Re: Windows versus Unix packages in CRAN (Was Re: [R] Rmetrics)
And it seems that this vicious circle continues forever. Before
posting these kind of messages can you please read the INSTRUCTIONS.
fBasics_190.10051.zip is a COMPILED version of the package, not
a source as you claim to be!
It works with no problems; well, at least under Linux.
Janusz.
Richard A. O'Keefe wrote:
Prof Brian Ripley [EMAIL PROTECTED] wrote:
mkdir fBasics
unzip fBasics.zip -d fBasics
rm fBasics/src/*.o
R CMD check fBasics
and that took me about 3 minutes.
Now me, I just did
unzip -a fBasics_190.10051.zip
R CMD INSTALL fBasics
rm -rf fBasics
in a naive and trusting manner. It took me considerably longer than 3
minutes to learn that this was what I should do, and when I did learn,
I wondered if it's this simple, why can't R CMD INSTALL do it?
Now I discover that it isn't that simple. The installation apparently
went smoothly. This is R, right? Never occurred to me that there might
be problems.
Now, B-G--R! It turns out that core stuff is supplied as .dll files,
which of course my UltraSPARC can do nothing with.
The author of the Rmetrics code has a perfect right to provide his code
in any form he wants under any conditions he wants (subject to GPL c).
In particular, if he wants to provide a distribution which only works under
Windows, that's perfectly OK.
**BUT** when a distribution is peculiar to one operating system, that really
should be highlighted in big bold letters: this is a WINDOWS BINARY
version, so that people who can't use Windows .DLL files are spared a day
of trying to figure out how to unpack and of doing an installation which
reports no errors at all and of them finding that things do not work.
There is *NOTHING* on http://www.itp.phys.ethz.ch/econophysics/R/download.htm
that says Windows only. Click on I acceptand the page you arrive at has
nothing in the text anywhere that says Windows only or what to do if not
Windows. (The http://.../R/bin/windows/contrib/1.9 address of the page
was, in retrospect, a big clue, sigh.)
It would of course be nice if the developers had done
R CMD check fBasics
But if you go into the Sources directory, which I suppose you must have,
for each of {fBasics,fExtremes,fOptions,fSeries} there is an
xxx-00check.log.txt, so they _did_ run R CMD check.
and sorted out the errors, then
R CMD build fBasics
Those same check logs show errors (like failure to build .dvi files).
Will it work if I download the Sources packages?
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Re: [R] symbol size in plot
On 19 May 2004 at 12:04, Ulrich Leopold wrote: Dear list, I have been reading the archives already but I do not manage to plot the correct size of symbols without running into other problems. When I use the syntax below I get the size of symbols and text right but the text overlays on top of the axis rather than be in the right position when you using the defaults for plot. Furthermore the ticks of the axis appear to be too small. Is there a way of getting things correct like in the default plot? Hi I am not sure what do you want to accomplish. What is wrong on default plot. If you want to shrink just points use cex in par(mfrow=c(2,2)) plot(x,y, pch=16, cex=0.2) and if you want to enlarge some characters in plot use cex.axis or cex according to par help page e.g. plot(x,y, pch=16, cex=0.2, cex.lab=2, cex.axis=2) par(mfrow=c(2,2)) plot(1:10,1:10) plot(1:10,1:10, cex=.2) plot(1:10,1:10, cex=.2, cex.axis=2) plot(1:10,1:10, cex=.2, cex.axis=2, cex.lab=2) I suppose that in your definition of par you first shrink all points and characters in plot to 0.2 of their default size and then you increase the size of some 5 times e.g. to the default size, but I may be wrong. Cheers Petr par(mfrow=c(2,2),cex=0.2, cex.main=5, cex.sub=5, cex.axis=5,pch=16) plot(x,y) Regards, Ulrich __ [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 Petr Pikal [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] Finding indices where
On 19 May 2004 at 13:26, Ravi Varadhan wrote: Hi: Suppose I have the following vector: x - c(1,4:8,11,13:14,17,19,23:28,35:38) x [1] 1 4 5 6 7 8 11 13 14 17 19 23 24 25 26 27 28 35 36 37 38 and I would like to pick out the first and last indices of all the consecutive runs of integers, where the length of a run is no smaller than a specified value, say, nmin. That is, in the above example, for nmin=4, I would like to get the following 3 by 2 matrix: 4 8 23 28 35 38 For nmin=5, I would get the following 2 by 2 matrix 4 8 23 28 and for nmin=6, I would get the following 1 by 2 matrix 23 28 Is there an efficient and elegant way to do this? Hallo not complete maybe not ellegant but y-rle(diff(x)) res1-x[(cumsum(y$length))[y$length1]]+1 res2-res1-y$length[y$length1] gives you the numbers you want in two vectors (res1, res2). Than you can do any formating and selection you want. Cheers Petr Thanks very much for any help/suggestions. Ravi. __ [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 Petr Pikal [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
[R] function for running MS-DOS from R
I had downloaded the program that runs on MS-DOS. Is it possible for MS-DOS to be run in R such as WinBugs1.4? I wonder whether there is the R function for running MS-DOS from R. _ . MSN . __ [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] quadratic problem with quadratic constraint
Sure -- just use a Lagrangian multiplier to bring the constraint into the objective function and then use a QP routine like quadproog (in the quadprog library). You will need to run an *outer* optimisation to find the value of the Langrangian multiplier. -Original Message- From: Ramzi TEMANNI [mailto:[EMAIL PROTECTED] Sent: 14 May 2004 11:27 To: [EMAIL PROTECTED] Subject: [R] quadratic problem with quadratic constraint Hi all, Can we solve Quadratic Program with Quadratic Constraint in R ? Regards, TEMANNI Ramzi DEA Student LimBio http://www.limbio-paris13.org UFR de Santé, Médecine et Biologie Humaine (SMBH) Léonard de Vinci 74, rue Marcel Cachin 93017 Bobigny Cedex France. Tél : 01.48.38.73.07 Tél : 06.21.43.27.59 [EMAIL PROTECTED] http://temanni.ramzi.free.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] function for running MS-DOS from R
bang jeong sook quietroom78 at hotmail.com writes: I had downloaded the program that runs on MS-DOS. Is it possible for MS-DOS to be run in R such as WinBugs1.4? I wonder whether there is the R function for running MS-DOS from R. On my XP system this works: R system(cmd) to drop into the Windows command line and exit at the Windows command line get you back. One can slso do this: R system(cmd /c dir listing.txt) R listing - readLines(listing.txt) __ [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: [R] column sorting a matrix with indices returned
A possible solution is using apply + order: apply(x,2,order) [,1] [,2] [,3] [1,]323 [2,]132 [3,]211 apply(x,2,function(x)x[order(x)]) [,1] [,2] [,3] [1,]235 [2,]347 [3,]468 best, vito - Original Message - From: Rajarshi Guha [EMAIL PROTECTED] To: R [EMAIL PROTECTED] Sent: Thursday, May 20, 2004 4:11 PM Subject: [R] column sorting a matrix with indices returned Hi, I'm trying to translate some Matlab code to R and I'm trying to implement the behavior of Matlab's sort() which when applied to a matrix will sort the columns returning the column sorted matrix as well as a matrix of permuted indices. Doing: x - matrix(c(3,4,2,6,3,4,8,7,5), nr=3) x [,1] [,2] [,3] [1,]368 [2,]437 [3,]245 What I want after sorting x are two matrices: (the column sorted x) 2 3 5 3 4 7 4 6 8 and (the index matrix) 3 2 3 1 3 2 2 1 1 Doing, sx - apply(x, c(2), sort, index.return=T) results in sx being a series of lists. I know I could then go through the list and create a sorted matrix and an index matrix. But is there a neater way to do this? Thanks, --- Rajarshi Guha [EMAIL PROTECTED] http://jijo.cjb.net GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE --- Accuracy, n.: The vice of being right __ [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] column sorting a matrix with indices returned
On Thu, 2004-05-20 at 10:11, Rajarshi Guha wrote:
Hi,
I'm trying to translate some Matlab code to R and I'm trying to
implement the behavior of Matlab's sort() which when applied to a matrix
will sort the columns returning the column sorted matrix as well as a
matrix of permuted indices.
Doing:
x - matrix(c(3,4,2,6,3,4,8,7,5), nr=3)
x
[,1] [,2] [,3]
[1,]368
[2,]437
[3,]245
What I want after sorting x are two matrices:
(the column sorted x)
2 3 5
3 4 7
4 6 8
and (the index matrix)
3 2 3
1 3 2
2 1 1
I worked out a way:
sorted - apply(x, c(2), sort, index.return=T)
sortedmatrix - matrix(unlist(lapply(sorted, function(x) { x$x })),
nr=length(sortstruct))
sortedindices - matrix(unlist(lapply(sorted, function(x) { x$ix })),
nr=length(sorted))
Is this efficient, as the matrices will be large (or can it be made
into a 1 liner)?
---
Rajarshi Guha [EMAIL PROTECTED] http://jijo.cjb.net
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
---
A man is known by the company he organizes.
-- Ambrose Bierce
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RE: [R] mixed models for analyzing survey data with unequal selec tion probability
Han-Lin I don't think I have seen a reply so I will suggest that maybe you could try a different approach than what you are thinking about doing. I believe the current best practice is to use the weights as a covariate in a regression model - and bytheway - the weights are the inverse of the probabilities of selection - not the probabilities. Fundamentally, there is a difficulty in making sense out of 'random effects' in a finite population setting. (plagiarized from some unknown source) See: 9. Pfeffermann, D. , Skinner, C. J. , Holmes, D. J. , Goldstein, H. , and Rasbash, J. (1998), ``Weighting for unequal selection probabilities in multilevel models (Disc: p41-56)'', Journal of the Royal Statistical Society, Series B, Methodological, 60 , 23-40 which refers back to: 29. Pfeffermann, D. , and LaVange, L. (1989), ``Regression models for stratified multi-stage cluster samples'', Analysis of Complex Surveys, 237-260 If you don't like statistical papers, then see section 4.5 of 8. Korn, Edward Lee , and Graubard, Barry I. (1999), ``Analysis of health surveys'', John Wiley Sons (New York; Chichester) They explain the idea of using weights in a model fairly simply. Bob -Original Message- From: Han-Lin Lai [mailto:[EMAIL PROTECTED] Sent: Wednesday, May 19, 2004 12:47 PM To: [EMAIL PROTECTED] Subject: [R] mixed models for analyzing survey data with unequal selection probability Hi, I need the help on this topic because this is out of my statistical trianing as biologist. Here is my brief description of the problem. I have a survey that VESSELs are selected at random with the probability of p(j). Then the tows within the jth VESSEL are sampled at random with probability of p(i|j). I write my model as y = XB + Zb + e where XB is fixed part, Zb is for random effect (VESSEL) and e is within-vessel error. I feel that I should weight the Zb part by p(j) and the e-part by p(i,j)=p(j)*p(i|j). Is this a correct weighting? How can I implement the weightings in nlme (or lme)? I think that p(i,j) can be specified by nlme(..., weights=p(i,j),...)? Where is p(j) to be used in nlme? I appreciate anyone can provide examples and literature for this problem. Cheers! Han __ [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] mixed models for analyzing survey data with unequal selec tion probability
On Thu, 20 May 2004, Baskin, Robert wrote: Han-Lin I don't think I have seen a reply so I will suggest that maybe you could try a different approach than what you are thinking about doing. I believe the current best practice is to use the weights as a covariate in a regression model - and bytheway - the weights are the inverse of the probabilities of selection - not the probabilities. Fundamentally, there is a difficulty in making sense out of 'random effects' in a finite population setting. I would have thought that it matters why you are fitting a mixed model. Often people use mixed models when they are just interested in inference about the mean and need to model the covariances to get valid standard errors. In that situation you could use an ordinary survey regression to get a design-based result. If you are actually interested in variance components then you need some other approach, and putting the weights into the model as a covariate will presumably give a valid model-based result (since the weights carry all the biased sampling information --- like a propensity score). Presumably this is also more efficient. However, it could well be that you don't want those variables in the model. If the sampling depends on a variable Z correlated with Y and X and you want to model the distribution of Y given X, not the distribution of Y given X and Z, you are still in trouble. -thomas (plagiarized from some unknown source) See: 9. Pfeffermann, D. , Skinner, C. J. , Holmes, D. J. , Goldstein, H. , and Rasbash, J. (1998), ``Weighting for unequal selection probabilities in multilevel models (Disc: p41-56)'', Journal of the Royal Statistical Society, Series B, Methodological, 60 , 23-40 which refers back to: 29. Pfeffermann, D. , and LaVange, L. (1989), ``Regression models for stratified multi-stage cluster samples'', Analysis of Complex Surveys, 237-260 If you don't like statistical papers, then see section 4.5 of 8. Korn, Edward Lee , and Graubard, Barry I. (1999), ``Analysis of health surveys'', John Wiley Sons (New York; Chichester) They explain the idea of using weights in a model fairly simply. Bob -Original Message- From: Han-Lin Lai [mailto:[EMAIL PROTECTED] Sent: Wednesday, May 19, 2004 12:47 PM To: [EMAIL PROTECTED] Subject: [R] mixed models for analyzing survey data with unequal selection probability Hi, I need the help on this topic because this is out of my statistical trianing as biologist. Here is my brief description of the problem. I have a survey that VESSELs are selected at random with the probability of p(j). Then the tows within the jth VESSEL are sampled at random with probability of p(i|j). I write my model as y = XB + Zb + e where XB is fixed part, Zb is for random effect (VESSEL) and e is within-vessel error. I feel that I should weight the Zb part by p(j) and the e-part by p(i,j)=p(j)*p(i|j). Is this a correct weighting? How can I implement the weightings in nlme (or lme)? I think that p(i,j) can be specified by nlme(..., weights=p(i,j),...)? Where is p(j) to be used in nlme? I appreciate anyone can provide examples and literature for this problem. Cheers! Han __ [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 Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ [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] 'start' argument for fitdistr()
Could someone please help me understand the 'start' argument for fitdistr(), perhaps with a couple of examples? (The examples in the online Help are ones that do not require 'start'.) JTW [[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] POSIX to ts and back to POSIX
On Wed, May 19, 2004 at 03:24:38PM -0400, [EMAIL PROTECTED] wrote: I am trying to use POSIX datetime objects rather than chron datetime objects but am having difficulty with POSIX in a time series. My question: Once a POSIXct vector is bound to a time series, is there a function to convert back to POSIXct? The following code demonstrates what I am trying to do. ts(as.POSIXct(strptime(tmp,%m/%d/%Y %H:%M:%S)),freq=1440) Time Series: Start = c(1, 1) End = c(1, 10) Frequency = 1440 [1] 1074022572 1074022632 1074022693 1074022753 1074022813 1074022874 1074022934 1074022994 1074023055 1074023115 attr(,tzone) [1] ... for the reverse process, something like ## UNTESTED! yourts - ts(as.POSIXct(strptime(tmp,%m/%d/%Y %H:%M:%S)),freq=1440) ISOdate(1970,1,1,0,0,0,UTC) + time(yourts) Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [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
[R] Help with hclust() and plot()
Hi When I use plot(hclust(dist..)...)...) etc to create a dendrogram of a hierarchial cluster analysis, I end up with a vertical tree. What do I need to do to get a horizontal tree? Also, my users are used to seeing trees who's leaves all end at the same place (eg. Like in minitab). Is this possible in R? Thanks Mick Michael Watson Head of Informatics Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berkshire RG20 7NN UK Phone : +44 (0)1635 578411 ext. 2535 Mobile: +44 (0)7990 827831 E-mail: [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] Help with hclust() and plot()
michael watson (IAH-C) wrote: Hi When I use plot(hclust(dist..)...)...) etc to create a dendrogram of a hierarchial cluster analysis, I end up with a vertical tree. What do I need to do to get a horizontal tree? Also, my users are used to seeing trees who's leaves all end at the same place (eg. Like in minitab). Is this possible in R? Thanks Mick Mick, If you use as.dendrogram first then the plot method for dendrograms has a horizontal option: data(USArrests) hc - hclust(dist(USArrests), ave) dend1 - as.dendrogram(hc) plot(dend1, horiz = TRUE) This also puts the leave at the end. R version 1.9.0, 2004-05-06 Windows 2000 --sundar __ [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] irregular time series
On Thu, May 20, 2004 at 02:23:46PM +0930, McClatchie, Sam (PIRSA-SARDI) wrote: [long time series, broken in two with a gap] I realise that I could just break each series into two segments and cross-correlate with the shorter series, but I'd rather deal with the whole series to increase the nyquist frequency. I think the its function in the irregular time series package will create a class its object with the right time stamps, but can this then be used in the same was as a class ts object for the correlation and spectral anayses? its does some nice things for storing, plotting, and manipulating irregular time series, but isn't long on the analysis. A few options: 1) Analyze the two sub-series separately. 2) There is some merit to de-mean or de-trending both series, zero-padding the shorter so its length matches the longer, and performing spectral analysis that way. Frequencies near zero should be treated with suspicion, however. 3) Jim Lindsey has some continuous ARMA and Kalman filter routines on his site (Google for Lindsey and rmutil, which is the name of one of those packages). 4) I'm working on an R version of the Lomb periodogram, which was built for irregular series, but I've no guarantees when I'll roll it up - rather busy most days. I do remember seeing an S version on someone's web page, but that was a while ago, and it was the direct or slow method. Hope that helps Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [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] Repeated measures ANOVA
On Wed, May 19, 2004 at 11:11:46PM -0600, GIDEON WASSERBERG wrote:
Dear friends
I am not sure that I am conducting this analysis correctly.
I would really appreciate if someone can verify what I've done.
I conducted repeated measures ANOVA for some bugs data.
These bugs were measured repeatedly over 32 weeks at the
same trapping plots. I want to test a full model for the
effect of time (week) (the within subject variable),
and the main effects are: place, station,species, and all
the interactions thereof.
Since there's likely some serious time and location dependence
here, I suggest you get a copy of Pinheiro and Bates.
@Book{PinheiroBates2000,
author = {Jos\'e C. Pinheiro and Douglas M. Bates},
title =Mixed-Effects Models in S and S-PLUS,
publisher ={Springer-Verlag},
year = {2000},
address = {New York}
}
Since performing statistical consulting for free is a
dangerous prescedent to the profession, I'll leave it
at that :)
Cheers
Jason
--
Indigo Industrial Controls Ltd.
http://www.indigoindustrial.co.nz
64-21-343-545
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[R] write in fixed format
DeaR useRs: I have a problem, because I have a file in fixed width format and I can read it with 'read.fwf' and after I can use these data to do generate new columns (variables) and when I am going to write this set of data (data.frame) I can't find a function which storages my data.frame in fixed width format. Can you help me? Thanks in advance. Agustín Pérez Universidad Miguel Hernández de Elche. __ [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] mixed models for analyzing survey data with unequal selec tion probability
Cassel, Sarndal and Wretman (1977) Foundations of Inference in Survey Sampling (Krieger) insisted that for infinite population inference (what Deming called an 'analytic study'), the sampling probabilities should be ignored UNLESS they related somehow to something of interest in the model. In other words, is the sampling informative or noninformative? If noninformative, the sampling probabilities do not appear in the likelihood and therefore should not affect inference. As I recall, Cassel, Sarndal and Wretman said that if stratified random sampling is used, and if the stratification system is included in the model, then the sampling is noninformative, and the sampling probabilities should not affect inference. From this paradigm, using weights inversely proportional to sampling probabilities is (primarily?) a tool for finite population inference -- what Deming called an 'enumerative study'. For an enumerative study, the purpose is to make inference about a fixed, finite population, e.g., how to feed the people in Japan who would otherwise starve within the next week or month, which was the situation when Deming directed a survey there shortly after World War II. For an analytic study, the purpose is more long term, e.g., how to design a national alimentary system to feed the people who will be there 10 or 30 years from now. Since most of my work has dealt processed that will create the future, rather than dealing with fixed, finite populations, I have ignored sampling probabilities in most of my work (though I have not worked much recently with sample surveys). Is this still consistent with current thinking? Is it feasible to summarize in a few words what Pferrermann, Korn et al. say about this? Thanks, spencer graves Thomas Lumley wrote: On Thu, 20 May 2004, Baskin, Robert wrote: Han-Lin I don't think I have seen a reply so I will suggest that maybe you could try a different approach than what you are thinking about doing. I believe the current best practice is to use the weights as a covariate in a regression model - and bytheway - the weights are the inverse of the probabilities of selection - not the probabilities. Fundamentally, there is a difficulty in making sense out of 'random effects' in a finite population setting. I would have thought that it matters why you are fitting a mixed model. Often people use mixed models when they are just interested in inference about the mean and need to model the covariances to get valid standard errors. In that situation you could use an ordinary survey regression to get a design-based result. If you are actually interested in variance components then you need some other approach, and putting the weights into the model as a covariate will presumably give a valid model-based result (since the weights carry all the biased sampling information --- like a propensity score). Presumably this is also more efficient. However, it could well be that you don't want those variables in the model. If the sampling depends on a variable Z correlated with Y and X and you want to model the distribution of Y given X, not the distribution of Y given X and Z, you are still in trouble. -thomas (plagiarized from some unknown source) See: 9. Pfeffermann, D. , Skinner, C. J. , Holmes, D. J. , Goldstein, H. , and Rasbash, J. (1998), ``Weighting for unequal selection probabilities in multilevel models (Disc: p41-56)'', Journal of the Royal Statistical Society, Series B, Methodological, 60 , 23-40 which refers back to: 29. Pfeffermann, D. , and LaVange, L. (1989), ``Regression models for stratified multi-stage cluster samples'', Analysis of Complex Surveys, 237-260 If you don't like statistical papers, then see section 4.5 of 8. Korn, Edward Lee , and Graubard, Barry I. (1999), ``Analysis of health surveys'', John Wiley Sons (New York; Chichester) They explain the idea of using weights in a model fairly simply. Bob -Original Message- From: Han-Lin Lai [mailto:[EMAIL PROTECTED] Sent: Wednesday, May 19, 2004 12:47 PM To: [EMAIL PROTECTED] Subject: [R] mixed models for analyzing survey data with unequal selection probability Hi, I need the help on this topic because this is out of my statistical trianing as biologist. Here is my brief description of the problem. I have a survey that VESSELs are selected at random with the probability of p(j). Then the tows within the jth VESSEL are sampled at random with probability of p(i|j). I write my model as y = XB + Zb + e where XB is fixed part, Zb is for random effect (VESSEL) and e is within-vessel error. I feel that I should weight the Zb part by p(j) and the e-part by p(i,j)=p(j)*p(i|j). Is this a correct weighting? How can I implement the weightings in nlme (or lme)? I think that p(i,j) can be specified by nlme(..., weights=p(i,j),...)? Where is p(j) to be used in nlme? I appreciate anyone can provide examples and literature for this problem.
RE: [R] Help with hclust() and plot()
Hi Thanks for that! BUT if I use as.dendrogram, I can't use my labels anymore! plot(hclust(...etc), labels=p[,1]) Works fine. But: plot(as.dendrogram(hclust(...etc)), labels=p[,1]) Gives me errors: Error in axis(side, at, labels, tick, line, pos, outer, font, vfont, lty, : location and label lengths differ, 6 != 24 I have 24 labels. I have no idea where it gets 6 from! My 'dendrogram' has '2 branches and 24 members total'. SOOO, how do I get my dendrogram horizontal, or vertical for that matter, with useful labels instead of 1,2,3,4,5,etc Thanks in advance for your help! Mick -Original Message- From: Sundar Dorai-Raj [mailto:[EMAIL PROTECTED] Sent: 20 May 2004 16:49 To: michael watson (IAH-C) Cc: R-Help (E-mail) Subject: Re: [R] Help with hclust() and plot() michael watson (IAH-C) wrote: Hi When I use plot(hclust(dist..)...)...) etc to create a dendrogram of a hierarchial cluster analysis, I end up with a vertical tree. What do I need to do to get a horizontal tree? Also, my users are used to seeing trees who's leaves all end at the same place (eg. Like in minitab). Is this possible in R? Thanks Mick Mick, If you use as.dendrogram first then the plot method for dendrograms has a horizontal option: data(USArrests) hc - hclust(dist(USArrests), ave) dend1 - as.dendrogram(hc) plot(dend1, horiz = TRUE) This also puts the leave at the end. R version 1.9.0, 2004-05-06 Windows 2000 --sundar __ [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] R 1.8.1 - 1.9.0 incompatability: Underscore in syntactically valid names
Dear R-gang, I have a question about handling underscores in names in R 1.8.1 and 1.9.0. I recently installed 1.9.0 on a machine and found that many codes no longer work as a result of the changed behavior in make.names. I have numerous data files that have dashes, periods and underscores in the header row. I've got numerous R codes that read those files with read.table and read.csv and then use the names expecting the underscores and dashes to be changed to periods in the column names. Since this no longer happens in 1.9.0, lots of codes are failing. One way to work around this is to repair a lot of codes to take this backward incompatibility into account (both R scripts and data sources, so that is a significant project, here at least). Or I can stay with 1.8.1, but that is just a sure route to eventual incomparability with something else, so I'll gradually start migrating code over and adding version checks. Can anyone suggest a way to maintain compatibility between R versions? I suppose I could write a wrapper around make.names to replace _ with ., but I'm not sure what that might break in 1.9.0 that now expects the new behavior. I'd appreciate any suggestions. Mike -- Michael A. Miller [EMAIL PROTECTED] Imaging Sciences, Department of Radiology, IU School of Medicine __ [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] Get Slot from a Class
Hello, everyone, I don't quite understand the following message: TTT - t.test(1:10, y=c(7:20)) class(TTT) [1] htest [EMAIL PROTECTED] Error: Trying to get slot p.value from an object whose class (htest) is not defined TTT$p.value [1] 1.855282e-05 Why the message says the class of TTT is not defined while class(TTT) gets htest? I appreciate the explanations? -Minghua [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] write in fixed format
Perez Martin, Agustin wrote: DeaR useRs: I have a problem, because I have a file in fixed width format and I can read it with 'read.fwf' and after I can use these data to do generate new columns (variables) and when I am going to write this set of data (data.frame) I can't find a function which storages my data.frame in fixed width format. Can you help me? Thanks in advance. Agustín Pérez Universidad Miguel Hernández de Elche. See ?write.matrix in package MASS. Uwe Ligges __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Get Slot from a Class
Yao, Minghua wrote: Hello, everyone, I don't quite understand the following message: TTT - t.test(1:10, y=c(7:20)) class(TTT) [1] htest [EMAIL PROTECTED] Error: Trying to get slot p.value from an object whose class (htest) is not defined TTT$p.value [1] 1.855282e-05 Why the message says the class of TTT is not defined while class(TTT) gets htest? I appreciate the explanations? Well, you are mixing S3 with S4 classes. The slot extractor @ epects an S4 class. And htest is an S3 class Uwe Ligges -Minghua [[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
[R] Spearman probabilities and SuppDists
cor.test and SuppDists give me different P-values for the same Spearman's rho. Which is correct, or am I doing something wrong? x - c(44.4, 45.9, 41.9, 53.3, 44.7, 44.1, 50.7, 45.2, 60.1) y - c( 2.6, 3.1, 2.5, 5.0, 3.6, 4.0, 5.2, 2.8, 3.8) cor.test(x,y,method=spearman) Spearman's rank correlation rho data: x and y S = 48, p-value = 0.0968 alternative hypothesis: true rho is not equal to 0 sample estimates: rho 0.6 2*(1-pSpearman(.6,9)) [1] 0.08572531 Drew Hoysak __ [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] ifelse when test is shorter than yes/no
Hi, It turns out that the 'test' vector in ifelse(test, yes, no) is not recycled if it is shorter than the other arguments, e.g. ifelse(TRUE, seq(10), -seq(10)) [1] 1 Is there any particular reason it is not recycled? If there is one indeed a warning message might be in order when someone calls ifelse with a shorter 'test'. This is R1.8.1 on RH-7.3 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
Re: [R] Help with hclust() and plot()
michael watson (IAH-C) wrote: Hi Thanks for that! BUT if I use as.dendrogram, I can't use my labels anymore! plot(hclust(...etc), labels=p[,1]) Works fine. But: plot(as.dendrogram(hclust(...etc)), labels=p[,1]) Gives me errors: Error in axis(side, at, labels, tick, line, pos, outer, font, vfont, lty, : location and label lengths differ, 6 != 24 I have 24 labels. I have no idea where it gets 6 from! My 'dendrogram' has '2 branches and 24 members total'. SOOO, how do I get my dendrogram horizontal, or vertical for that matter, with useful labels instead of 1,2,3,4,5,etc Thanks in advance for your help! Mick Mick, Change the labels in hclust first: data(USArrests) hc - hclust(dist(USArrests), ave) hc$labels - 1:50 dend1 - as.dendrogram(hc) plot(dend1, horiz = TRUE) --sundar __ [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] GUI data browsers
Gabor Grothendieck wrote: This is not a full answer to what you are looking for but you might try ?browseEnv Seems to be among the best answers out there :). There is a TODO item in browseEnv regarding using Tk, so if I am up to the challenge... ?str is helpful too W __ [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] GUI data browsers
foobar wwsprague at ucdavis.edu writes: ?str is helpful too If you are interested in str then you might also be interested in dput. __ [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] Spearman probabilities and SuppDists
cor.test is giving Pr(x0.6), SuppDists is giving Pr(x=0.6). My recollection is that it is the custom in R for discrete distributions to include the point in the left tail. Drew Hoysak wrote: cor.test and SuppDists give me different P-values for the same Spearman's rho. Which is correct, or am I doing something wrong? x - c(44.4, 45.9, 41.9, 53.3, 44.7, 44.1, 50.7, 45.2, 60.1) y - c( 2.6, 3.1, 2.5, 5.0, 3.6, 4.0, 5.2, 2.8, 3.8) cor.test(x,y,method=spearman) Spearman's rank correlation rho data: x and y S = 48, p-value = 0.0968 alternative hypothesis: true rho is not equal to 0 sample estimates: rho 0.6 2*(1-pSpearman(.6,9)) [1] 0.08572531 Drew Hoysak __ [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 -- Bob Wheeler --- http://www.bobwheeler.com/ ECHIP, Inc. --- Randomness comes in bunches. __ [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] for() to lapply()
Hi dear R-users:
I have the following problem:
I have a list of data.frames (12 variables and 6 rows, each)
I have to merge from an specific point of the list to the
end of the list, I am doing so with a for() loop but it is
too inefficient and it exhausts memory.
How can I convert this for() loop in a function and then use
lapply?
-
LIST: list of data frames.
m:point of start merging.
result-merge(LIST[[m]],LIST[[m+1]],by=key,all.x=T)
for (i in (m+2):length(LIST))
{
result-merge(result,LIST[[i]],by=key,all.x=T)
}
The problem is the acumulative: result-merge(result,...)
I can think in a function like this:
mergeListelem-function(i,LS,m)
{
merge(LS[[m]],LS[[i]],by=key,all.x=T)
}
ind-m:length(LIST)
lapply(ind,mergeListelem,LIST,m)
But I just obtain a list of merged data.frames,
and I dont know how to join all the elements
of the list in just one final data.frame.
Thank you for your help
--
Kenneth Cabrera
Universidad Nacional de Colombia
Tel Of 430 9351
Cel 315 504 9339
Medelln
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RE: [R] ifelse when test is shorter than yes/no
From: Vadim Ogranovich Hi, It turns out that the 'test' vector in ifelse(test, yes, no) is not recycled if it is shorter than the other arguments, e.g. ifelse(TRUE, seq(10), -seq(10)) [1] 1 Is there any particular reason it is not recycled? If there is one indeed a warning message might be in order when someone calls ifelse with a shorter 'test'. ?ifelse says: Value: A vector of the same length and attributes (including class) as 'test' and data values from the values of 'yes' or 'no'. ... Seems to me it works as documented. Why do you expected otherwise? Andy This is R1.8.1 on RH-7.3 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 __ [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] ifelse when test is shorter than yes/no
It does work as documented. My question was why it was designed to work
this way. I can not think of a practical situation when someone might
want to ifelse() on a 'test' that is shorter than yes/no w/o expecting
'test' to recycle (therefore I was asking for a warning).
I find this behavior inconsistent with the (spirit of) R's recycling
rules. For example if 'test', 'yes', 'no' are all of the same length
then the following two expressions are equivalent:
1.
x - ifelse(test, yes, no)
2.
x - no; x[test] - yes[test]
This equivalence breaks when 'test' is shorter than yes/no: in the
second case 'test' will be recycled. And I don't see a good reason for
having them behave differently.
If I had to implement ifelse() I'd probably do:
ifelse2 - function(test, yes, no) {
x - rep(no, length.out=max(length(test), length(yes),
length(no)))
x[test] - yes[test]
x
}
(If there is interest I can extend it to take care of NA-s and submit as
a (trivial) patch)
Here is a simple test:
ifelse2(c(TRUE, FALSE), seq(10), -seq(5))
[1] 1 -2 3 -4 5 -1 7 -3 9 -5
Maybe it will help if I tell how I stumbled upon this problem. I had two
m*n matrices, 'yes' and 'no', and a 'test' vector of length m. I wanted
to create a m*n matrix which has 'yes' rows where test==TRUE and 'no'
rows otherwise. So I did
x - matrix(ifelse(test, yes, no), nrow(yes), ncol(yes))
priding myself for doing it the whole object way ... and 'test' did
not recycle (in full accordance with the help page) w/o a warning.
Thanks,
Vadim
-Original Message-
From: Liaw, Andy [mailto:[EMAIL PROTECTED]
Sent: Thursday, May 20, 2004 2:20 PM
To: Vadim Ogranovich; R-Help
Subject: RE: [R] ifelse when test is shorter than yes/no
From: Vadim Ogranovich
Hi,
It turns out that the 'test' vector in ifelse(test, yes, no) is not
recycled if it is shorter than the other arguments, e.g.
ifelse(TRUE, seq(10), -seq(10))
[1] 1
Is there any particular reason it is not recycled? If there is one
indeed a warning message might be in order when someone
calls ifelse
with a shorter 'test'.
?ifelse says:
Value:
A vector of the same length and attributes (including class) as
'test' and data values from the values of 'yes' or 'no'. ...
Seems to me it works as documented. Why do you expected otherwise?
Andy
This is R1.8.1 on RH-7.3
Thanks,
Vadim
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Re: [R] for() to lapply()
On Thu, May 20, 2004 at 03:52:22PM -0500, Kenneth Cabrera wrote:
Hi dear R-users:
I have the following problem:
I have a list of data.frames (12 variables and 6 rows, each)
I have to merge from an specific point of the list to the
end of the list, I am doing so with a for() loop but it is
too inefficient and it exhausts memory.
How can I convert this for() loop in a function and then use
lapply?
There's still a better way to do it, I'm sure, but something
like...
##untested!
myMerge - function(x,y,...) {
zz - merge(x,y,...)
gc()
}
foo - lapply(my.df.list[[-1]],myMerge,my.df.list[[1]])
Cheers
Jason
--
Indigo Industrial Controls Ltd.
http://www.indigoindustrial.co.nz
64-21-343-545
[EMAIL PROTECTED]
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[R] Memory usage of R on Windows XP
I am running R 1.8.1 on windows xp. I have been using the 'apply' R
function to run a short function against a matrix of 19000 x 340 rows ...
yes it is a big matrix. every item in the matrix is a float that can have a
maximum value of 2^16 ~ 65k.
The function:
mask256 - function(value) {
if (value 256) {
result = 0
}
else {
result = 1
}
result
}
what happens is that the memory required for the session to run starts
ballooning. The matrix with a few other objects starts at about 160M, but
then quickly goes up to 750M, and stays there when the function has completed
I am fairly new to R. Is there something I should know about writing
functions , i.e. do I need to clean-up at the end of the function? It seems
R can not release the memory once it has been used. When I close the R
application and open the R application again then the memory is back down
to what it is supposed to be, the size of the workspace, plus any new
objects that I have created
Does anybody know what is going on?
Peter
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Re: [R] for() to lapply()
I have the following problem: I have a list of data.frames (12 variables and 6 rows, each) I have to merge from an specific point of the list to the end of the list, I am doing so with a for() loop but it is too inefficient and it exhausts memory. How about: a - list( data.frame(a=1), data.frame(a=2), data.frame(a=3), data.frame(a=4) ) do.call(rbind, a) do.call(rbind, a[3:4]) (assuming that the data frames have the same variables) Hadley __ [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: Windows versus Unix packages in CRAN (Was Re: [R] Rmetrics)
Hello all:
On my linux platform, I ran the commands,
mkdir fBasics
unzip fBasics.zip -d fBasics
rm fBasics/src/*.o
R CMD check fBasics
That was 3 minutes. Next, I copied the files contained in
fBasics.Rcheck/fBasics to the R library.
library(fBasics)
fBasics:Markets, Basic Statistics, Date and TimeError in
try(winMenuAdd(Rmetrics)) : couldn't find function winMenuAdd
So, how do I get it to work with no problems in Linux??
Thanks,
Andrew
Janusz Kawczak wrote:
And it seems that this vicious circle continues forever. Before
posting these kind of messages can you please read the INSTRUCTIONS.
fBasics_190.10051.zip is a COMPILED version of the package, not
a source as you claim to be!
It works with no problems; well, at least under Linux.
Janusz.
Richard A. O'Keefe wrote:
Prof Brian Ripley [EMAIL PROTECTED] wrote:
mkdir fBasics
unzip fBasics.zip -d fBasics
rm fBasics/src/*.o
R CMD check fBasics
and that took me about 3 minutes.
Now me, I just did
unzip -a fBasics_190.10051.zip
R CMD INSTALL fBasics
rm -rf fBasics
in a naive and trusting manner. It took me considerably longer than 3
minutes to learn that this was what I should do, and when I did learn,
I wondered if it's this simple, why can't R CMD INSTALL do it?
Now I discover that it isn't that simple. The installation apparently
went smoothly. This is R, right? Never occurred to me that there might
be problems.
Now, B-G--R! It turns out that core stuff is supplied as .dll files,
which of course my UltraSPARC can do nothing with.
The author of the Rmetrics code has a perfect right to provide his code
in any form he wants under any conditions he wants (subject to GPL c).
In particular, if he wants to provide a distribution which only works under
Windows, that's perfectly OK.
**BUT** when a distribution is peculiar to one operating system, that really
should be highlighted in big bold letters: this is a WINDOWS BINARY
version, so that people who can't use Windows .DLL files are spared a day
of trying to figure out how to unpack and of doing an installation which
reports no errors at all and of them finding that things do not work.
There is *NOTHING* on http://www.itp.phys.ethz.ch/econophysics/R/download.htm
that says Windows only. Click on I acceptand the page you arrive at has
nothing in the text anywhere that says Windows only or what to do if not
Windows. (The http://.../R/bin/windows/contrib/1.9 address of the page
was, in retrospect, a big clue, sigh.)
It would of course be nice if the developers had done
R CMD check fBasics
But if you go into the Sources directory, which I suppose you must have,
for each of {fBasics,fExtremes,fOptions,fSeries} there is an
xxx-00check.log.txt, so they _did_ run R CMD check.
and sorted out the errors, then
R CMD build fBasics
Those same check logs show errors (like failure to build .dvi files).
Will it work if I download the Sources packages?
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[R] function for running MS-DOS on R
I had downloaded the program that runs on MS-DOS. Is it possible for MS-DOS to be run in R such as WinBugs1.4? I wonder whether there is the R function for running MS-DOS from R such as the 'bug.r' function to make Winbugs practicable in R. I had heard Rterm.exe that runs on MS-DOS. However, What I need is to run MS-DOS in R but to run R in MS-DOS. _ MSN Hotmail . http://loginnet.passport.com/login.srf?id=2svc=mailcbid=24325msppjph=1lc=1042 __ [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] function for running MS-DOS on R
Perhaps you could use the R2WinBugs package? --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:r-help- [EMAIL PROTECTED] Behalf Of bang jeong sook Sent: Thursday, May 20, 2004 19:9 PM To: [EMAIL PROTECTED] Subject: [R] function for running MS-DOS on R I had downloaded the program that runs on MS-DOS. Is it possible for MS-DOS to be run in R such as WinBugs1.4? I wonder whether there is the R function for running MS-DOS from R such as the 'bug.r' function to make Winbugs practicable in R. I had heard Rterm.exe that runs on MS-DOS. However, What I need is to run MS-DOS in R but to run R in MS-DOS. _ MSN Hotmail . http://loginnet.passport.com/login.srf?id=2svc=mailcbid=24325msppjph=1lc =1042 __ [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: Windows versus Unix packages in CRAN (Was Re: [R] Rmetrics)
Here is what I get:
R : Copyright 2004, The R Foundation for Statistical Computing
Version 1.9.0 (2004-04-12), ISBN 3-900051-00-3
.
[Previously saved workspace restored]
library(fBasics)
---
fLibraries: A SOFTWARE COLLECTION FOR FINANCIAL ENGINEERS
fBasics:Markets, Basic Statistics, Date and Time
---
(there were no alterations done to the above output except where
occurs!)
You simply need to remove the stuff related to MS Win from zzz.R;
in partricular the lines after if( ) to clear your message.
As you can see, the info relates to the WinMenu under MS Win.
Hope this helps.
Janusz.
On Fri, 21 May 2004, Andrew Criswell wrote:
Hello all:
On my linux platform, I ran the commands,
mkdir fBasics
unzip fBasics.zip -d fBasics
rm fBasics/src/*.o
R CMD check fBasics
That was 3 minutes. Next, I copied the files contained in
fBasics.Rcheck/fBasics to the R library.
library(fBasics)
fBasics:Markets, Basic Statistics, Date and TimeError in
try(winMenuAdd(Rmetrics)) : couldn't find function winMenuAdd
So, how do I get it to work with no problems in Linux??
Thanks,
Andrew
Janusz Kawczak wrote:
And it seems that this vicious circle continues forever. Before
posting these kind of messages can you please read the INSTRUCTIONS.
fBasics_190.10051.zip is a COMPILED version of the package, not
a source as you claim to be!
It works with no problems; well, at least under Linux.
Janusz.
Richard A. O'Keefe wrote:
Prof Brian Ripley [EMAIL PROTECTED] wrote:
mkdir fBasics
unzip fBasics.zip -d fBasics
rm fBasics/src/*.o
R CMD check fBasics
and that took me about 3 minutes.
Now me, I just did
unzip -a fBasics_190.10051.zip
R CMD INSTALL fBasics
rm -rf fBasics
in a naive and trusting manner. It took me considerably longer than 3
minutes to learn that this was what I should do, and when I did learn,
I wondered if it's this simple, why can't R CMD INSTALL do it?
Now I discover that it isn't that simple. The installation apparently
went smoothly. This is R, right? Never occurred to me that there might
be problems.
Now, B-G--R! It turns out that core stuff is supplied as .dll files,
which of course my UltraSPARC can do nothing with.
The author of the Rmetrics code has a perfect right to provide his code
in any form he wants under any conditions he wants (subject to GPL c).
In particular, if he wants to provide a distribution which only works under
Windows, that's perfectly OK.
**BUT** when a distribution is peculiar to one operating system, that really
should be highlighted in big bold letters: this is a WINDOWS BINARY
version, so that people who can't use Windows .DLL files are spared a day
of trying to figure out how to unpack and of doing an installation which
reports no errors at all and of them finding that things do not work.
There is *NOTHING* on http://www.itp.phys.ethz.ch/econophysics/R/download.htm
that says Windows only. Click on I acceptand the page you arrive at has
nothing in the text anywhere that says Windows only or what to do if not
Windows. (The http://.../R/bin/windows/contrib/1.9 address of the page
was, in retrospect, a big clue, sigh.)
It would of course be nice if the developers had done
R CMD check fBasics
But if you go into the Sources directory, which I suppose you must have,
for each of {fBasics,fExtremes,fOptions,fSeries} there is an
xxx-00check.log.txt, so they _did_ run R CMD check.
and sorted out the errors, then
R CMD build fBasics
Those same check logs show errors (like failure to build .dvi files).
Will it work if I download the Sources packages?
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Re: [R] Memory usage of R on Windows XP
On 20 May 2004 at 20:58, Peter Wilkinson wrote:
I am running R 1.8.1 on windows xp. I have been using the 'apply' R
function to run a short function against a matrix of 19000 x 340 rows
... yes it is a big matrix. every item in the matrix is a float that
can have a maximum value of 2^16 ~ 65k.
Hi
I would go for computing only, should be quicker.
(yourmatrix=256)*1
will give you 1 on places where was number greater or equal 256 and 0 where it
was lower.
Not sure about memory issues but I suppose better performance than if else apply
construction.
Cheers
Petr
The function:
mask256 - function(value) {
if (value 256) {
result = 0
}
else {
result = 1
}
result
}
what happens is that the memory required for the session to run starts
ballooning. The matrix with a few other objects starts at about 160M,
but then quickly goes up to 750M, and stays there when the function
has completed
I am fairly new to R. Is there something I should know about writing
functions , i.e. do I need to clean-up at the end of the function? It
seems R can not release the memory once it has been used. When I close
I suppose R is doing it best but Windows does not take it back.
the R application and open the R application again then the memory is
back down to what it is supposed to be, the size of the workspace,
plus any new objects that I have created
Does anybody know what is going on?
Peter
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Petr Pikal
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