yellow, with red the lowest value, and yellow the highest
value. What if i want a reverse palette, with green the lowest value
:
palette(rev(palette()))
palette()
[1] grayyellow magenta cyanbluegreen3 red
[8] black
and yellow middle values and red highest value??? Or much more simple,
just yellow lowest value and red highest value???
See also the CRAN package RColorBrewer
Kjetil Halvorsen
Thank you for assistance,
Monica
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RE: [R] Ordered logit/probit
Anyone Knows how Shoud I Fit a Mixed Effects Ordered Logistic Model in R? (lme?) []s Leonard Assis Estatístico - CONFE 7439 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Valentin Stanescu Sent: quarta-feira, 24 de março de 2004 15:15 To: [EMAIL PROTECTED] Subject: [R] Ordered logit/probit Hello everyone I am trying to fit an ordered probit/logit model for bank rating prediction. Besides polr() in MASS package which is not written especially for this as far as I know, do you know how else I can do this? I already found the modified polr () version on the Valentin STANESCU Enrst and Young Tel. 402 4000 -- The information contained in this communication is intended solely for the use of the individual or entity to whom it is addressed and others authorized to receive it. It may contain confidential or legally privileged information. If you are not the intended recipient you are hereby notified that any disclosure, copying, distribution or taking any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this communication in error, please notify us immediately by responding to this email and then delete it from your system. Ernst Young is neither liable for the proper and complete transmission of the information contained in this communication nor for any delay in its receipt. Note: If you have received a delivery failure report, it may be due to the change in the Ernst Young e-mail domain from eyi.com to ey.com. Could you please make the necessary amendment, if required, and resend the message. [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Ordered logit/probit
On 24 Mar 2004 at 20:14, Valentin Stanescu wrote: Hello everyone I am trying to fit an ordered probit/logit model for bank rating The CRAN package MCMCpack has at least ordered probit. Kjetil Halvorsen prediction. Besides polr() in MASS package which is not written especially for this as far as I know, do you know how else I can do this? I already found the modified polr () version on the Valentin STANESCU Enrst and Young Tel. 402 4000 -- The information contained in this communication is intended solely for the use of the individual or entity to whom it is addressed and others authorized to receive it. It may contain confidential or legally privileged information. If you are not the intended recipient you are hereby notified that any disclosure, copying, distribution or taking any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this communication in error, please notify us immediately by responding to this email and then delete it from your system. Ernst Young is neither liable for the proper and complete transmission of the information contained in this communication nor for any delay in its receipt. Note: If you have received a delivery failure report, it may be due to the change in the Ernst Young e-mail domain from eyi.com to ey.com. Could you please make the necessary amendment, if required, and resend the message. [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] binding vectors or matrix using their names
Goodness Patrick, this must surely qualify for the obfuscated R competition finals. I love it! There are two solutions I can think of with do.call and here they are: x - 1 x2 - runif(10) x12 - c(x, x2) do.call(cbind, lapply(x12, as.name)) x x2 [1,] 1 0.99327265 [2,] 1 0.63260097 [3,] 1 0.17411170 [4,] 1 0.54635634 [5,] 1 0.75603670 [6,] 1 0.27739270 [7,] 1 0.32125068 [8,] 1 0.01326344 [9,] 1 0.37519602 [10,] 1 0.11133052 do.call(cbind, lapply(x12, get)) [,1] [,2] [1,]1 0.99327265 [2,]1 0.63260097 [3,]1 0.17411170 [4,]1 0.54635634 [5,]1 0.75603670 [6,]1 0.27739270 [7,]1 0.32125068 [8,]1 0.01326344 [9,]1 0.37519602 [10,]1 0.11133052 I suspect the first offers a few advantages over the second, (which some other people have implicitly suggested). The first preserves the names in the result. Also, if the vectors are large, the second constructs a large language object and then evaluates it to get a large result. The first uses the names rather than the objects themselves, so at least the language object is small, even if the result is not. A more serious, philosophical word on Patrick's solution. It is rarely necessary (in my limited experience, sure) to have to use parse() like this. Where it provides a quick (kludgy?) solution I often find it a useful exercise to consider alternatives. They often come out simpler and you nearly always pick up something useful in the process. Bill V. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Patrick Burns Sent: Thursday, 25 March 2004 7:02 AM To: Stephane DRAY Cc: [EMAIL PROTECTED]; Stephane DRAY; Tom Blackwell Subject: Re: [R] binding vectors or matrix using their names I think you are looking for the eval-parse-text idiom: eval(parse(text=paste(cbind(, paste(my.names, collapse=, ), Patrick Burns Burns Statistics [EMAIL PROTECTED] +44 (0)20 8525 0696 http://www.burns-stat.com (home of S Poetry and A Guide for the Unwilling S User) Stephane DRAY wrote: Hi Tom, Your approach did not work, do.call(cbind, as.list(my.names)) [,1] [,2] [1,] x x2 but it helps me a lot to find the good one: do.call(cbind, as.list(parse(text=my.names))) Thanks, At 14:56 24/03/2004, Tom Blackwell wrote: I believe the syntax is result - do.call(cbind, as.list(my.names)) Haven't checked this on your example, though. - tom blackwell - u michigan medical school - ann arbor - On Wed, 24 Mar 2004, Stephane DRAY wrote: Hello list, I have two vectors x and x2: x=runif(10) x2=runif(10) and one vectors with their names : my.names=c(x,x2) I would like to cbind these two vectors using their names contained in the vector my.names. I can create a string with comma ncomma=paste(my.names,collapse=,) and now, I just need a function to transform this string into a adequate argument for cbind: cbind(afunction(ncomma)) Is there in R a function that can do the job ? If not, how can I do it ?? Thanks in advance, Sincerely. Stéphane DRAY - - Département des Sciences Biologiques Université de Montréal, C.P. 6128, succursale centre-ville Montréal, Québec H3C 3J7, Canada Tel : 514 343 6111 poste 1233 E-mail : [EMAIL PROTECTED] - - Web http://www.steph280.freesurf.fr/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Stéphane DRAY -- Département des Sciences Biologiques Université de Montréal, C.P. 6128, succursale centre-ville Montréal, Québec H3C 3J7, Canada Tel : 514 343 6111 poste 1233 E-mail : [EMAIL PROTECTED] -- Web http://www.steph280.freesurf.fr/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide!
[R] if exists with regex return
Hello
I am trying for an hour now,
p - c:/data/
or
p - c:/data/abc.hig
d - sub((.+/.+?/)(.+),\\1,p,perl=TRUE)
f - sub((.+/.+?/)(.+)?,\\2,p,perl=TRUE)
if (exists(f)){ #why this gives TRUE no mater what?
do this with d and f
} else {
do that with d
}
thanks
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RE: [R] if exists with regex return
You assigned `f' whatever the result of
sub((.+/.+?/)(.+)?,\\2,p,perl=TRUE) is. The only way for `f' not to
exist after that assignment (that I can think of anyway) is if there was an
error raised in the sub() call. Otherwise `f' will always exist! You
should simply check what value `f' has. My guess is that you really want
something like:
if (f == ) ...
or maybe:
if (nchar(f) == 0) ...
Andy
From: Fred J.
Hello
I am trying for an hour now,
p - c:/data/
or
p - c:/data/abc.hig
d - sub((.+/.+?/)(.+),\\1,p,perl=TRUE)
f - sub((.+/.+?/)(.+)?,\\2,p,perl=TRUE)
if (exists(f)){ #why this gives TRUE no mater what?
do this with d and f
} else {
do that with d
}
thanks
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RE: [R] statistical significance test for cluster agreement
From: Alexander Sirotkin [at Yahoo] [mailto:[EMAIL PROTECTED]
Christian,
I think I understand your point, but I do not
completely agree with you. I also did not describe
my problem clear enough.
If you see two
clusterings on the same
data, they are identical, if they are 100%
identical, and if not, then
not.
What you are actually saying is that all values of
Rand index for cluster agreement other then 1
inidicate that clusters do not agree. I believe
that many people would disagree with this statement.
Let me explain my problem in a little bit more detail.
I have some classified data set. These classes were
ontained using non-statistical methods. What I'm
trying
to do is run some clustering algorithm and compare
it's results to this known classification.
I think that this is not very different from
calculating mean and comparing it to some known value.
AFAICS they are most definitely not the same. The hypotheses in statistical
tests are about `true', unknown, population mean, not the sample mean
observed in the data. What exactly would be the hypotheses you intend to
test? If you are testing whether the clustering algorithm produces
something that disagree with the non-statistical classification, then one
disagreement would have settled it, no? Before you think about what
statistic to use, do try to figure out how you would write the null and
alternative hypotheses, mathematically.
Andy
I think that is should be theoretically possible to
use
Rand index as a test statistic.
Or maybe I'm missing something...
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Re: [R] Status of Rmpi--Good with tweaks
On 24 Mar 2004, Ross Boylan outgrape: By the way, I'm in the dark about (r)sprng. From some of the snow docs, I thought that was really snow's business. But your site notes that the Rmpi packages are withough SPRNG support. And Tony Rossini's pages (I think) had a slightly cryptic remark that SPRNG under MPI was a bit dicey. rsprng works like this: each process calls the function init.sprng, with three pieces of information: 1) the total number of processes; 2) the rank of current process; 3) a seed that is the same for all processes. An alternative is that the master generates say ten streams, and send one stream to each slave (and keep track of who gets what, to ensure reproducibility). Only very little (and simple) inter-process communication is required for SPRNG. The communication layer is orthogonal of SPRNG itself. rsprng can be used with Rmpi just fine. (SPRNG can be used in serial code as well.) If you look at SPRNG source, it has some sort of MPI support, which is disabled when I compile SPRNG. See this note: http://www.biostat.umn.edu/~nali/RsprngNotes.php Cheers, Michael __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] debugging a code
Using debugger() for post-mortem debugging is the best way to chase down
the immediate cause of an error, which seems to be the issue here.
If you use debug() (which is not a `dubuger') you need to single-step
(with n), and look at values just before the line in which the error
occurs.
There are a lot of good books out there and, `Fred J.', it looks to be
time you started reading them as you are asking a lot of questions they do
answer.
On Wed, 24 Mar 2004, Liaw, Andy wrote:
Well, you can insert `browser()' right above the offending line, then run
the code again. It will stop with the `browse' prompt right before that
line. You can then check which value(s) give you the problem.
Have you tried Mark Bravington's `debug' package on CRAN? There's an
article on it in the most recent issue of R News.
Andy
From: Fred J.
Hello
just learned HowTo but R, reminded me with the way
Perl does it but with much less on-line commands, R
AFAIK has n, c, Q and where and cann't debug outside
the {}.
1) is there a more versatile/flexable debugging method
for R?
I have saved 2 functions in an ASCII file digfun.
getdata function calls squash function and both
use loops. In another file.R I have
source(digfun)
debug(getdata)
data - getdata(c:/data/)
Browse[1] c
Error in if (d[i, V3] == d[i + 1, V3] d[i,
V4] == d[i + 1, V4] :
missing value where TRUE/FALSE needed
traceback()
2: squash(dt1)
1: getdata(c:/data/)
to dubug this I need to know the value of some
variable at this particular loop/sub-fun loop case,
and since the dubuger terminated by showing
prompt, how then I am going to debug this error?
You are not even in the `debugger', sic.
--
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University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [R] if block and brackets
On Wed, 24 Mar 2004, Fred J. wrote:
Hello
the maunal states When the if statement is not in a
block the else, if present, must appear on the same
line as statement1. Otherwise the new line at the end
of statement1 yields a syntactically complete
statement that is evaluated.
well, what is wrong with this if structure? I am
getting an error on the line where else is
The else is inside a { } block.
If you use a good editor and proper indentation such errors will be
obvious to you.
thanks
if (exists(f)){
dt - read.csv(file.path(d,f),header=F)#data frame
builddl(dt,f)
else
for (i in dir(d)){
dt -
read.csv(file.path(c:/data,i),header=F)#data frame
an - sub(([^.]+)(\\..+),\\1, i))
builddl(dt,an)
}
}
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University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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[R] geoR - help for bayesian modelling
Dear Monica Guess the reason for the problem you are seeing is that you are requiring simulations from the predictive distribution. geoR is doing this simulation in a joint step, simulating from the joint predictive distriubtion [as far as I know some other geostatistical software packages are doing such simulation in a sequential way, where a point the grid is added at a time]. For a relatively large grid the covariance matrix needed for this joint simulation is large [in your example a matrix of size 7500 by 7500]. Possible solutions : * Do you really want simulations from the multivariate predictive distribution ? What do you want to do with them ? Most summaries you would want of the predictive distribution are summaries of the univariate distributions at individual locations. * Do you really need to predict in a 150 by 250 grid ? If possible, then reduce the size of your grid. The error you are seeing is related to the cholesky factorisation of the covariance matrix, which is needed to do the joint simulations. If you do not require these simulations, the error will disappear. As you write, the error is probably due to some locations being very close to data locations. As I remember there is an internal handling in the package of prediction locations close to data locations, but your locations are not sufficiently near to the data locations to be handled by this. Maybe you should change the prediction coordinates in question such that they actually do coincide with the data locations. Hope this is helpful Cheers Ole *** Hi, I am trying to do a bayesian prediction for soil pollution data above a certain threshold, using geoR. Everything is working fine until i am doing the krig.bayes. I tried to do the prediction on a grid 67 by 113 cells and my computer is freezing to death. At larger numbers of cells it tells me after a while that it reaches the max. memory of 511 Mb. My computer has only 512 Mb of RAM. What RAM capacity should i look for to do a 150 x 250 cell grid??? If i want to do the prediction on my initial data locations (well, actually the prediction points are shifted 1 m in X and respectively Y direction, so the raw data coordinates don't coincide with the prediction coordinates) i am getting the following error using the command: zn.bayes - krige.bayes(zn.gdata, loc = xy, model = model.control(cov.model = exponential, lambda = 0), prior = prior.control(phi.prior =exponential, phi = 89.1894), output=output.control(n.predictive=2, mean.var = TRUE, quantile = c(0.025,0.25, 0.5, 0.75, 0.975), threshold = c(300))) Error in cond.sim(env.loc = base.env, env.iter = iter.env, loc.coincide = get(loc.coincide, : chol: matrix not pos def, diag[13]= -1.279220e-018 I will really appreciate any suggestion you may have. Thank you so much, Monica -- Ole F. Christensen Center for Bioinformatik Aarhus Universitet Ny Munkegade, Bygning 540 8000 Aarhus C __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] First Variable in lm
I want to take the first variable (column) of a data frame and regress
it against all other variables.
bla - function (dat) {
reg - lm(whateverthefirstofthevariablenamesis ~., data=dat)
return(reg)
}
Thanks to all who answered my question:
Prof. Brian Ripley:
---
bla - function (dat)
eval(substitute(lm(foo ~., data=dat), list(foo=as.name(names(dat)[1]
which has the advantage of embedding a clean value of $call.
[EMAIL PROTECTED]:
lm(formula = dat)
[EMAIL PROTECTED]:
-
for(j in 1:ncol(dat)) {
fff - as.formula(paste(names(dat)[j],~,
paste(names(dat)[-j],collapse=+)))
nm - paste(rslt,j,sep=.)
assign(nm,lm(fff,data=dat))
}
[EMAIL PROTECTED]
---
data(longley)
lm( longley[,7] ~. , data = longley[,-7] )
You cannot call data() inside a function:
data(dat)
reg - lm(dat[,1] ~ dat[,-1])
Error in model.frame(formula, rownames, variables, varnames, extras,
extranames, :
invalid variable type
In addition: Warning message:
Data set 'dat' not found in: data(dat)
Regards
Christian
--
Dr.sc.math.Christian W. Hoffmann,
http://www.wsl.ch/staff/christian.hoffmann
Mathematics + Statistical Computing e-mail: [EMAIL PROTECTED]
Swiss Federal Research Institute WSL Tel: ++41-44-73922- -77 (office)
CH-8903 Birmensdorf, Switzerland -11(exchange), -15 (fax)
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