Re: [R] Cannot update some packages after upgrade to 2.1.1
-lf77blas is part of ATLAS, so I do suspect the RPM builder had ATLAS installed. lme4 needs a compatible Matrix installed. I do think installing from the sources would solve this, but probably you need to discuss this with the RPM maintainer as a dependency appears to be missing. On Fri, 15 Jul 2005, Kevin E. Thorpe wrote: I just upgraded to version 2.1.1 (from 2.0.1) today. R.version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major2 minor1.1 year 2005 month06 day 20 language R I am using SuSE 9.2 and did the upgrade using rpm -U with the RPM available on CRAN. After upgrading r-base, I ran update.packages(). Four previously installed packages failed to update: Matrix (0.95-5 to 0.97-4) gam (0.93 to 0.94) lme4 (0.95-3 to 0.96-1) mgcv (1.3-1 to 1.3-4) In the case of Matrix, gam and mgcv I get the message: [long path]/ld: cannot find -lf77blas In the case of lme4 the messages are: ** preparing package for lazy loading Error in setMethod(coef, signature(object = lmList), function(object, : no existing definition for function 'coef' Error: unable to load R code in package 'lme4' Execution halted ERROR: lazy loading failed for package 'lme4' I have searched the SuSE repository for any package that provides f77blas but came up empty. I also could not identify any relevant messages in the mailing list archives. Is R looking for that library because it was present on the machine the RPM was built on? Would building R myself solve the missing library problem or did I do something wrong? -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.971.2462 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- 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 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Coxph with factors
Thank you for your help. In any case, to specify f.pom You need it to be a factor with the same set of levels. You don't say what the lowest level of pom is, but if it is, say, -3. f.pom=factor(-3, levels=seq(-3,2.5, by=0.5)) For this particular model, f.pom starts at -5.5 going to 2 in 0.5 increments. I seem to have misunderstood your explanation, as R is still producing an error. final-coxph(Surv(time.sec,done)~f.pom+vo+po,data=DATA) final.surv-survfit((final), data.frame(po=0,vo=1,f.pom=factor(-5.5,levels=seq(-5.5,2,by=0.5)),individual=T)) summary(final.surv) Error in x2 %*% coef : non-conformable arguments Execution halted I would first note that the survival function at zero covariates is not a very useful thing and is usually numerically unstable, and it's often more useful to get the survival function at some reasonable set of covariates. Please correct me if I'm wrong, I was under the impression that the survival function at zero covariates gave the baseline distribution. I.e. if given the baseline prob.,S_0, at time t, one could calculate the survival prob for specified covariates by S_0^exp(beta(vo)*specified(vo)+beta(po)*specified(po)+beta(f.pom at the level of interest)) for time t. Since I was unable to get survfit to work with specified covariates, I was using the survival probs of the 'avg' covariates, S(t), to determine the baseline at time t, i.e. S(t)^(1/exp(beta(vo)*mean(vo)+beta(po)*mean(po)+beta(f.pom-5.5)*mean(f.pom-5.5)+beta(f.pom-5.0)*mean(f.pom-5.0)+). And then proceeding as mention in the above paragraph (clearly not an efficient way of doing things). - Original Message - From: Thomas Lumley [EMAIL PROTECTED] To: Kylie-Anne Richards [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Sent: Saturday, July 16, 2005 12:31 AM Subject: Re: [R] Coxph with factors On Fri, 15 Jul 2005, Kylie-Anne Richards wrote: FIRST Q: The default uses the mean of 'vo' and mean of 'po', but what is it using for the factors?? Is it the sum of the coef of the factors divided by the number of factors?? It uses the mean of each factor variable. The $means component of the fit gives the values it uses. SECOND Q: For a model with covariates I would normally specify: final.surv-survfit((final), data.frame(po=0,vo=0,pom=0,individual=T)) to get the baseline survival prob.; what would I specify for a model with a factor, i.e., 'f.pom' ?? I would first note that the survival function at zero covariates is not a very useful thing and is usually numerically unstable, and it's often more useful to get the survival function at some reasonable set of covariates. In any case, to specify f.pom You need it to be a factor with the same set of levels. You don't say what the lowest level of pom is, but if it is, say, -3. f.pom=factor(-3, levels=seq(-3,2.5, by=0.5)) =thomas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] cbind a list of matrices
Dear users, I have a list of several matrices with the same number of columns, how do I rbind them all with a vectorized command? A related simpler question is, how do I vectorize the instruction that rbinds together several copies of the same matrix? Thanks. -- Mauro Gasparini __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R: to the power
At 10:11 12/7/2005, [EMAIL PROTECTED] wrote: hi all why does R do this: (-8)^(1/3)=NaN the answer should be : -2 Allan In my computer: (-8)^(1/3) [1] NaN -8^(1/3) [1] -2 -(8^(1/3)) [1] -2 The problem is -8 or the problem is (-8) ? []s Tura -- No virus found in this outgoing message. Checked by AVG Anti-Virus. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] cbind a list of matrices
On 16-Jul-05 Mauro Gasparini wrote: Dear users, I have a list of several matrices with the same number of columns, how do I rbind them all with a vectorized command? A related simpler question is, how do I vectorize the instruction that rbinds together several copies of the same matrix? Didn't you simply try: A-matrix(c(1.1,1.2,1.3,1.4,1.5,1.6),ncol=3) B-matrix(c(2.1,2.2,2.3,2.4,2.5,2.6),ncol=3) C-matrix(c(3.1,3.2,3.3,3.4,3.5,3.6),ncol=3) A [,1] [,2] [,3] [1,] 1.1 1.3 1.5 [2,] 1.2 1.4 1.6 B [,1] [,2] [,3] [1,] 2.1 2.3 2.5 [2,] 2.2 2.4 2.6 C [,1] [,2] [,3] [1,] 3.1 3.3 3.5 [2,] 3.2 3.4 3.6 rbind(A,B,C) [,1] [,2] [,3] [1,] 1.1 1.3 1.5 [2,] 1.2 1.4 1.6 [3,] 2.1 2.3 2.5 [4,] 2.2 2.4 2.6 [5,] 3.1 3.3 3.5 [6,] 3.2 3.4 3.6 rbind(A,A,A) [,1] [,2] [,3] [1,] 1.1 1.3 1.5 [2,] 1.2 1.4 1.6 [3,] 1.1 1.3 1.5 [4,] 1.2 1.4 1.6 [5,] 1.1 1.3 1.5 [6,] 1.2 1.4 1.6 If there's an exception under which the above does not work, I'd be interested to hear of it! Best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 16-Jul-05 Time: 10:29:59 -- XFMail -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] cbind a list of matrices
(Ted Harding) [EMAIL PROTECTED] writes: On 16-Jul-05 Mauro Gasparini wrote: Dear users, I have a list of several matrices with the same number of columns, how do I rbind them all with a vectorized command? A related simpler question is, how do I vectorize the instruction that rbinds together several copies of the same matrix? Didn't you simply try: A-matrix(c(1.1,1.2,1.3,1.4,1.5,1.6),ncol=3) B-matrix(c(2.1,2.2,2.3,2.4,2.5,2.6),ncol=3) C-matrix(c(3.1,3.2,3.3,3.4,3.5,3.6),ncol=3) A [,1] [,2] [,3] [1,] 1.1 1.3 1.5 [2,] 1.2 1.4 1.6 B [,1] [,2] [,3] [1,] 2.1 2.3 2.5 [2,] 2.2 2.4 2.6 C [,1] [,2] [,3] [1,] 3.1 3.3 3.5 [2,] 3.2 3.4 3.6 rbind(A,B,C) [,1] [,2] [,3] [1,] 1.1 1.3 1.5 [2,] 1.2 1.4 1.6 [3,] 2.1 2.3 2.5 [4,] 2.2 2.4 2.6 [5,] 3.1 3.3 3.5 [6,] 3.2 3.4 3.6 rbind(A,A,A) [,1] [,2] [,3] [1,] 1.1 1.3 1.5 [2,] 1.2 1.4 1.6 [3,] 1.1 1.3 1.5 [4,] 1.2 1.4 1.6 [5,] 1.1 1.3 1.5 [6,] 1.2 1.4 1.6 If there's an exception under which the above does not work, I'd be interested to hear of it! If the matrices literally are in a list, you might need do.call(rbind, l) which for multiple copies (5, say) of the same matrix might be done via M - matrix(1:4,2) MM - do.call(rbind,replicate(5, M, simplify=FALSE)) although it might be more efficient with MM - matrix(t(M),5*2,2,byrow=T) -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Can't get sample function from An Introduction to R to work
When you copied it into MS Word, did you Copy - paste special -
unformatted text? This trick sometimes might expose (or eliminate)
nonprinting characters or characters with special attributes that might
have created the problem.
spencer graves
David Groos wrote:
Thank you-all very much for your help, your responses and help has been
very encouraging. The following doesn't close the case but it tables
it...
First I copied Ken's code into my R Console and...it worked great!
That was baffling as it looked identical to mine.
I did not explicitly say earlier that the code I sent out I had copied
from the console, pasted into MS Word, changed font size, then pasted
it into the e-mail--in other words, that was a copy of one of the codes
that didn't work.
Anyway, I then copied the non-working, pasted it into Console,
expecting that it would say Error: syntax error upon pressing the
return key at the end of this line:
+ tst-(yb1-yb2)/sqrt(s*(1/n1+1/n2))
but it didn't! and the code worked this time, also!
I then went about doing what I could to replicate the error from before
and was as unsuccessful in doing that as I was in making it work,
earlier.
On Jul 15, 2005, at 4:43 PM, Peter Dalgaard wrote:
Bret Collier [EMAIL PROTECTED] writes:
David,
If below is exactly what you typed, check your code again, I think you
are missing a '}' after the last 2 parentheses.
That's not supposed to cause a syntax error, just another '+'.
(right! that's what I thought...)
I can copy and paste the code as written and not get an error:
twosam-function(y1, y2) {
+ n1-length(y1);n2 -length(y2)
+ yb1-mean(y1); yb2-mean(y2)
+ s1-var(y1);s2-var(y2)
+ s-((n1-1)*s1 + (n2-1)*s2)/(n1+n2-2)
+ tst-(yb1-yb2)/sqrt(s*(1/n1+1/n2))
+ }
Perhaps this was the 1st time David got his typing right? The error is
of the sort you'd get if you had
s-((n1-1)*s1 + (n2-1)*s2/(n1+n2-2)
Interestingly enough, I did try this line when first I was trying to
make the code work and with just 1 ) at the end I didn't get the
error message, but then again I wasn't able to make the whole program
work, either.
In conclusion, I can't explain why it didn't first work time nor why I
couldn't replicate the error. I think I ought to e-mail the Mac R
folks about this.
Again, Thanks,
-David
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Re: [R] rmpi in windows
Uzuner, Tolga wrote: Hi Folks, Has anyone been able to get rmpi to work under windows ? Rmpi uses the LAM implementation of MPI. See http://www.lam-mpi.org/faq/category12.php3 and read FAQ 2 which implicitly tells us that there is no native port, hence you cannot run it under Windows. The package maintainer may know better. Uwe Ligges BTW: Why do you ask twice (in private message and on R-help)? I am reading R-help anyway ... Thanks, Tolga Please follow the attached hyperlink to an important disclaimer http://www.csfb.com/legal_terms/disclaimer_europe.shtml == Please access the attached hyperlink for an important electronic communications disclaimer: http://www.csfb.com/legal_terms/disclaimer_external_email.shtml __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Proportion test in three-chices experiment
Have you considered BTm in library(BradleyTerry)? Consider the following example: cond1 - data.frame(winner=rep(LETTERS[1:3], e=2), + loser=c(B,C,A,C,A,B), + Freq=1:6) cond2 - data.frame(winner=rep(LETTERS[1:3], e=2), + loser=c(B,C,A,C,A,B), + Freq=6:1) fit1 - BTm(cond1~..) fit2 - BTm(cond2~..) fit12 - BTm(rbind(cond1, cond2)~..) Dev12 - (fit1$deviance+fit2$deviance + -fit12$deviance) pchisq(Dev12, 2, lower=FALSE) [1] 0.8660497 This says the difference between the two data sets, cond1 and cond2, are not statistically significant. Do you present each subject with onely one pair? If yes, then this model is appropriate. If no, then the multiple judgments by the same subject are not statistically independent, as assumed by this model. However, if you don't get statistical significance via this kind of computation, it's unlikely that a better model would give you statistical significance. If you get a p value of, say, 0.04, then the difference is probably NOT statistically significant. The p value you get here would be an upper bound. You could get a lower bound by using only one of the three pairs presented to each subject selected at random. If that p value were statistically significant, then I think it is safe to say that your two sets of conditions are significantly different. For any value in between, it would depend on how independent the three choices by the same subject. You might, for example, delete one of the three pairs at random and use the result of that comparison. There are doubtless better techniques, but I'm not familiar with them. Perhaps someone else will reply to my reply. spencer graves Rafael Laboissiere wrote: Hi, I wish to analyze with R the results of a perception experiment in which subjects had to recognize each stimulus among three choices (this was a forced-choice design). The experiment runs under two different conditions and the data is like the following: N1 : count of trials in condition 1 p11, p12, p13: proportions of choices 1, 2, and 3 in condition 1 N2 : count of trials in condition 2 p21, p22, p23: proportions of choices 1, 2, and 3 in condition 2 How can I test whether the triple (p11,p12,p13) is different from the triple (p21,p22,p23)? Clearly, prop.test does not help me here, because it relates to two-choices tests. I apologize if the answer is trivial, but I am relatively new to R and could not find any pointers in the FAQ or in the mailing list archives. Thanks in advance for any help, -- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA [EMAIL PROTECTED] www.pdf.com http://www.pdf.com Tel: 408-938-4420 Fax: 408-280-7915 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] cbind a list of matrices
Didn't you simply try: A-matrix(c(1.1,1.2,1.3,1.4,1.5,1.6),ncol=3) B-matrix(c(2.1,2.2,2.3,2.4,2.5,2.6),ncol=3) C-matrix(c(3.1,3.2,3.3,3.4,3.5,3.6),ncol=3) A [,1] [,2] [,3] [1,] 1.1 1.3 1.5 [2,] 1.2 1.4 1.6 B [,1] [,2] [,3] [1,] 2.1 2.3 2.5 [2,] 2.2 2.4 2.6 C [,1] [,2] [,3] [1,] 3.1 3.3 3.5 [2,] 3.2 3.4 3.6 rbind(A,B,C) [,1] [,2] [,3] [1,] 1.1 1.3 1.5 [2,] 1.2 1.4 1.6 [3,] 2.1 2.3 2.5 [4,] 2.2 2.4 2.6 [5,] 3.1 3.3 3.5 [6,] 3.2 3.4 3.6 rbind(A,A,A) [,1] [,2] [,3] [1,] 1.1 1.3 1.5 [2,] 1.2 1.4 1.6 [3,] 1.1 1.3 1.5 [4,] 1.2 1.4 1.6 [5,] 1.1 1.3 1.5 [6,] 1.2 1.4 1.6 This would be adequate for low dimensional dataset e.g. the example you have give. What if you have a list of thousands of matrices. Is there an efficient way of doing this other than looping? __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Padding in lattice plots
On Friday 15 July 2005 17:00, Deepayan Sarkar wrote: On 7/15/05, Federico Gherardini [EMAIL PROTECTED] wrote: On Friday 15 July 2005 14:42, you wrote: Hi all, I've used the split argument to print four lattice plots on a single page. The problem now is that I need to reduce the amount of white space between the plots. I've read other mails in this list about the new trellis parameters layout.heights and layout.widhts but I haven't been able to use them properly. I've tried to input values between 0 and 1 as the padding value (both left and right and top and bottom) but nothing changed. It seems I can only increase the padding by using values 1. Any ideas? Thanks in advance for your help Federico Gherardini It seems like I've found an answer myself you have to use negative values to decrease the padding. I thought it was something like the cex parameter which acts like a multiplier I thought so too. but this is not the case. Could you post what you used? There are several different padding parameters you need to set to 0, did you change them all? Deepayan Hi Deepayan This is what I used I don't know if I did everything the proper way but at least I got the result I was seeking! :) trellis.par.set(list(layout.heights = list(top.padding = -1))) trellis.par.set(list(layout.heights = list(bottom.padding = -1, axis.xlab.padding = 1, xlab = -1.2))) trellis.par.set(list(layout.widths = list(left.padding = -1))) trellis.par.set(list(layout.widths = list(right.padding = -1, ylab.axis.padding = -0.5))) Do these settings make any sense? Federico __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] summary: cbind a list of matrices
Thanks to all kind people who answered. Attached is a useful reply,
among many others.
--
Mauro Gasparini
Professore Straordinario di Statistica
Dipartimento di Matematica, Politecnico di Torino
Corso Duca degli Abruzzi 24 I-10129 Torino, Italy
tel: +39 011 564 7546
fax: +39 011 564 7599
email: [EMAIL PROTECTED]
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Centro Universitario di Statistica per le Scienze Biomediche
dell'Università Vita-Salute San Raffaele di Milano
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---BeginMessage---
Two different techniques for the two questions:
do.call('rbind', list.of.matrices)
orig.mat[rep(1:nrow(orig.mat), 5), ]
See S Poetry for details.
Patrick Burns
[EMAIL PROTECTED]
+44 (0)20 8525 0696
http://www.burns-stat.com
(home of S Poetry and A Guide for the Unwilling S User)
Mauro Gasparini wrote:
Dear users,
I have a list of several matrices with the same number of columns,
how do I rbind them all with a vectorized command?
A related simpler question is, how do I vectorize the instruction
that rbinds together several copies of the same matrix?
Thanks.
---End Message---
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Re: [R] Can't get sample function from An Introduction to R to work
On Fri, 15 Jul 2005, David Groos wrote: Thank you-all very much for your help, your responses and help has been very encouraging. The following doesn't close the case but it tables it... First I copied Ken's code into my R Console and...it worked great! That was baffling as it looked identical to mine. I did not explicitly say earlier that the code I sent out I had copied from the console, pasted into MS Word, changed font size, then pasted it into the e-mail--in other words, that was a copy of one of the codes that didn't work. Mysterious syntax errors on OS X can result from copying and pasting into R. Files that look perfectly innocent can contain Windows line endings (\r\n) or en-dashes instead of hyphens. These might well be transparently fixed in the process of converting to email. If you actually typed into the R console then this won't explain it, of course. -thomas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Coxph with factors
On Sat, 16 Jul 2005, Kylie-Anne Richards wrote: Thank you for your help. In any case, to specify f.pom You need it to be a factor with the same set of levels. You don't say what the lowest level of pom is, but if it is, say, -3. f.pom=factor(-3, levels=seq(-3,2.5, by=0.5)) For this particular model, f.pom starts at -5.5 going to 2 in 0.5 increments. I seem to have misunderstood your explanation, as R is still producing an error. In the model you showed, there were no factor levels below -2.5. You need to make sure that the levels are the same in the initial data and the data supplied to survfit. Check this with levels(). I would first note that the survival function at zero covariates is not a very useful thing and is usually numerically unstable, and it's often more useful to get the survival function at some reasonable set of covariates. Please correct me if I'm wrong, I was under the impression that the survival function at zero covariates gave the baseline distribution. I.e. if given the baseline prob.,S_0, at time t, one could calculate the survival prob for specified covariates by S_0^exp(beta(vo)*specified(vo)+beta(po)*specified(po)+beta(f.pom at the level of interest)) for time t. Since I was unable to get survfit to work with specified covariates, I was using the survival probs of the 'avg' covariates, S(t), to determine the baseline at time t, i.e. S(t)^(1/exp(beta(vo)*mean(vo)+beta(po)*mean(po)+beta(f.pom-5.5)*mean(f.pom-5.5)+beta(f.pom-5.0)*mean(f.pom-5.0)+). And then proceeding as mention in the above paragraph (clearly not an efficient way of doing things). Yes, but you don't need to go via the baseline. The survival curves for any two covariate vectors z1 and z2 are related by S(t; z1)= S(t; z2)^(z1-z2) For convenience of mathematical notation, mathematical statisticians write everything in terms of z2=0, and call this the baseline. In the real world, though, you are better off with a baseline defined at a covariate value somewhere in the vicinity of the actual data. If, as if often the case, the zero covariate value is a long way from the observed data, both the computation of the survival curve at zero and the transformation to the covariates you want are numerically ill-conditioned. So, you can use the baseline returned by survfit(z2), which is at z2=fit$means, to do anything you can do with the baseline at z=0, and the computations will be more accurate. -thomas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R: to the power
On Sat, 16 Jul 2005, Bernardo Rangel Tura wrote: At 10:11 12/7/2005, [EMAIL PROTECTED] wrote: hi all why does R do this: (-8)^(1/3)=NaN the answer should be : -2 Yes and no. The problem is that the reciprocal of 3 is not exactly representable as a floating point number (it has an infinite binary expansion .010101010101...) So the R expression 1/3 actually returns a number slightly different from one-third. It is a fraction with denominator a power of two (probably 2^53). Now, -8 to power that is a fraction with denominator a power of 2 is not a real number, so, NaN. It would be nice if R could realize that you meant the cube root of -8, but that requires either magical powers or complicated and unreliable heuristics. The real solution might be a function like root(x,a,b) to compute x^(a/b), where a and b could then be exactly representable integers. If someone wants to write one -thomas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Coxph with factors
On Sat, 16 Jul 2005, Thomas Lumley wrote: Yes, but you don't need to go via the baseline. The survival curves for any two covariate vectors z1 and z2 are related by S(t; z1)= S(t; z2)^(z1-z2) Actually S(t; z1)=S(t;z2) ^(beta'(z1-z2)) of course. -thomas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Proportion test in three-chices experiment
I suspect that there are more direct ways to do this test, but it is unclear to me just what the issue is. For example, if there are many subjects and very few stimuli for each, you might want to get some sort of measure of ability for each subject (many possibilities here, then test the measure across subjects with a t test. The measure must be chosen so that you can specify a null hypothesis. It must be directional. If you have a few subjects and many trials per subject, then you could do a significance test for each subject. You want a directional test, because you have a specific hypothesis, namely, that the correct answer will occur more often than predicted from the marginal frequencies in the 3x3 table. (I assume it is a 3x3 table with stimuli as rows and responses ad columns, and you want to show that the diagonal cells are higher than predicted.) One possibility is kappa, which is in the vcd package, and also in psy and concord, in somewhat different forms. Usually in this sort of experiment, though, there isn't much of an issue about whether subjects are transmitting information at all. Rather the issue is testing alternative models of what they are doing. Jon On 07/16/05 06:33, Spencer Graves wrote: Have you considered BTm in library(BradleyTerry)? Consider the following example: cond1 - data.frame(winner=rep(LETTERS[1:3], e=2), + loser=c(B,C,A,C,A,B), + Freq=1:6) cond2 - data.frame(winner=rep(LETTERS[1:3], e=2), + loser=c(B,C,A,C,A,B), + Freq=6:1) fit1 - BTm(cond1~..) fit2 - BTm(cond2~..) fit12 - BTm(rbind(cond1, cond2)~..) Dev12 - (fit1$deviance+fit2$deviance + -fit12$deviance) pchisq(Dev12, 2, lower=FALSE) [1] 0.8660497 This says the difference between the two data sets, cond1 and cond2, are not statistically significant. Do you present each subject with onely one pair? If yes, then this model is appropriate. If no, then the multiple judgments by the same subject are not statistically independent, as assumed by this model. However, if you don't get statistical significance via this kind of computation, it's unlikely that a better model would give you statistical significance. If you get a p value of, say, 0.04, then the difference is probably NOT statistically significant. The p value you get here would be an upper bound. You could get a lower bound by using only one of the three pairs presented to each subject selected at random. If that p value were statistically significant, then I think it is safe to say that your two sets of conditions are significantly different. For any value in between, it would depend on how independent the three choices by the same subject. You might, for example, delete one of the three pairs at random and use the result of that comparison. There are doubtless better techniques, but I'm not familiar with them. Perhaps someone else will reply to my reply. spencer graves Rafael Laboissiere wrote: Hi, I wish to analyze with R the results of a perception experiment in which subjects had to recognize each stimulus among three choices (this was a forced-choice design). The experiment runs under two different conditions and the data is like the following: N1 : count of trials in condition 1 p11, p12, p13: proportions of choices 1, 2, and 3 in condition 1 N2 : count of trials in condition 2 p21, p22, p23: proportions of choices 1, 2, and 3 in condition 2 How can I test whether the triple (p11,p12,p13) is different from the triple (p21,p22,p23)? Clearly, prop.test does not help me here, because it relates to two-choices tests. I apologize if the answer is trivial, but I am relatively new to R and could not find any pointers in the FAQ or in the mailing list archives. Thanks in advance for any help, -- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA [EMAIL PROTECTED] www.pdf.com http://www.pdf.com Tel: 408-938-4420 Fax: 408-280-7915 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] topical guide to R packages
I would like to see R packages arranged by topic. CRAN Task Views are at http://lib.stat.cmu.edu/R/CRAN/src/contrib/Views/ , but I'd like something more detailed. For example, the IMSL Fortran library, version 4 is easy to navigate and has procedures arranged according to following topics: Basic Statistics Regression Correlation Analysis of Variance Categorical and Discrete Data Analysis Nonparametric Statistics Tests of Goodness of FIt and Randomness Time Series Analysis and Forecasting Covariance Structures and Factor Analysis Discriminant Analysis Cluster Analysis Sampling Survival Analysis, Life Testing, and Reliability Multidimensional Scaling Density and Hazard Estimation Line Printer Graphics Probability Distribution Functions and Inverses Random Number Generation Utilities As a start, here are the R packages I know of for time series analysis: dyn: Time Series Regression dynlm: Dynamic Linear Regression GeneTS: Microarray Time Series and Network Analysis its: Irregular Time Series sspir: State Space Models in R tseries: Time series analysis and computational finance urca: Unit root and cointegration tests for time series data uroot: Unit root tests and graphics for seasonal time series I would like to see lists corresponding to other categories of IMSL. Another classification system is GAMS at http://gams.nist.gov/Classes.plain . Section L, Statistics, probability, would be relevant. Regards, Vivek Rao __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] xlabel and ylabel in ROC curve ??
When I draw a ROC curve, the xlabel is '1-spec:', and ylabel is 'sens:' . My question is: can I specify them to '1-specificity', and 'sensitivity' ? thanks for your help. Lu. __ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Confidence Intervals for Arbitrary Functions
I have a rather basic background in statistics, and am looking for assistance in solving what I expect is a common type of problem. I have measurements of physical processes, and mathematical models of those processes that I want to feed the measurements into. A simple case is using measurements of electric power entering and leaving a power conversion device, sampled at regular intervals, and summed to estimate energy in and out, and dividing the energy out by the energy in to get an estimate of efficiency. I know that power efficiency varies with power level, but for this calculation I am interested in the quantifying the overall efficiency rather than the instantaneous efficiency. If the energy quantities are treated as a normally-distributed random variable (per measurement uncertainty), is there a package that simplifies the determination of the probability distribution function for the quotient of these values? Or, in the general sense, if I have a function that computes a measure of interest, are such tools general enough to handle this? (The goal being to determine a confidence interval for the computed quantity.) As an attempt to understand the issues, I have used SQL to generate discrete sampled normal distributions, and then computed new abscissa values using a function such as division and computing the joint probability as the ordinate, and then re-partitioned the result into new bins using GROUP BY. This is general enough to handle non-normal distributions as well, though I don't know how to quantify the numerical stability/accuracy of this computational procedure. However, this is pretty tedious... it seems like R ought to have some straightforward solution to this problem, but I don't seem to know what search terms to use. --- Jeff NewmillerThe . . Go Live... DCN:[EMAIL PROTECTED]Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] topical guide to R packages
On 7/16/2005 1:17 PM, Vivek Rao wrote: I would like to see R packages arranged by topic. CRAN Task Views are at http://lib.stat.cmu.edu/R/CRAN/src/contrib/Views/ , but I'd like something more detailed. For example, the IMSL Fortran library, version 4 is easy to navigate and has procedures arranged according to following topics: Basic Statistics Regression Correlation Analysis of Variance Categorical and Discrete Data Analysis Nonparametric Statistics Tests of Goodness of FIt and Randomness Time Series Analysis and Forecasting Covariance Structures and Factor Analysis Discriminant Analysis Cluster Analysis Sampling Survival Analysis, Life Testing, and Reliability Multidimensional Scaling Density and Hazard Estimation Line Printer Graphics Probability Distribution Functions and Inverses Random Number Generation Utilities As a start, here are the R packages I know of for time series analysis: dyn: Time Series Regression dynlm: Dynamic Linear Regression GeneTS: Microarray Time Series and Network Analysis its: Irregular Time Series sspir: State Space Models in R tseries: Time series analysis and computational finance urca: Unit root and cointegration tests for time series data uroot: Unit root tests and graphics for seasonal time series I would like to see lists corresponding to other categories of IMSL. Another classification system is GAMS at http://gams.nist.gov/Classes.plain . Section L, Statistics, probability, would be relevant. I don't see a Task View for time series, so why don't you write it, for a start? Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] PBSmapping and shapefiles
Hi, Is there a way, preferably with R, to read shapefiles and transform them in a format that I could then use with package PBSmapping? I have been able to read such files into R with maptools' read.shape and plot it with plot.Map, but I'd like to bring the data to PBSmapping and plot from there. I also looked at the package shapefile, but it does not seem to do what I want either. Sincerely, Denis Chabot __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Confidence Intervals for Arbitrary Functions
On 7/16/05, Jeff Newmiller [EMAIL PROTECTED] wrote: I have a rather basic background in statistics, and am looking for assistance in solving what I expect is a common type of problem. I have measurements of physical processes, and mathematical models of those processes that I want to feed the measurements into. A simple case is using measurements of electric power entering and leaving a power conversion device, sampled at regular intervals, and summed to estimate energy in and out, and dividing the energy out by the energy in to get an estimate of efficiency. I know that power efficiency varies with power level, but for this calculation I am interested in the quantifying the overall efficiency rather than the instantaneous efficiency. If the energy quantities are treated as a normally-distributed random variable (per measurement uncertainty), is there a package that simplifies the determination of the probability distribution function for the quotient of these values? Or, in the general sense, if I have a function that computes a measure of interest, are such tools general enough to handle this? (The goal being to determine a confidence interval for the computed quantity.) As an attempt to understand the issues, I have used SQL to generate discrete sampled normal distributions, and then computed new abscissa values using a function such as division and computing the joint probability as the ordinate, and then re-partitioned the result into new bins using GROUP BY. This is general enough to handle non-normal distributions as well, though I don't know how to quantify the numerical stability/accuracy of this computational procedure. However, this is pretty tedious... it seems like R ought to have some straightforward solution to this problem, but I don't seem to know what search terms to use. There is some discussion about the ratio of normals at: http://www.pitt.edu/~wpilib/statfaq.html but you may just want to use bootstrapping: library(boot) library(simpleboot) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R: to the power
[Thomas Lumley] It would be nice if R could realize that you meant the cube root of -8, but that requires either magical powers or complicated and unreliable heuristics. The real solution might be a function like root(x,a,b) to compute x^(a/b), where a and b could then be exactly representable integers. If someone wants to write one... While this could be done with moderate difficulty for the simpler cases, one cannot reasonably ask R to be and do everything. :-) So far, I see R more on the numerical side of things. If you want precise, exact solutions to various mathematical problems, you might consider installing a Computer Algebra System on your machine, next to R, for handling the symbolic side of things. One such system which is both free and very capable might be Maxima. Its convoluted story is rooted 40 years in the past. Some may say it lacks some chrome and be mislead; don't be, the engine is pretty solid. Peek at http://maxima.sourceforge.net if you think you need such a beast. Beware: to use it, you need either GCL or Clisp pre-installed. -- François Pinard http://pinard.progiciels-bpi.ca __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] xfig device - depth
Hi, I hope this is the right list for my posting, since I've never posted to any R list before. I'm quite extensively using the xfig graphics device and as far as I figured out this device writes all the objects into xfig layer 100 (based on what I saw in the devPS.c file -if this is the file to output to xfig format - depth 100 is hardcoded). Are the any plans to implement xfig layer depth control in the xfig graphics device or am I just missing something. Thanks a lot in advance Thomas Zanon -- * Thomas Zanon 2116 Hamerschlag Hall Department of Electrical and Computer Engineering Carnegie Mellon University 5000 Forbes Avenue Pittsburgh, PA 15213-3890 phone office: (412) 268-6638 fax: (412) 268-3204 email+UID:[EMAIL PROTECTED] homepage: http://www.ece.cmu.edu/~zanon * -- No virus found in this outgoing message. Checked by AVG Anti-Virus. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Time Series Count Models
Hello, I'm trying to model the entry of certain firms into a larger number of distinct markets over time. I have a short time series, but a large cross section (small T, big N). I have both time varying and non-time varying variables. Additionally, since I'm modeling entry of firms, it seems like the number of existing firms in the market at time t should depend on the number of firms at (t-1), so I would like to include the lagged cumulative count as well. My basic question is whether it is appropriate (in a statistical sense) to include both the time varying variables and the lagged cumulative count variable. The lagged count aside, I know there are standard extensions to count models to handle time series. However, I'm not sure if anything changes when lagged values of the cumulative dependent variable are added (i.e. are the regular standard errors correct, are estimates consistent, etc) I would greatly appreciate it if anyone can direct me to relevant material on this. As a note, I have already looked at Cameron and Trivedi's book. Many thanks, Brett __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Time Series Count Models
Hello, I'm trying to model the entry of certain firms into a larger number of distinct markets over time. I have a short time series, but a large cross section (small T, big N). I have both time varying and non-time varying variables. Additionally, since I'm modeling entry of firms, it seems like the number of existing firms in the market at time t should depend on the number of firms at (t-1), so I would like to include the lagged cumulative count. My basic question is whether it is appropriate (in a statistical sense) to include both the time varying variables and the lagged cumulative count variable. The lagged count aside, I know there are standard extensions to count models to handle time series. However, I'm not sure if anything changes when lagged values of the cumulative dependent variable are added (i.e. are the regular standard errors correct, are estimates consistent, etc). Can I still use one of the time series count models while including this lagged cumulative value? I would greatly appreciate it if anyone can direct me to relevant material on this. As a note, I have already looked at Cameron and Trivedi's book. Many thanks, Brett __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Is it possible to coerce R to continue proceeding the next command in a loop after an error message ?
Hello R-users, In a loop, if a function, such as nls, gives an error, is it possible to coerce R to continue proceeding the next command with the same loop? Thanks so much for your advice! Hanna Lu [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Is it possible to coerce R to continue proceeding the next command in a loop after an error message ?
Yimeng Lu wrote: Hello R-users, In a loop, if a function, such as nls, gives an error, is it possible to coerce R to continue proceeding the next command with the same loop? Yes, see the try() function. The basic usage is something like value - try( some calculation ) if (inherits(value, try-error)) handle the error else handle a correct calculation Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Is it possible to coerce R to continue proceeding the next command in a loop after an error message ?
?try spencer graves Yimeng Lu wrote: Hello R-users, In a loop, if a function, such as nls, gives an error, is it possible to coerce R to continue proceeding the next command with the same loop? Thanks so much for your advice! Hanna Lu [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA [EMAIL PROTECTED] www.pdf.com http://www.pdf.com Tel: 408-938-4420 Fax: 408-280-7915 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] nlme and spatially correlated errors
Have you tried anova(fit1, fit2), where
fit1 - lme(one model...)
fit2 - lme(a submodel ... )
This anova does about the best that anyone knows how to do -- or at
lest did 7 years ago when it was written. If the submodel changes the
fixed effects, you should use method='ML'. If the submodel changes
the noise model specification, use method='REML'. See Pinheiro and
Bates (2000) Mixed-Effect Models in S and S-Plus (Springer). If you
need something more precise than the standard approximations, try
simulate.lme.
buena suerte!
spencer graves
Patricia Balvanera wrote:
Dear R users,
I am using lme and nlme to account for spatially correlated errors as
random effects. My basic question is about being able to correct F, p, R2
and parameters of models that do not take into account the nature of such
errors using gls, glm or nlm and replace them for new F, p, R2 and
parameters using lme and nlme as random effects.
I am studying distribution patterns of 50 tree species along a gradient.
That gradient
was sampled through 27 transects, with 10 plots within each transect. For
each plot I
have data on presence/absence, abundance and basal area of the species. I
also have data
for 4 environmental variables related to water availability (soil water
retention
capacity, slope, insolation, altitude) and X and Y coordinates for each
plot. I explored
wether the relationship between any of the response variables
(presence/absence,
abundance, basal area) and the environmental variables was linear,
polinomial, or
non-linear.
My main interest in this question is that I proceeded to correct for spatial
autocorrelation (both within transects and overall) following the
procedures suggest by
Crawley 2002 for linear models
e.g. (GUAMAC = a species, CRAS = soil water retention capacity, TRANSECTO =
transect)
model1-gls(GUAMAC ~ CRAS)
model2-lme(GUAMAC ~ CRAS, random = ~ 1 | TRANSECTO)
model3-lme(GUAMAC ~ CRAS, random = GUAMAC ~ CRAS | TRANSECTO)
model4-lme(GUAMAC ~ CRAS, random = GUAMAC ~ CRAS -1 | TRANSECTO)
AIC(model1,model2,model3,model4)
df AIC
model1 3 3730.537
model2 4 3698.849
model3 6 3702.408
model4 4 3704.722
plot(Variogram(model2, form = ~ X + Y))
model5-update(model2,corr=corSpher(c(30,0.8), form = ~ X + Y, nugget = T))
plot(Variogram(modelo7, resType = n))
summary(model5)
In this case I obtain new F for the independent variable INSOLACION, new R2
for the whole model and new parameters for the linear model.
I have also applied this procedure to polinomial models and to glms with
binomial errors
(presence/absence) with no problem.
I am nevertheless stuck with non-linear models. I am using the protocols
you suggested
in the 1998 manuals by Pinheiro and Bates, and those suggested by Crawley
2002.
Please find enclose an example with an
exponential model (which I chose for being simple). In fact the linear
models I am using
are a bit more complicated.
(HELLOT is a species, INSOLACION = INSOLATION, basal = basal area of the
species, TRANSECTO = transect)
HELLOT ~ exp(A + (B * INSOLACION))
basal.HELLOT -function(A,B,INSOLACION) exp(A + (B * INSOLACION))
HELLOT ~ basal.HELLOT(A,B,INSOLACION)
basal.HELLOT- deriv(~ exp(A + (B * INSOLACION))
+ , LETTERS [1:2], function(A, B, INSOLACION){})
model1- nlme(model = HELLOT ~ exp(A + (B * INSOLACION)), fixed = A + B
~ 1,
random = A + B ~ 1, groups = ~ TRANSECTO, start = list(fixed = c(5.23,
-0.05)))
It runs perfectly and gives new values for parameters A and B, but would
only give me F for fixed effects of A and B, while what I am really looking
for is F for fixed effects of INSOLACION and the R2 of the new model.
Thank you so much in advance for your help
Dra. Patricia Balvanera
Centro de Investigaciones en Ecosistemas, UNAM-Campus Morelia
Apdo. Postal 27-3, Xangari
58090 Morelia, Michoacán, Mexico
Tel. (52-443)3-22-27-07, (52-55) 56-23-27-07
FAX (52-443) 3-22-27-19, (52-55) 56-23-27-19
__
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--
Spencer Graves, PhD
Senior Development Engineer
PDF Solutions, Inc.
333 West San Carlos Street Suite 700
San Jose, CA 95110, USA
[EMAIL PROTECTED]
www.pdf.com http://www.pdf.com
Tel: 408-938-4420
Fax: 408-280-7915
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[R] printing the name of the arguments passed to a function
R2.1.1
Win 2k
I have a function, B, within a function, A.
I would like to have B print the name of the argument passed to it (not
the value of the arguments).
i.e.,
A-function()
{
B-function(x,y)
{
fit1-lm(y~x,data=jo)
print(summary(fit1)
I want B to print the string age and the string height.
}
B(age,height)
}
I would like have function B print the name of the arguments passed to
it, i.e. I want B to print the word
age
and the word
height
I would appreciate any suggestions that would help me accomplish this
task.
Thanks,
John
John Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
Baltimore VA Medical Center GRECC and
University of Maryland School of Medicine Claude Pepper OAIC
University of Maryland School of Medicine
Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
410-605-7119
- NOTE NEW EMAIL ADDRESS:
[EMAIL PROTECTED]
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Re: [R] Can't get sample function from An Introduction to R to work
On Jul 16, 2005, at 9:58 AM, Thomas Lumley wrote: On Fri, 15 Jul 2005, David Groos wrote: Thank you-all very much for your help, your responses and help has been very encouraging. The following doesn't close the case but it tables it... First I copied Ken's code into my R Console and...it worked great! That was baffling as it looked identical to mine. I did not explicitly say earlier that the code I sent out I had copied from the console, pasted into MS Word, changed font size, then pasted it into the e-mail--in other words, that was a copy of one of the codes that didn't work. Mysterious syntax errors on OS X can result from copying and pasting into R. Files that look perfectly innocent can contain Windows line endings (\r\n) or en-dashes instead of hyphens. These might well be transparently fixed in the process of converting to email. I'll put this, as well as the copying/pasting as unformatted text as recommends Spencer, into my bag of tricks. If you actually typed into the R console then this won't explain it, of course. And indeed, I did type right into the R console, so the mystery remains... Thanks, David -thomas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] 2D contour predictions
It's not so simple, but consider the following: x=rep(1:6, each=2, length=24) y=rep(1:6, each=4) z=rep(0:1, length=24) set.seed(1) tstDF - data.frame(x=x, y=y, z=z, w=(x-3.5)^2+(y-3.5)+z+0.1*rnorm(24)) fit - lm(w~x+y+z+I(x^2)+I(y^2), tstDF) x0 - seq(1, 5, .5) y0 - seq(1, 6, .5) Grid - expand.grid(x=x0, y=y0) Grid$z - rep(0.5, dim(Grid)[1]) pred - predict(fit, Grid) contour(x0, y0, array(pred, dim=c(length(x0), length(y0 This kind of thing is discussed in Venables and Ripley (2002) Modern Applied Statistics with S, 4th ed. (Springer). I highly recommend this book. spencer graves Michael Hopkins wrote: Hi All I have been fitting regression models and would now like to produce some contour image plots from the predictors. Is there an easy way to do this? My current (newbie) experience with R would suggest there is but that it's not always easy to find it! f3 - lm( fc ~ poly( speed, 2 ) + poly( torque, 2 ) + poly( sonl, 2 ) + poly( p_rail, 2 ) + poly( pil_sep, 2 ) + poly( maf, 2 ) + (speed + torque + sonl + p_rail + pil_sep + maf)^2 ) hat - predict( f3 ) contour( sonl, maf, hat ) Error in contour.default(sonl, maf, hat) : increasing 'x' and 'y' values expected image(sonl, maf, hat) Error in image.default(sonl, maf, hat) : increasing 'x' and 'y' values expected I have tried naïve sorting but no luck with that. I suspect I may need to produce a data grid of some kind but I'm not clear how I would use R to specify such a 2D slice in the 6D design space. TIA Michael P.S. Whilst I'm asking the list - is there an easier way of expressing a full 2nd order model than the one I used above? I'm sure there is but finding it etc etc... _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/_/ _/_/_/ Hopkins Research Ltd _/_/ _/_/ _/_/_/_/ _/_/_/ http://www.hopkins-research.com/ _/_/ _/ _/ _/_/ _/ _/ 'touch the future' _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA [EMAIL PROTECTED] www.pdf.com http://www.pdf.com Tel: 408-938-4420 Fax: 408-280-7915 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] printing the name of the arguments passed to a function
How about the following:
tstFn - function(x){
+ xName - deparse(substitute(x))
+ cat(xName)
+ done
+ }
tstFn(Varname)
Varname[1] done
tstF1 - function(x){
+ tstF2 - function(y){
+ cat(deparse(substitute(y)),
+ doesn't work\n)
+ }
+ tstF2(x)
+ xName - deparse(substitute(x))
+ tstF3 - function(y, yName){
+ cat(yName, works\n)
+ }
+ tstF3(x, xName)
+ done
+ }
tstF1(Varname)
x doesn't work
Varname works
[1] done
spencer graves
John Sorkin wrote:
R2.1.1
Win 2k
I have a function, B, within a function, A.
I would like to have B print the name of the argument passed to it (not
the value of the arguments).
i.e.,
A-function()
{
B-function(x,y)
{
fit1-lm(y~x,data=jo)
print(summary(fit1)
I want B to print the string age and the string height.
}
B(age,height)
}
I would like have function B print the name of the arguments passed to
it, i.e. I want B to print the word
age
and the word
height
I would appreciate any suggestions that would help me accomplish this
task.
Thanks,
John
John Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
Baltimore VA Medical Center GRECC and
University of Maryland School of Medicine Claude Pepper OAIC
University of Maryland School of Medicine
Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
410-605-7119
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--
Spencer Graves, PhD
Senior Development Engineer
PDF Solutions, Inc.
333 West San Carlos Street Suite 700
San Jose, CA 95110, USA
[EMAIL PROTECTED]
www.pdf.com http://www.pdf.com
Tel: 408-938-4420
Fax: 408-280-7915
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[R] Strange problems with lattice plots
Dear r-help, I need to draw some lattice plots and have stuck in strange problems. I have a data frame of 405 rows: str(dframe) `data.frame': 405 obs. of 4 variables: $ year : num 1990 1990 1990 1990 1990 1990 1990 1990 1990 1990 ... $ month: num 1 2 3 4 5 6 7 8 9 10 ... $ V_A2 : num NA NA NA NA NA ... $ V_A3 : num NA NA NA NA NA ... Variable month changes from 1 to 27 as the data frame includes monthly measurements and some aggregations of them. Variable year varies from 1990 to 2004. Variables V_A2 and V_A3 contain floating point values and several NAs (as sometimes measurements were unavailable). I draw plots: xyplot((V_A3/25)~year| factor(month,labels=c(month.name,Annual mean, Annual integral,Integral (Jan-Mar),Integral (Apr-Jun),Integral (Jul-Sep),Integral (Oct-Dec), Integral (Jan-Feb),Integral (Jan-Mar),Integral (Jan-Apr),Integral (Jan-May),Integral (Jan-Jun), Integral (Jan-Jul),Integral (Jan-Aug),Integral (Jan-Sep),Integral (Jan-Oct))), data=dfame,as.table=TRUE,type=c(o,g,r),layout=c(3,9), ylab=Flow, Sv,xlab=NULL) However, instead of plots I am getting the following error Error in do.call(pmax, lapply(cond, is.na)) : symbol print-name too long Shortening factor labels doesn't help. Removing them at all solves the problem, but this doesn't meet my needs, as I have to explain the meaning of each plot. Could you, please, explain me, what does it mean, and what should I do to avoid this and get my plots? The ways to solve my task I see now are either to make subsets (I wonder if it will work with the only addition of subset parameter to call of xyplot) or to add captions to the plots to the picture in the graphic editor. I would like to avoid these. Thank you very much in helping me to solve the problem! --- Best regards, Wladimirmailto:[EMAIL PROTECTED] == Research Scientist, PhD Leninsky Prospect 33, Space Monitoring Ecoinformation Systems Sector, Moscow, Russia, 119071, Institute of Ecology, Phone: (095) 135-9972; Russian Academy of Sciences Fax: (095) 135-9972 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Strange problems with lattice plots
Yes!!! I have overcome it! The solution is xyplot((V_A3/25)~year|factor(month), strip=strip.custom(factor.levels=c(month.name,Annual mean, Annual integral,Integral (Jan-Mar),Integral (Apr-Jun),Integral (Jul-Sep),Integral (Oct-Dec), and so on... Sorry to disturb. WE Dear r-help, WE I need to draw some lattice plots and have stuck in strange problems. WEI have a data frame of 405 rows: str(dframe) WE `data.frame': 405 obs. of 4 variables: WE $ year : num 1990 1990 1990 1990 1990 1990 1990 1990 1990 1990 ... WE $ month: num 1 2 3 4 5 6 7 8 9 10 ... WE $ V_A2 : num NA NA NA NA NA ... WE $ V_A3 : num NA NA NA NA NA ... WE Variable month changes from 1 to 27 as the data frame includes monthly WE measurements and some aggregations of them. WE Variable year varies from 1990 to 2004. WE Variables V_A2 and V_A3 contain floating point values and several NAs (as WE sometimes measurements were unavailable). WE I draw plots: WE xyplot((V_A3/25)~year| WEfactor(month,labels=c(month.name,Annual mean, WE Annual integral,Integral WE (Jan-Mar),Integral (Apr-Jun),Integral (Jul-Sep),Integral WE (Oct-Dec), WE Integral (Jan-Feb),Integral WE (Jan-Mar),Integral (Jan-Apr),Integral (Jan-May),Integral WE (Jan-Jun), WE Integral (Jan-Jul),Integral WE (Jan-Aug),Integral (Jan-Sep),Integral (Jan-Oct))), WEdata=dfame,as.table=TRUE,type=c(o,g,r),layout=c(3,9), WEylab=Flow, Sv,xlab=NULL) WE However, instead of plots I am getting the following error WE Error in do.call(pmax, lapply(cond, is.na)) : WE symbol print-name too long __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
