Re: [R] polr problem solved
On Fri, 8 Oct 2004, Peter Flom wrote: I'd like to thank John Fox and Chuck Cleland for their help in resovling this issue. It turned out to be something simple, but perhaps others have had similar problems In my original data frame, I had 4 categories of race/ethnicity. One of the categories (other) was very small, and not similar to any of the other three categories, so I created a new data frame deleting those people. However, the level other was still there, with no one in it. This didn't cause a problem for glm or lm, but it did for polr. When I eliminated that level, the problem disappeared. How did you use `glm or lm' for an order factor response? An empty factor level will certainly cause glm problems, depending which one it is. An empty level will always cause polr problems, as there is no MLE under those circumstances. I will add a sanity check in due course. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Survey of moving window statistical functions - still looking f or fast mad function
On Fri, 8 Oct 2004, Tuszynski, Jaroslaw W. wrote: [...] Finally a question: I still need to get moving windows mad function faster my runmad function is not that much faster than apply/embed combo, and that I used before, and this is where my code spends most of its time. I need something like runmed but for a mad function. Any suggestions? Write your own C-level implementation, as runmed and most of the other fast functions you cite are. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Adding factor variable to a CoxPH
On Sat, Oct 09, 2004 at 09:03:23AM +0800, Neil Leonard wrote: I think this is a pretty basic statistic question: If I have a variable which has 4 factors how can I add it to a coxph model? I have other variables added which have digits 1-4 instead of four factors. If I recode the variable will that work? ?factor ?as.factor Thanks Neil __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Göran Broströmtel: +46 90 786 5223 Department of Statistics fax: +46 90 786 6614 Umeå University http://www.stat.umu.se/egna/gb/ SE-90187 Umeå, Sweden e-mail: [EMAIL PROTECTED] __ [EMAIL PROTECTED] 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] which() and value replacement in a matrix
Hi, I cannot go through the archives with which() as key-word... so common. Though I am sure to have seen something about this subject in the past could somebody put me on the track. I have a matrix (actually a data.frame) in which I would replace the non-null values by 1. I tried the following: indices-which(myforetbin 0,arr.ind=T) myforetbin[indices[,1],indices[,2]]-1 and get the message: myforetbin[indices[,1],indices[,2]]-1 Error in [-.data.frame(`*tmp*`, indices[, 1], indices[, 2], value = 1) : duplicate subscripts for columns I get the same with myforetbin[indices]-1 However, with: myforetbin[indices] I well get a vector with the corresponding non-null values. Can somebody put me on the track? All the best, Patrick __ [EMAIL PROTECTED] 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] polr problem solved
Prof Brian Ripley [EMAIL PROTECTED] 10/09/04 3:18 AM asked How did you use `glm or lm' for an order factor response? An empty factor level will certainly cause glm problems, depending which one it is. An empty level will always cause polr problems, as there is no MLE under those circumstances. I will add a sanity check in due course. The analyses were part of a paper I am writing, illustrating that, when the DV is oddly distributed (the DV in question was a count, with many 0's, and a long right tail) that the 'usual' methods not only are wrong for statisically reasaons (such as grossly violating model assumptions) but also give bad results. While this is widely known to statisticians, in the fields in which I work, people sometimes analyze such variables using either OLS regression (hence lm), or by categorizing the DV into something like 0, 1, 2, more than 2 (hence the need for polr). I also tried Poisson regression and negative binomial regression (hence glm). The empty level of the IV only caused a problem for polr Thanks Peter Peter Peter L. Flom, PhD Assistant Director, Statistics and Data Analysis Core Center for Drug Use and HIV Research National Development and Research Institutes 71 W. 23rd St www.peterflom.com New York, NY 10010 (212) 845-4485 (voice) (917) 438-0894 (fax) __ [EMAIL PROTECTED] 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] Shangai ranking of world Universities
Dear all, this is somewhat off-topic, but given the audience of this mailling list this might interest some people here. I have imported under R the data used in 2004 by Liu et al. from Shanghai Jiao Tong University to build their Academic Ranking of World Universities, see: http://ed.sjtu.edu.cn/rank/2004/2004Main.htm The following R code: loadURL(http://pbil.univ-lyon1.fr/R/donnees/shangai.RData;, mode = wb) should import a dataframe called shangai in your workspace. If you are interested I have also a draft Sweave-generated document based on this dataframe, but all comments are in french. I would be interested by references of scientific articles about this ranking. Best, Jean Lobry -- Jean R. Lobry([EMAIL PROTECTED]) Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I, 43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE allo : +33 472 43 12 87 fax: +33 472 43 13 88 http://pbil.univ-lyon1.fr/members/lobry/ __ [EMAIL PROTECTED] 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] which() and value replacement in a matrix
Use the index vector directly, rather than breaking it up: x - matrix(sample(30), 10, 3) idx - which(x 25, arr.ind=TRUE) idx row col [1,] 6 1 [2,] 9 1 [3,] 4 2 [4,] 6 2 [5,] 4 3 x[idx] - 999 x [,1] [,2] [,3] [1,]7 14 16 [2,] 20 248 [3,] 17 18 11 [4,] 19 999 999 [5,] 234 15 [6,] 999 9995 [7,] 219 12 [8,] 2223 [9,] 999 131 [10,]6 10 25 HTH, Andy From: Patrick Giraudoux Hi, I cannot go through the archives with which() as key-word... so common. Though I am sure to have seen something about this subject in the past could somebody put me on the track. I have a matrix (actually a data.frame) in which I would replace the non-null values by 1. I tried the following: indices-which(myforetbin 0,arr.ind=T) myforetbin[indices[,1],indices[,2]]-1 and get the message: myforetbin[indices[,1],indices[,2]]-1 Error in [-.data.frame(`*tmp*`, indices[, 1], indices[, 2], value = 1) : duplicate subscripts for columns I get the same with myforetbin[indices]-1 However, with: myforetbin[indices] I well get a vector with the corresponding non-null values. Can somebody put me on the track? All the best, Patrick __ [EMAIL PROTECTED] mailing list https://stat.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://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] problem Installing R 2.0.0 on SuSe 9.1
Hello: I first tried it by using ./configure with the source files, but found that there is a huge problem with the gcc-g77 package, then I tried using the RPM obtained from CRAN, getting the following, the first of which appears to be another manifestation of the g77 problem: linux:/tmp # rpm -i R-base-2.0.0-1.i586.rpm warning: R-base-2.0.0-1.i586.rpm: V3 DSA signature: NOKEY, key ID a3278da3 error: Failed dependencies: libg2c.so.0 is needed by R-base-2.0.0-1 libglade-gnome.so.0 is needed by R-base-2.0.0-1 libglade.so.0 is needed by R-base-2.0.0-1 Do you have a suggestion about what I (a suse beginner) should do in order to get R up and running under suse 9.1? I have done some looking around and I do not see any package on suse for version 3.3.3 of the gcc-g77 package that corresponds to the gcc-g++ version 3.3.3, and I don't know if I am up to changing the versions of everything, so I hope I don't have to do that. Thanks in advance. I'm not a Suse user, but this probably means you are missing a couple packages that a required for the install. On a Fedora 2 box : [EMAIL PROTECTED] albert]$ rpm -qf /usr/lib/libg2c.so.0 libf2c-3.3.3-7 [EMAIL PROTECTED] albert]$ rpm -qf /usr/lib/libglade-gnome.so.0 libglade-0.17-13.2.1 [EMAIL PROTECTED] albert]$ rpm -qf /usr/lib/libglade.so.0 libglade-0.17-13.2.1 [EMAIL PROTECTED] albert]$ Do you have those files? If not, you might just need to install a couple of rpms, libf2c and libglade. They seem to be available for 9.1: http://www.suse.com/us/private/products/suse_linux/prof/packages_profess ional/libglade.html http://www.suse.de/en/private/products/suse_linux/prof/packages_professi onal/f2c.html What does rpm -q f2c libglade tell you? Chris __ [EMAIL PROTECTED] 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] RE: zero-inflated count models (was polr problem solved)
Dear Peter, -Original Message- . . . The analyses were part of a paper I am writing, illustrating that, when the DV is oddly distributed (the DV in question was a count, with many 0's, and a long right tail) that the 'usual' methods not only are wrong for statisically reasaons (such as grossly violating model assumptions) but also give bad results. While this is widely known to statisticians, in the fields in which I work, people sometimes analyze such variables using either OLS regression (hence lm), or by categorizing the DV into something like 0, 1, 2, more than 2 (hence the need for polr). I also tried Poisson regression and negative binomial regression (hence glm). From your description, it seems possible that there are too many zeros for a Poisson or negative-binomial model. Since the focus of your paper is the methodology, you might want to try a zero-inflated Poisson or negative-binomial model. Though I haven't tried them, I'm aware of two sources of R functions for zero-inflated count models -- zeroinfl(), from Simon Jackman's web site http://pscl.stanford.edu/content.html, and gnlr() in Jim Lindsey's gnlm package, which is not available on CRAN but at www.luc.ac.be/~jlindsey/rcode.html. I hope this helps, John John Fox Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox __ [EMAIL PROTECTED] 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] which() and value replacement in a matrix
Thanks for the clue. Actually the trouble comes when refering to a data.frame. If I use the matrix from the data.frame (matrix(mydataframe)), everything goes smoothly... So I wrote: indices-which(myforetbin 0,arr.ind=T) myforetbin-as.matrix(myforetbin) myforetbin[indices]-1 myforetbin-as.data.frame(myforetbin) It works but I wonder if there are no more simple ways... All the best, Patrick - Original Message - From: Liaw, Andy [EMAIL PROTECTED] To: 'Patrick Giraudoux' [EMAIL PROTECTED]; r-help [EMAIL PROTECTED] Sent: Saturday, October 09, 2004 3:00 PM Subject: RE: [R] which() and value replacement in a matrix Use the index vector directly, rather than breaking it up: x - matrix(sample(30), 10, 3) idx - which(x 25, arr.ind=TRUE) idx row col [1,] 6 1 [2,] 9 1 [3,] 4 2 [4,] 6 2 [5,] 4 3 x[idx] - 999 x [,1] [,2] [,3] [1,]7 14 16 [2,] 20 248 [3,] 17 18 11 [4,] 19 999 999 [5,] 234 15 [6,] 999 9995 [7,] 219 12 [8,] 2223 [9,] 999 131 [10,]6 10 25 HTH, Andy From: Patrick Giraudoux Hi, I cannot go through the archives with which() as key-word... so common. Though I am sure to have seen something about this subject in the past could somebody put me on the track. I have a matrix (actually a data.frame) in which I would replace the non-null values by 1. I tried the following: indices-which(myforetbin 0,arr.ind=T) myforetbin[indices[,1],indices[,2]]-1 and get the message: myforetbin[indices[,1],indices[,2]]-1 Error in [-.data.frame(`*tmp*`, indices[, 1], indices[, 2], value = 1) : duplicate subscripts for columns I get the same with myforetbin[indices]-1 However, with: myforetbin[indices] I well get a vector with the corresponding non-null values. Can somebody put me on the track? All the best, Patrick __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. -- __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] conversion of a data.frame of numerics to a data.frame of factors
Hi,
I am trying to convert a data.frame of numerics (this could be a matrix as well in
this case) into a data.frame of factors.
I did it in a way that is less than direct...
myforet2-t(myforet)
for (i in 1:length(myforet2[1,])) {
if (i == 1)myforetfact-list(as.factor(myforet2[,i]))
else myforetfact-c(myforetfact,list(as.factor(myforet2[,i])))
}
myforetfact-data.frame(myforetfact)
names(myforetfact)-row.names(myforet)
Here again, I wonder if there are no easier way to go through (the loop is not R
style, for the least). However, I cannot do
it otherway so far...
Cheers,
Patrick
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[R] inst directory
R CMD check now balks at my inst directory. It contains a single folder doc, but apparently any folder causes the problem. If inst is empty, the project checks OK. This was not a problem before 1.9. I've checked the documentation, but don't see a change. What am I missing. -- Bob Wheeler --- http://www.bobwheeler.com/ ECHIP, Inc. --- Randomness comes in bunches. __ [EMAIL PROTECTED] 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] conversion of a data.frame of numerics to a data.frame of factors
On Sat, 9 Oct 2004, Patrick Giraudoux wrote:
mydf[] - lapply(mydf, as.factor)
would appear to be what you want.
For a matrix, I presume you want a factor matrix as the result. Something
like
my - matrix(1:12, 3, 4)
dmy - dim(my)
my - as.factor(my)
dim(my) - dmy
my
which does not print as a matrix but is one. If you want a data frame
result, convert to a data frame first.
Hi,
I am trying to convert a data.frame of numerics (this could be a matrix
as well in this case) into a data.frame of factors.
I did it in a way that is less than direct...
myforet2-t(myforet)
for (i in 1:length(myforet2[1,])) {
if (i == 1)myforetfact-list(as.factor(myforet2[,i]))
else myforetfact-c(myforetfact,list(as.factor(myforet2[,i])))
}
myforetfact-data.frame(myforetfact)
names(myforetfact)-row.names(myforet)
Here again, I wonder if there are no easier way to go through (the loop is not
R style, for the least). However, I cannot do
it otherway so far...
Cheers,
Patrick
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--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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[R] [R-pkgs] Publishing R package descriptions in JSS
More and more R packages come with a corresponding article in the Journal of Statistical Software (www.jstatsoft.org). Achim Zeileis, our TeXnical Editor, has recently contributed jss style files for issues, bookreviews, software reviews, and code snippets. They can be downloaded from http://www.jstatsoft.org/JSSstyle.zip Package authors who want to transform their package into a published article are encouraged to use these style files. === Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8125 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] homepage: http://gifi.stat.ucla.edu - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ [EMAIL PROTECTED] 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] [R-pkgs] verfication package announcement
The verification package has recently been posted to CRAN. This package was initially developed by people in the Verification Group at the National Center for Atmospheric Research to verfiy and study weather models and forecasts. It has been written in general terms to be applicable to other fields of study. Functions include receiver operating characteristic curves attribute diagrams reliability plots spatial scale and frequency plots conditional quantile plots and more. Suggestions and comments on the package can be directed to me at [EMAIL PROTECTED] More information on verification (with a somewhat meteorolgical perspective) can be found at http://www.bom.gov.au/bmrc/wefor/staff/eee/verif/verif_web_page.html. Thanks, Matt # Matt Pocernich NCAR - Research Applications Program 303-497-8312 ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ [EMAIL PROTECTED] 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] [R-pkgs] R interface for MINPACK least squares optimization library
Hello guys. I've built and uploaded to CRAN an R interface to MINPACK Fortran library, which solves non-linear least squares problem by modification of the Levenberg-Marquardt algorithm. The package includes one R function, which passes all the necessary control parameters to the appropriate Fortran functions. The package location is http://cran.r-project.org/src/contrib/Descriptions/minpack.lm.html Best wishes, Timur. ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ [EMAIL PROTECTED] 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] inst directory
On Sat, 9 Oct 2004, Bob Wheeler wrote: R CMD check now balks at my inst directory. It contains a single folder doc, but apparently any folder causes the problem. If inst is empty, the project checks OK. This was not a problem before 1.9. I've checked the documentation, but don't see a change. What am I missing. Hard to tell. (What does `balk at' really mean? What OS? What is meant by `now'?: there is no `1.9' and 1.9.0 is six months ago. And so on.) There are many packages on CRAN with sub-directories of inst (I presume that is what you mean by `folder'), for example MASS, sm, spatstat, and several (e.g. strucchange) have an inst directory just containing a doc subdirectory. As I hope is clear we would need a lot more information. Also, I think R-devel is a more appropriate place to ask such questions. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] conversion of a data.frame of numerics to a data.frame of factors
This work perfectly with a data.frame. Actually my so-called data.frame was an
output of t(), and thus not a data.frame (what I
realise after trying Prof. Ripley's example). If applied to an output of t() (eg
t(df)), the result is quite unxpected (to me): a
strange list of 989 elements, each of them being a factor of one digit and one level
corresponding to each cell of the matrix 23
rows x 43 columns...
So in this particular case, advised to write:
mydf-as.data.frame(t(mydf0))
mydf[] - lapply(mydf, as.factor)
- Original Message -
From: Prof Brian Ripley [EMAIL PROTECTED]
To: Patrick Giraudoux [EMAIL PROTECTED]
Cc: r-help [EMAIL PROTECTED]
Sent: Saturday, October 09, 2004 4:32 PM
Subject: Re: [R] conversion of a data.frame of numerics to a data.frame of factors
On Sat, 9 Oct 2004, Patrick Giraudoux wrote:
mydf[] - lapply(mydf, as.factor)
would appear to be what you want.
For a matrix, I presume you want a factor matrix as the result. Something
like
my - matrix(1:12, 3, 4)
dmy - dim(my)
my - as.factor(my)
dim(my) - dmy
my
which does not print as a matrix but is one. If you want a data frame
result, convert to a data frame first.
Hi,
I am trying to convert a data.frame of numerics (this could be a matrix
as well in this case) into a data.frame of factors.
I did it in a way that is less than direct...
myforet2-t(myforet)
for (i in 1:length(myforet2[1,])) {
if (i == 1)myforetfact-list(as.factor(myforet2[,i]))
else myforetfact-c(myforetfact,list(as.factor(myforet2[,i])))
}
myforetfact-data.frame(myforetfact)
names(myforetfact)-row.names(myforet)
Here again, I wonder if there are no easier way to go through (the loop is
not R style, for the least). However, I
cannot
do
it otherway so far...
Cheers,
Patrick
__
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--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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[R] Clustering of variable
Hi! Does anybody know if there is any way to do clustering of variables? Thank you in advance, Clara. [[alternative HTML version deleted]] __ [EMAIL PROTECTED] 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] Chernoff faces
There is also an code which is more faithful (?) to the original one by S. Aoki although it is in a Japanese HP http://aoki2.si.gunma-u.ac.jp/R/face.html Quality? Judge yourself! Wolfram Fischer wrote: Kenneth == Kenneth Cabrera [EMAIL PROTECTED] writes: Kenneth Hello everybody: Does any one has a function to build Chernoff Kenneth faces? Many of us don't think it's worth them. But we know that opinions differ and gladly incorporate (good quality) submissions of source code. R *is* an open source project and to some extent a community effort. Please don't hesitate to contribute and enter the hall of fame of R contributors :-) Martin An example code from H.P. Wolf (2003) can be found at: http://www.wiwi.uni-bielefeld.de/~wolf/ : S/R - functions : faces Wolfram __ [EMAIL PROTECTED] mailing list https://stat.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://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] RE: zero-inflated count models (was polr problem solved)
John Fox wrote From your description, it seems possible that there are too many zeros for a Poisson or negative-binomial model. Since the focus of your paper is the methodology, you might want to try a zero-inflated Poisson or negative-binomial model. Though I haven't tried them, I'm aware of two sources of R functions for zero-inflated count models -- zeroinfl(), from Simon Jackman's web site http://pscl.stanford.edu/content.html, and gnlr() in Jim Lindsey's gnlm package, which is not available on CRAN but at www.luc.ac.be/~jlindsey/rcode.html. Indeed. I am going to use these, as well, and attempt to demonstrate that fitting the correct model not only is correct, statistically, but also give results that are substantively different than the 'usual' models. I hope that this will increase the use of appropriate models in the field (which, in case anyone is interested, is substance abuse research, and, in my particular case, the syringe-sharing behaviors of drug injectors). Peter Peter L. Flom, PhD Assistant Director, Statistics and Data Analysis Core Center for Drug Use and HIV Research National Development and Research Institutes 71 W. 23rd St www.peterflom.com New York, NY 10010 (212) 845-4485 (voice) (917) 438-0894 (fax) __ [EMAIL PROTECTED] 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] R-2.0.0 and tcltk package
there does not seem to be a package tcltk on CRAN for 2.0.0. I have successfully installed the same package for 1.9.1. In essence I require the package for a GUI interface to setwd. All work fine with 1.9.1. This is on a Linux Debian unstable kernel 2.4.20 The build version of R 2.0.0 (issuing version whithin R) has the following platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major2 minor0.0 year 2004 month10 day 04 language R However, the build version of 1.9.1. has the paltform as i386 platform i386-pc-linux-gnu arch i386 os linux-gnu system i386, linux-gnu status major1 minor9.1 year 2004 month06 day 21 language R Thank you for all the help, Jean, __ [EMAIL PROTECTED] 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 safe? Cochran etc
I have the following contingency table
dat - matrix(c(1,506,13714,878702),nr=2)
And I want to test if their is an association between events
A:{a,not(a)} and B:{b,not(b)}
| b | not(b) |
+-++
a | 1 | 13714 |
+-++
not(a) | 506 | 878702 |
+-++
I am worried that prop.test and chisq.test are not valid given the low
counts and low probabilites associated with 'sucess' in each category.
Is it safe to use them, and what is the alternative? (given that
fisher.test can't handle this data... hold the phone...
I just found fisher.test can handle this data if the test is one-tailed
and not two-tailed.
I don't understand the difference between chisq.test, prop.test and
fisher.test when the hybrid=1 option is used for the fisher.test.
I was using the binomial distribution to test the 'extremity' of the
observed data, but now I think I know why that is inapropriate, however,
with the binomial (and its approximation) at least I know what I am
doing. And I can do it in perl easily...
Generally, how should I calculate fisher.test in perl (i.e. what are its
principles). When is it safe to approximate fisher to chisq?
I cannot get insight into this problem...
How come if I do...
dat - matrix(c(50,60,100,100),nr=2)
prop.test(dat)$p.value
chisq.test(dat)$p.value
fisher.test(dat)$p.value
I get
[1] 0.5173269
[1] 0.5173269
[1] 0.4771358
When I looked at the binomial distribution and the normal approximation
thereof with similar counts I never had a p-value difference 0.004
I am so fed up with this problem :(
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Re: [R] Is it safe? Cochran etc
Why can't I just use Log odds? Does the standard error of the logs score
depend on a similar chisq assumption?
On Sat, 9 Oct 2004, Dan Bolser wrote:
I have the following contingency table
dat - matrix(c(1,506,13714,878702),nr=2)
And I want to test if their is an association between events
A:{a,not(a)} and B:{b,not(b)}
| b | not(b) |
+-++
a | 1 | 13714 |
+-++
not(a) | 506 | 878702 |
+-++
I am worried that prop.test and chisq.test are not valid given the low
counts and low probabilites associated with 'sucess' in each category.
Is it safe to use them, and what is the alternative? (given that
fisher.test can't handle this data... hold the phone...
I just found fisher.test can handle this data if the test is one-tailed
and not two-tailed.
I don't understand the difference between chisq.test, prop.test and
fisher.test when the hybrid=1 option is used for the fisher.test.
I was using the binomial distribution to test the 'extremity' of the
observed data, but now I think I know why that is inapropriate, however,
with the binomial (and its approximation) at least I know what I am
doing. And I can do it in perl easily...
Generally, how should I calculate fisher.test in perl (i.e. what are its
principles). When is it safe to approximate fisher to chisq?
I cannot get insight into this problem...
How come if I do...
dat - matrix(c(50,60,100,100),nr=2)
prop.test(dat)$p.value
chisq.test(dat)$p.value
fisher.test(dat)$p.value
I get
[1] 0.5173269
[1] 0.5173269
[1] 0.4771358
When I looked at the binomial distribution and the normal approximation
thereof with similar counts I never had a p-value difference 0.004
I am so fed up with this problem :(
__
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[R] RSQLite query error
Dear R-helpers, I ran the following little test on RSQLite and got the data below from the query. Unless I've made some mistake, the results of both the where and order by statements have problems: library(RSQLite) con-dbConnect(dbDriver(SQLite),dbname=test) data(USArrests) dbWriteTable(con,arrests,USArrests,overwrite=TRUE) dbListTables(con) dbReadTable(con,arrests) dbGetQuery(con,paste(SELECT row_names,Murder,Rape FROM arrests, WHERE Rape30 ORDER BY Murder)) row_names Murder Rape 1 Alaska 10.0 44.5 2 New Mexico 11.4 32.1 3 Michigan 12.1 35.1 4 Nevada 12.2 46.0 5Florida 15.4 31.9 6 North Dakota0.8 7.3 7 New Hampshire2.1 9.5 8 Maine2.1 7.8 9 Rhode Island3.4 8.3 10 West Virginia5.7 9.3 11 Colorado7.9 38.7 12 Arizona8.1 31.0 13California9.0 40.6 I'm running R 2.0.0 on Windows XP. Should I make a bug report or can someone point to an error that I've made? cheers Mikkel __ [EMAIL PROTECTED] 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 safe? Cochran etc
Dan,
I don't know what is the theory behind this hybrid option and what
consists the Cochran conditions.
However, I think even if you suppose the asymptotic distribution is not
too accurate, because your sampled 1, there is a too strong association
of A and B, as this can be noticed by conservative methods such as using
the Yates continuity correction or Wald/Neyman tests (that usually does
not reject the null hypothesis of no interaction much more than the
Pearson/score test and likelihood ratio test, in this order) of the log
odds.
Both procedures inflate the pvalues, but not sufficiently to change your
conclusion as you can notice by:
chisq.test(dat,correct=FALSE)
Pearson's Chi-squared test
data: dat
X-squared = 6.0115, df = 1, p-value = 0.01421
chisq.test(dat)
Pearson's Chi-squared test with Yates' continuity correction
data: dat
X-squared = 5.1584, df = 1, p-value = 0.02313
1-pchisq( (log(878702/(13714*506))^2)/(1+1/878702+1/13714+1/506) ,1)
# Wald test of null log odds
[1] 0.03898049
The book Categorical data analysis from Agresti (2002) has an ample
discussion about tests like this on chapters 1 (basics and one sample)
and 3 (two variables). You may look there if you still have doubts about
this tests.
Sincerely,
--
Frederico Zanqueta Poleto
[EMAIL PROTECTED]
--
An approximate answer to the right problem is worth a good deal more than an exact answer
to an approximate problem. J. W. Tukey
Dan Bolser wrote:
Why can't I just use Log odds? Does the standard error of the logs score
depend on a similar chisq assumption?
On Sat, 9 Oct 2004, Dan Bolser wrote:
I have the following contingency table
dat - matrix(c(1,506,13714,878702),nr=2)
And I want to test if their is an association between events
A:{a,not(a)} and B:{b,not(b)}
| b | not(b) |
+-++
a | 1 | 13714 |
+-++
not(a) | 506 | 878702 |
+-++
I am worried that prop.test and chisq.test are not valid given the low
counts and low probabilites associated with 'sucess' in each category.
Is it safe to use them, and what is the alternative? (given that
fisher.test can't handle this data... hold the phone...
I just found fisher.test can handle this data if the test is one-tailed
and not two-tailed.
I don't understand the difference between chisq.test, prop.test and
fisher.test when the hybrid=1 option is used for the fisher.test.
I was using the binomial distribution to test the 'extremity' of the
observed data, but now I think I know why that is inapropriate, however,
with the binomial (and its approximation) at least I know what I am
doing. And I can do it in perl easily...
Generally, how should I calculate fisher.test in perl (i.e. what are its
principles). When is it safe to approximate fisher to chisq?
I cannot get insight into this problem...
How come if I do...
dat - matrix(c(50,60,100,100),nr=2)
prop.test(dat)$p.value
chisq.test(dat)$p.value
fisher.test(dat)$p.value
I get
[1] 0.5173269
[1] 0.5173269
[1] 0.4771358
When I looked at the binomial distribution and the normal approximation
thereof with similar counts I never had a p-value difference 0.004
I am so fed up with this problem :(
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] RSQLite query error
Mikkel Grum wrote: Dear R-helpers, I ran the following little test on RSQLite and got the data below from the query. Unless I've made some mistake, the results of both the where and order by statements have problems: This is due to the fact that SQLite as of version 2.8 is typeless and values are stored as ASCII strings. Most expressions are evaluated as string expressions, as in your query. For details see http://www.sqlite.org/datatypes.html (SQLite Version 2.8) and http://www.sqlite.org/datatype3.html (Version 3.0). You can use a trivial arithmetic expression to force numeric comparisons (awk users may recognize this trick): dbGetQuery(con, paste(select * from arrests where Rape+0.0 30, order by Murder+0.0)) row_names Murder Assault UrbanPop Rape 1 Colorado7.9 204 78 38.7 2Arizona8.1 294 80 31.0 3 California9.0 276 91 40.6 4 Alaska 10.0 263 48 44.5 5 New Mexico 11.4 285 70 32.1 6 Michigan 12.1 255 74 35.1 7 Nevada 12.2 252 81 46.0 8Florida 15.4 335 80 31.9 Regards, -- David library(RSQLite) con-dbConnect(dbDriver(SQLite),dbname=test) data(USArrests) dbWriteTable(con,arrests,USArrests,overwrite=TRUE) dbListTables(con) dbReadTable(con,arrests) dbGetQuery(con,paste(SELECT row_names,Murder,Rape FROM arrests, WHERE Rape30 ORDER BY Murder)) row_names Murder Rape 1 Alaska 10.0 44.5 2 New Mexico 11.4 32.1 3 Michigan 12.1 35.1 4 Nevada 12.2 46.0 5Florida 15.4 31.9 6 North Dakota0.8 7.3 7 New Hampshire2.1 9.5 8 Maine2.1 7.8 9 Rhode Island3.4 8.3 10 West Virginia5.7 9.3 11 Colorado7.9 38.7 12 Arizona8.1 31.0 13California9.0 40.6 I'm running R 2.0.0 on Windows XP. Should I make a bug report or can someone point to an error that I've made? cheers Mikkel __ [EMAIL PROTECTED] mailing list https://stat.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://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-2.0.0 and tcltk package
On Sat, 9 Oct 2004, Jean Eid wrote: there does not seem to be a package tcltk on CRAN for 2.0.0. It is part of the R tarball, so library(tcltk) should do something. It has never been on CRAN, to my knowledge. See the R FAQ 5.1.1 (as the posting guide suggests). -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://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 safe? Cochran etc
Dan Bolser wrote:
I have the following contingency table
dat - matrix(c(1,506,13714,878702),nr=2)
And I want to test if their is an association between events
A:{a,not(a)} and B:{b,not(b)}
| b | not(b) |
+-++
a | 1 | 13714 |
+-++
not(a) | 506 | 878702 |
+-++
I am worried that prop.test and chisq.test are not valid given the low
counts and low probabilites associated with 'sucess' in each category.
test - matrix( c(1,506, 13714, 878702), 2,2)
test
[,1] [,2]
[1,]1 13714
[2,] 506 878702
chisq.test(test)
Pearson's Chi-squared test with Yates' continuity correction
data: test
X-squared = 5.1584, df = 1, p-value = 0.02313
chisq.test(test,sim=TRUE)
Pearson's Chi-squared test with simulated p-value (based on 2000
replicates)
data: test
X-squared = 6.0115, df = NA, p-value = 0.02099
chisq.test(test,sim=TRUE, B=20)
# To rule out simulation uncertainty
Pearson's Chi-squared test with simulated p-value (based on 20
replicates)
data: test
X-squared = 6.0115, df = NA, p-value = 0.01634
N - sum(test)
rows - rowSums(test)
cols - colSums(test)
E - rows %o% cols/N
E
[,1] [,2]
[1,] 7.787351 13707.21
[2,] 499.212649 878708.79
None of the expected'eds are lesser than 5, an often used rule of thumb
(which might even be
to conservative. Just to check on the distribution:
rows - round(rows)
cols - round(cols)
pvals - sapply(r2dtable(10, rows, cols), function(x)
chisq.test(x)$p.value)
hist(pvals)
# not very good approximation to uniform histogram, but:
sum(pvals 0.05)/10
[1] 0.03068
sum(pvals 0.01)/10
[1] 0.00669
So the true levels are not very far from the calculated by te chisq
approximation, and it seems safe to use it.
All of this to show that with R you are not anymore dependent on old
rules os thumb,
you can investigate for yourself.
Kjetil
Is it safe to use them, and what is the alternative? (given that
fisher.test can't handle this data... hold the phone...
I just found fisher.test can handle this data if the test is one-tailed
and not two-tailed.
I don't understand the difference between chisq.test, prop.test and
fisher.test when the hybrid=1 option is used for the fisher.test.
I was using the binomial distribution to test the 'extremity' of the
observed data, but now I think I know why that is inapropriate, however,
with the binomial (and its approximation) at least I know what I am
doing. And I can do it in perl easily...
Generally, how should I calculate fisher.test in perl (i.e. what are its
principles). When is it safe to approximate fisher to chisq?
I cannot get insight into this problem...
How come if I do...
dat - matrix(c(50,60,100,100),nr=2)
prop.test(dat)$p.value
chisq.test(dat)$p.value
fisher.test(dat)$p.value
I get
[1] 0.5173269
[1] 0.5173269
[1] 0.4771358
When I looked at the binomial distribution and the normal approximation
thereof with similar counts I never had a p-value difference 0.004
I am so fed up with this problem :(
__
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--
Kjetil Halvorsen.
Peace is the most effective weapon of mass construction.
-- Mahdi Elmandjra
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Re: [R] Clustering of variable
clara gonçalves wrote: Hi! Does anybody know if there is any way to do clustering of variables? Thank you in advance, varclust() in Hmisc Kjetil Clara. [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Kjetil Halvorsen. Peace is the most effective weapon of mass construction. -- Mahdi Elmandjra __ [EMAIL PROTECTED] 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] which() and value replacement in a matrix
Use matrix indexing, instead of generating the index vector: x - as.data.frame(x) x[x 25] - -999 x V1 V2 V3 1 7 14 16 220 248 317 18 11 419 -999 -999 5234 15 6 -999 -9995 7219 12 82223 9 -999 131 106 10 25 Andy From: Patrick Giraudoux Thanks for the clue. Actually the trouble comes when refering to a data.frame. If I use the matrix from the data.frame (matrix(mydataframe)), everything goes smoothly... So I wrote: indices-which(myforetbin 0,arr.ind=T) myforetbin-as.matrix(myforetbin) myforetbin[indices]-1 myforetbin-as.data.frame(myforetbin) It works but I wonder if there are no more simple ways... All the best, Patrick - Original Message - From: Liaw, Andy [EMAIL PROTECTED] To: 'Patrick Giraudoux' [EMAIL PROTECTED]; r-help [EMAIL PROTECTED] Sent: Saturday, October 09, 2004 3:00 PM Subject: RE: [R] which() and value replacement in a matrix Use the index vector directly, rather than breaking it up: x - matrix(sample(30), 10, 3) idx - which(x 25, arr.ind=TRUE) idx row col [1,] 6 1 [2,] 9 1 [3,] 4 2 [4,] 6 2 [5,] 4 3 x[idx] - 999 x [,1] [,2] [,3] [1,]7 14 16 [2,] 20 248 [3,] 17 18 11 [4,] 19 999 999 [5,] 234 15 [6,] 999 9995 [7,] 219 12 [8,] 2223 [9,] 999 131 [10,]6 10 25 HTH, Andy From: Patrick Giraudoux Hi, I cannot go through the archives with which() as key-word... so common. Though I am sure to have seen something about this subject in the past could somebody put me on the track. I have a matrix (actually a data.frame) in which I would replace the non-null values by 1. I tried the following: indices-which(myforetbin 0,arr.ind=T) myforetbin[indices[,1],indices[,2]]-1 and get the message: myforetbin[indices[,1],indices[,2]]-1 Error in [-.data.frame(`*tmp*`, indices[, 1], indices[, 2], value = 1) : duplicate subscripts for columns I get the same with myforetbin[indices]-1 However, with: myforetbin[indices] I well get a vector with the corresponding non-null values. Can somebody put me on the track? All the best, Patrick __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. -- __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Mac: importing saved PDF figures into Illustrator CS
Rene Bertin wrote:
Hello,
This is a usage question for others with experience of R under the
Aqua Mac OS
X interface.
Basically, I don't succeed in importing PDF files (created with the
'Save As'
menu to Quartz device windows) into Illustrator. Versions up to (and
including?) 10 loose paths (lines/polygons) and or fill them in
black. Version
CS (11) on the Mac imports almost correctly, but, to preserve
appearance,
some text has been outlined. In other words: *all* text in the
figure is
converted to polygons. Somewhat annoying if one plans to edit the
text, and in
general change the appearance. I've asked on both the Apple and Adobe
Illustrator forums
(http://www.adobeforums.com/cgi-bin/webx?
[EMAIL PROTECTED]@.3bb6383d/0),
but have not yet received any reply. Maybe someone here has found a
way to
tell Illustrator not to outline ('preserve editability', in their
jargon), or
some other workaround?
Thanks in advance, René Bertin
No real solution but try the pdf command instead of saving with the menu
pdf(file='~/Desktop/figure.pdf')
curve(x^2)
dev.off()
the resulting pdf file can be read into Illustrator CS without
outlining the text (Mac OS X 10.3.5 with R 1.9.1) but each character is
in a separate text frame.
As far as I remember the paths were not lost in Illustrator 10 but just
were invisible. Selecting everything inside the plot region and setting
the opacity to 100% (can be done in the transparency window) solved the
problem.
Tilo
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[R] functions
Does anyone know of a list of functions that R already knows? I can't seem to find this anywhere in the help documentation. For example, I want to count the number of occurences of a certain value in a column of a data frame: What do I have to do to tell R to Count? Thanks, Ben Osborne -- Botany Department University of Vermont 109 Carrigan Drive Burlington, VT 05405 [EMAIL PROTECTED] phone: 802-656-0297 fax: 802-656-0440 __ [EMAIL PROTECTED] 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] functions
On Sat, 9 Oct 2004 18:12:20 -0400, Benjamin M. Osborne
[EMAIL PROTECTED] wrote:
Does anyone know of a list of functions that R already knows? I can't seem to
find this anywhere in the help documentation. For example, I want to count the
number of occurences of a certain value in a column of a data frame: What do I
have to do to tell R to Count?
There are several such lists. The one you want is probably the one
the help system uses. For example,
help.search('count')
lists a number of functions that count various things. I don't think
any of them is exactly what you want, which could be accomplished in a
couple of ways:
table(x)
gives counts of all the different values in x;
length(x[x==3])
gives the count of occurences of 3 in x.
Duncan Murdoch
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[R] Fatal error: unable to restore saved data in .Rdata
Dear Sir/Madam: I'm currently running R 1.9.1 on a Mac OS 10.3. I have been able to use it fine for a while now. But for some reason, it now crashes each time I open it with the error: Fatal error: unable to restore saved data in .Rdata I read on the online help forum that I can just delete the bad .Rdata file. But I cannot find it. I even tried to delete everything related to R and reinstalling but the problem has not gone away. Please HELP! Thank you, Susan Yeh __ [EMAIL PROTECTED] 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] How to install a package that needs to see oher pkg dependencies:
Hi, I am trying to install the genetics package on a server with Linux, Fedora. I installed it in a PC and worked fine. In a server since I am not used with R, I am not sure what do I need to change so genetics pkg can see some package dependencies: Any suggestion is appreciated, Aldi Note: genetics expects gregmisc and mvtnorm to be installed already. gregmisc creates gdata etc dependencies. So here is what I have done: Retrieved the base R and installed and compiled it with make under : /users/genetics/aldi/r/R/R-2.0.0 Under it directories: /mvtnorm /gregmisc /genetics are created. Installed mvtnorm and gregmisc with no problem, but genetics is not recognizing the location of /gregmisc/gdata The command I am using to install genetics package is the following: ../bin/R CMD ../bin/INSTALL genetics_1.1.0.tar.gz Here is the problem: [EMAIL PROTECTED]:/users/genetics/aldi/r/R-2.0.0/genetics% ../bin/R CMD ../bin/INSTALL -l . genetics_1.1.0.tar.gz * Installing *source* package 'genetics' ... ** R ** data ** inst ** preparing package for lazy loading Error in loadNamespace(i[[1]], c(lib.loc, .libPaths()), keep.source) : There is no package called 'gdata' Execution halted ERROR: lazy loading failed for package 'genetics' [EMAIL PROTECTED]:/users/genetics/aldi/r/R-2.0.0/genetics% __ [EMAIL PROTECTED] 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-2.0.0 and tcltk package
On Sat, Oct 09, 2004 at 12:36:51PM -0400, Jean Eid wrote: there does not seem to be a package tcltk on CRAN for 2.0.0. I have successfully installed the same package for 1.9.1. In essence I require the package for a GUI interface to setwd. All work fine with 1.9.1. This is on a Linux Debian unstable kernel 2.4.20 If you were using the pre-built Debian package, you'd have the tcltk package: [EMAIL PROTECTED]:~ dpkg -L r-base-core | grep tcltk/ | wc -l 48 [EMAIL PROTECTED]:~ dpkg -L r-base-core | grep tcltk/ | head /usr/lib/R/library/tcltk/R /usr/lib/R/library/tcltk/R/tcltk /usr/lib/R/library/tcltk/R/tcltk.rdb /usr/lib/R/library/tcltk/R/tcltk.rdx /usr/lib/R/library/tcltk/NAMESPACE /usr/lib/R/library/tcltk/DESCRIPTION /usr/lib/R/library/tcltk/Meta /usr/lib/R/library/tcltk/Meta/package.rds /usr/lib/R/library/tcltk/Meta/nsInfo.rds /usr/lib/R/library/tcltk/Meta/Rd.rds As you seem to prefer to roll your own (which you could also base on the Debian package sources which enforce build-time dependencies so that these things work), I highly recommend to fetch the output of the build process (e.g. via script(1)) so that you can go back and check what configure told you -- for it will have almost surely have told you if and when it missed headers or libraries for tcl/tk. Hope this helps, regards, Dirk -- Those are my principles, and if you don't like them... well, I have others. -- Groucho Marx __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
