Re: [R] ANOVA non-sphericity test and corrections (eg, Greenhouse-Geisser)
DarrenWeber wrote: I'm an experimental psychologist and when I run ANOVA analysis in SPSS, I normally ask for a test of non-sphericity (Box's M-test). I also ask for output of the corrections for non-sphericity, such as Greenhouse-Geisser and Huhn-Feldt. These tests and correction factors are commonly used in the journals for experimental and other psychology reports. I have been switching from SPSS to R for over a year now, but I realize now that I don't have the non-sphericity test and correction factors. This can be done using anova.mlm() and mauchly.test() which work on mlm objects, i.e., lm() output where the response is a matrix. There is no theory, to my knowledge, to support it for general aov() models, the catch being that you need to have a within-subject covariance matrix. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Random numbers from skewed distributions
Dear Friends, I was wondering if there is any package to get random numbers from the Burr 10 distribution. I checked the rmutil and actuar package. Both seems to implement the Burr 12 distribution. thanks in advance Regards Anup - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Source code for rlogis
Anup Nandialath wrote: Dear friends, I was trying to read the source code for rlogis but ran into a roadblock. It shows [[1]] function (n, location = 0, scale = 1) .Internal(rlogis(n, location, scale)) environment: namespace:stats Is is possible to access the source code for the same. Yes, but as it is .Internal, you have to look in the (C code) sources for R itself. You can access that either by getting the source files for R and unpacking them somewhere on your computer, or by browsing e.g. https://*svn*.*R*-project.org/*R*/tags/R-2-5-0 or https://svn.r-project.org/R/branches/R-2-5-branch. Specifically, src/nmath/rlogis.c. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ANOVA non-sphericity test and corrections (eg, Greenhouse-Geisser)
On Mon, 2007-06-25 at 17:53 +1000, Simon Blomberg wrote: If you use lme, you can fit a general correlation structure to the within-subject data, and compare the fit to a model assuming uncorrelated within-subjects errors. That should tell you whether your data are ... correlated... (damn email gremlins.) Aren't the G-G and H-F corrections only approximate fixes? Surely it is better to work with a model that actually fits your data, rather than using ad hoc adjustments towards a model that doesn't quite fit. But I'm no psychologist. :-) Cheers, Simon. On Mon, 2007-06-25 at 08:22 +0200, Peter Dalgaard wrote: DarrenWeber wrote: I'm an experimental psychologist and when I run ANOVA analysis in SPSS, I normally ask for a test of non-sphericity (Box's M-test). I also ask for output of the corrections for non-sphericity, such as Greenhouse-Geisser and Huhn-Feldt. These tests and correction factors are commonly used in the journals for experimental and other psychology reports. I have been switching from SPSS to R for over a year now, but I realize now that I don't have the non-sphericity test and correction factors. This can be done using anova.mlm() and mauchly.test() which work on mlm objects, i.e., lm() output where the response is a matrix. There is no theory, to my knowledge, to support it for general aov() models, the catch being that you need to have a within-subject covariance matrix. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician Faculty of Biological and Chemical Sciences The University of Queensland St. Lucia Queensland 4072 Australia Room 320, Goddard Building (8) T: +61 7 3365 2506 email: S.Blomberg1_at_uq.edu.au The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. - John Tukey. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to run mathematica or c programs in R?
Hallo, I just know a solution if you use MATLAB. Here you need the library R.matlab and there the functions writeMat and readMat. You can download the package on CRAN. Corinna ** Corinna Schmitt, Dipl.Inf.(Bioinformatik) Fraunhofer Institut für Grenzflächen- Bioverfahrenstechnik Nobelstrasse 12, B 3.24 70569 Stuttgart Germany phone: +49 711 9704044 fax: +49 711 9704200 e-mail: [EMAIL PROTECTED] http://www.igb.fraunhofer.de -Ursprüngliche Nachricht- Von: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Im Auftrag von Zhang Jian Gesendet: Freitag, 22. Juni 2007 23:26 An: r-help Betreff: [R] How to run mathematica or c programs in R? I have some programs which were writen in mathematica or c language, but I donot know how to use these software. So I want to run them in R. Can I do it ? How to run mathematica or c programs in R? Jian Zhang [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ANOVA non-sphericity test and corrections (eg, Greenhouse-Geisser)
If you use lme, you can fit a general correlation structure to the within-subject data, and compare the fit to a model assuming uncorrelated within-subjects errors. That should tell you whether your data are Aren't the G-G and H-F corrections only approximate fixes? Surely it is better to work with a model that actually fits your data, rather than using ad hoc adjustments towards a model that doesn't quite fit. But I'm no psychologist. :-) Cheers, Simon. On Mon, 2007-06-25 at 08:22 +0200, Peter Dalgaard wrote: DarrenWeber wrote: I'm an experimental psychologist and when I run ANOVA analysis in SPSS, I normally ask for a test of non-sphericity (Box's M-test). I also ask for output of the corrections for non-sphericity, such as Greenhouse-Geisser and Huhn-Feldt. These tests and correction factors are commonly used in the journals for experimental and other psychology reports. I have been switching from SPSS to R for over a year now, but I realize now that I don't have the non-sphericity test and correction factors. This can be done using anova.mlm() and mauchly.test() which work on mlm objects, i.e., lm() output where the response is a matrix. There is no theory, to my knowledge, to support it for general aov() models, the catch being that you need to have a within-subject covariance matrix. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician Faculty of Biological and Chemical Sciences The University of Queensland St. Lucia Queensland 4072 Australia Room 320, Goddard Building (8) T: +61 7 3365 2506 email: S.Blomberg1_at_uq.edu.au The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. - John Tukey. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] adding lines to stripchart
James Root wrote:
I have two points of collection across 20 subjects (pre and post for each),
so 20 pairs of data points. I would like to plot the actual raw data points
for each subject for both pre and post and connect lines between these two
points (20 in all) to depict real change between the two timepoints.
I have tried using stripchart which adequately plots the two lines of
subject data points. Attempting to use segments however has been
difficult. It seems that the segments command gives too many coordiate
points - so where segments has:
x0, y0, x1, y1
I really only have two coordinates for each point -
pre to post
I am sure that I am misusing the command but not sure if I should continue
to try with segments or if there is another command that would be more
appropriate.
As always, thanks for any help.
Here is how you might use segments() and stripchart():
df - data.frame(pre = runif(20), post = runif(20))
stripchart(x = list(df$pre, df$post), vertical=TRUE,
group.names=c(Pre,Post))
for(i in 1:nrow(df)){segments(1, df$pre[i], 2, df$post[i])}
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Chuck Cleland, Ph.D.
NDRI, Inc.
71 West 23rd Street, 8th floor
New York, NY 10010
tel: (212) 845-4495 (Tu, Th)
tel: (732) 512-0171 (M, W, F)
fax: (917) 438-0894
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-2.5.0 compilation problem on Linux powerpc
Is this ppc32 or ppc64? (What does uname -a say?) If the former, you might need to set CPICFLAGS and FPICFLAGS to -fPIC (rather than -fpic): please look these up in the R-admin.html file (which INSTALL points you to). For ppc64 configure should have found -fPIC. On Mon, 25 Jun 2007, Vivek Menon wrote: Hello everybody,I am having an error while compiling R-2.5.0 on Linux powerpc. This is what I see when I do a make: gcc -std=gnu99 -shared -L/usr/local/lib -o grDevices.so chull.o devNull.o devPicTeX.o devPS.o devQuartz.o init.o ../../../../library/grDevices/libs/grDevices.so is unchanged make[5]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0/src/library/grDevices/src' make[4]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0 /src/library/grDevices/src' Warning: unable to load shared library '/home/vivekv/sw_alg/R-2.5.0 /modules//lapack.so': /home/vivekv/sw_alg/R- 2.5.0/modules//lapack.so: R_PPC_REL24 relocation at 0x0e65d7e4 for symbol `strlen' out of range Error in solve.default(rgb) : lapack routines cannot be loaded Error: unable to load R code in package 'grDevices' Execution halted make[3]: *** [all] Error 1 make[3]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0 /src/library/grDevices' make[2]: *** [R] Error 1 make[2]: Leaving directory `/home/vivekv/sw_alg/R- 2.5.0/src/library' make[1]: *** [R] Error 1 make[1]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0/src' make: *** [R] Error 1 Please let me know what needs to be done for a successful installation. Thanks, Vivek [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Re : Half of a heatmap
I am trying to produce a heatmap of pairwise correlations, but since the matrix is symmetric, I only need either the upper or the lower triangle. I have scoured the web and R documentation, but I have not been able to find a way to produce such a figure. Is there a simple way to produce a heat map with only the part above or below the diagonal? You might want to check out the LDheatmap() package which can generate the plots you describe. The help indicates that it accepts a matrix of pair-wise linkage disequilibrium measures, one of which is R^2 (the correlation coefficient between loci), but I suspect you could simply pass it a matrix of correlation coefficents. Hope that helps, Neil -- In mathematics you don't understand things. You just get used to them. - Johann von Neumann Email - [EMAIL PROTECTED] / [EMAIL PROTECTED] Website - http://slack.ser.man.ac.uk/ Photos - http://www.flickr.com/photos/slackline/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] fractional calculations
Hi All, is there a function in R that allows me to work with fractions without transforming them to floats (or whatever) in between? Something that would calculate something like: (1/2 + 1/8) * 1/2 = 5/16 without ever transforming to 0.5 and 0.125? Best, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] fractional calculations
require(MASS) ?as.fractions as.fractions(1/2+1/8) -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 Ohttp://maps.google.com/maps?f=qhl=enq=Curitiba,+Brazillayer=ie=UTF8z=18ll=-25.448315,-49.276916spn=0.002054,0.005407t=kom=1 On 25/06/07, Federico Calboli [EMAIL PROTECTED] wrote: Hi All, is there a function in R that allows me to work with fractions without transforming them to floats (or whatever) in between? Something that would calculate something like: (1/2 + 1/8) * 1/2 = 5/16 without ever transforming to 0.5 and 0.125? Best, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] fractional calculations
is there a function in R that allows me to work with fractions without transforming them to floats (or whatever) in between? You could use the ryacas (CAS) package: http://code.google.com/p/ryacas/ and/or http://cran.r-project.org/doc/vignettes/Ryacas/Ryacas.pdf e.g: library(Ryacas) yacas(expression((1/2 + 1/8) * 1/2 )) [1] Starting Yacas! expression(5/16) Stefan Something that would calculate something like: (1/2 + 1/8) * 1/2 = 5/16 without ever transforming to 0.5 and 0.125? __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] gam function in the mgcv library
I would like to fit a logistic regression using a smothing spline, where the spline is a piecewise cubic polynomial. Is the knots option used to define the subintervals for each piece of the cubic spline? If yes and there are k knots, then why does the coefficients field in the returned object from gam only list k coefficients? Shouldn't there be 4k -4 coefficients? Sincerely, Bill - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Re : Half of a heatmap
Thank you for your reply. I have looked at LDheatmap, but it does not seem to do what I want and seems to only work well for LD data. I was looking for something that would produce a figure identical to what heatmap.2 gives me, including the proper X and Y-axis labels and a dendogram, except that it would only have half of the map. Preferably, it would have the Color Key in the place where the other triangle of the heatmap would be, to save space. Jeff -Original Message- From: Neil Shephard [mailto:[EMAIL PROTECTED] Sent: Mon 6/25/2007 6:14 AM To: r-help@stat.math.ethz.ch Cc: Rosenfeld, Jeffrey Subject: Re : [R] Half of a heatmap I am trying to produce a heatmap of pairwise correlations, but since the matrix is symmetric, I only need either the upper or the lower triangle. I have scoured the web and R documentation, but I have not been able to find a way to produce such a figure. Is there a simple way to produce a heat map with only the part above or below the diagonal? You might want to check out the LDheatmap() package which can generate the plots you describe. The help indicates that it accepts a matrix of pair-wise linkage disequilibrium measures, one of which is R^2 (the correlation coefficient between loci), but I suspect you could simply pass it a matrix of correlation coefficents. Hope that helps, Neil -- In mathematics you don't understand things. You just get used to them. - Johann von Neumann Email - [EMAIL PROTECTED] / [EMAIL PROTECTED] Website - http://slack.ser.man.ac.uk/ Photos - http://www.flickr.com/photos/slackline/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Peter Moser ist außer Haus.
Ich werde ab 25.06.2007 nicht im Büro sein. Ich kehre zurück am 28.06.2007. in dringenden Fällen bin ich unter 079 79 73 74 6 erreichbar __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-excel
cf. R Data Import/Export file:///tmp/RtmpnFqONj/.R/doc/manual/R-data.htmlin the standard documentation. Christophe On 6/25/07, Erika Frigo [EMAIL PROTECTED] wrote: Good morning to everybody, I have a problem : how can I import excel files in R??? thank you very much Dr.sa. Erika Frigo Università degli Studi di Milano Facoltà di Medicina Veterinaria Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare (VSA) Via Grasselli, 7 20137 Milano Tel. 02/50318515 Fax 02/50318501 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Christophe Pallier (http://www.pallier.org) [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] fractional calculations
Henrique Dallazuanna wrote: require(MASS) ?as.fractions as.fractions(1/2+1/8) I thought that as.fractions did transform the fractions *first* into floats and *then* found the rational approssimation (a passage I'd rather avoid): fractionspackage:MASSR Documentation Rational Approximation Description: Find rational approximations to the components of a real numeric object using a standard continued fraction method. /F -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Help in HMM for count data
Respected Sir, I am Regina M.Verghis, Final Year PG in Biostatistics. My thesis is based on a count data. I am trying to fit the data using HMM. I have the count of new infectives each month. I am not considering any other covariates. I am using the 'chidden(repeated package)'. Can you explain about the estimation of the parameters. And how to estimate the initial values of 'mu' and 'pgamma'. I will be grateful to you for the help. Thanking You, Yours Faithfuly Regina M.Verghis -- [EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R-excel
Good morning to everybody, I have a problem : how can I import excel files in R??? thank you very much Dr.sa. Erika Frigo Università degli Studi di Milano Facoltà di Medicina Veterinaria Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare (VSA) Via Grasselli, 7 20137 Milano Tel. 02/50318515 Fax 02/50318501 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] JRI and Axis Web Service
On Jun 24, 2007, at 7:58 PM, Yifan (Eric) Jiang wrote: I've been asked to develop a Java Axis web service to retrieve an R-script file from the client side and then using JRI jar file in order to call the R program that installed on the web service server. After reading the online documentation, I've successfully installed the R program with rJava and JRI packages. In addition, I can call the R program to run the R-script by using org.rosuda.JRI.Rengine. Everything is running fine if this program is running as a normal Java application. However, I fail to obtain any return when I was trying to consume this method by using the Java Axis web service. So I am wondering if any one could share their experiences to using JRI in Axis web service. Your helps mean a lot to me and I've been struggled to fix this problem for days. We have developed a distributed computational infrastructure using R (and JRI) as the backend coupled with AXIS web services and have built a number of clients on top of this. You can browse the source code for the services from the Sourceforge repository located at http://svn.sourceforge.net/viewvc/cicc-grid/cicc-grid/rws/trunk/ (though the R code in the repository has not been updated recently) Examples of what functionality is available via the web services can be found at http://www.chembiogrid.org/projects/proj_statistics.html The page also lists a number of clients that make use of the web service infrastructure. --- Rajarshi Guha [EMAIL PROTECTED] GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE --- I'm related to people I don't relate to. -Calvin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-2.5.0 compilation problem on Linux powerpc
On Mon, 25 Jun 2007, Vivek Menon wrote: uname -a gives me this:== Linux 2.6.21.1-xserve #17 SMP Thu Jun 14 19:45:57 MDT 2007 ppc64 ppc64 ppc64 GNU/Linux === Also when I configure I see the foll. output: R is now configured for powerpc64-unknown-linux-gnu That might be the problem: 'powerpc64' not 'ppc64'. What Linux distro is this? Source directory: . Installation directory:/usr/local C compiler:gcc -std=gnu99 -g -O2 Fortran 77 compiler: gfortran -g -O2 C++ compiler: g++ -g -O2 Fortran 90/95 compiler:gfortran -g -O2 Obj-C compiler: Interfaces supported: External libraries:readline Additional capabilities: PNG, iconv, MBCS, NLS Options enabled: shared BLAS, R profiling, Java Recommended packages: yes Do you have any suggestions?? And what is the setting of the flags I mentioned? See the manual I pointed you to, or the Makeconf file? Thanks, Vivek On 6/25/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: Is this ppc32 or ppc64? (What does uname -a say?) If the former, you might need to set CPICFLAGS and FPICFLAGS to -fPIC (rather than -fpic): please look these up in the R-admin.html file (which INSTALL points you to). For ppc64 configure should have found -fPIC. On Mon, 25 Jun 2007, Vivek Menon wrote: Hello everybody,I am having an error while compiling R-2.5.0 on Linux powerpc. This is what I see when I do a make: gcc -std=gnu99 -shared -L/usr/local/lib -o grDevices.so chull.o devNull.o devPicTeX.o devPS.o devQuartz.o init.o ../../../../library/grDevices/libs/grDevices.so is unchanged make[5]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0/src/library/grDevices/src' make[4]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0 /src/library/grDevices/src' Warning: unable to load shared library '/home/vivekv/sw_alg/R-2.5.0 /modules//lapack.so': /home/vivekv/sw_alg/R- 2.5.0/modules//lapack.so: R_PPC_REL24 relocation at 0x0e65d7e4 for symbol `strlen' out of range Error in solve.default(rgb) : lapack routines cannot be loaded Error: unable to load R code in package 'grDevices' Execution halted make[3]: *** [all] Error 1 make[3]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0 /src/library/grDevices' make[2]: *** [R] Error 1 make[2]: Leaving directory `/home/vivekv/sw_alg/R- 2.5.0/src/library' make[1]: *** [R] Error 1 make[1]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0/src' make: *** [R] Error 1 Please let me know what needs to be done for a successful installation. Thanks, Vivek [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. -- 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 -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] transposing data.frames
Hello, This must be simple... Thanks a lot - Christoph # Imagine you have a list, e.g: K - list(1:10, 2:11, 9:18) K # Transforming to dataframe... KK - as.data.frame(K) # ... one obtaines the list elements as column. KK # But I need the list elements as rows # How can I achieve this? Is there a simple way to transpose data.frames? __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] gam function in the mgcv library
On Monday 25 June 2007 13:26, Bill Wheeler wrote: I would like to fit a logistic regression using a smothing spline, where the spline is a piecewise cubic polynomial. Is the knots option used to define the subintervals for each piece of the cubic spline? - if you use something like gam(y~s(x,bs=cr,k=5),family=binomial,knots=list(x=c(0,.1,.3,.4,.8)) then yes, k is the number of knots and the `knots' list specifies where they occur. If you use the default `bs=tp' then the spline basis functions are not really `knot' based, being instead an ordered set of eigenfunctions, that are optimal in a defined sense (see Wood, 2003, JRSSB). If yes and there are k knots, then why does the coefficients field in the returned object from gam only list k coefficients? Shouldn't there be 4k -4 coefficients? A k knot natural cubic spline only has k free coefficients, so that is all that mgcv:gam reports. If you are thinking about sections of cubic, then the other 3 coefficients of each section are determined by the spline continuity conditions + the conditions of having zero second derivative at the end knots. Exact details of the `mgcv' cr basis are given in section 4.1.2 of my 2006 book (see ?gam), but all you really need to know is that it's a natural cubic spline basis parameterized in terms of function heights at the knots (although there is a gam identifiability constraint absorbed into the parameterization which muddies this neat interpretability a little). best, Simon Sincerely, Bill - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK +44 1225 386603 www.maths.bath.ac.uk/~sw283 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-excel
http://cran.r-project.org/doc/manuals/R-data.html#Reading-Excel-spreadsheets plus there is a package xlsReadWrite that might be of your interest. Stefan Original Message Subject: [R] R-excel From: Erika Frigo [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Date: 25.06.2007 14:47 Good morning to everybody, I have a problem : how can I import excel files in R??? thank you very much Dr.sa. Erika Frigo Università degli Studi di Milano Facoltà di Medicina Veterinaria Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare (VSA) Via Grasselli, 7 20137 Milano Tel. 02/50318515 Fax 02/50318501 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. No virus found in this incoming message. Checked by AVG Free Edition. Version: 7.5.472 / Virus Database: 269.9.6/865 - Release Date: 24.06.2007 08:33 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-2.5.0 compilation problem on Linux powerpc
uname -a gives me this:== Linux 2.6.21.1-xserve #17 SMP Thu Jun 14 19:45:57 MDT 2007 ppc64 ppc64 ppc64 GNU/Linux === Also when I configure I see the foll. output: R is now configured for powerpc64-unknown-linux-gnu Source directory: . Installation directory:/usr/local C compiler:gcc -std=gnu99 -g -O2 Fortran 77 compiler: gfortran -g -O2 C++ compiler: g++ -g -O2 Fortran 90/95 compiler:gfortran -g -O2 Obj-C compiler: Interfaces supported: External libraries:readline Additional capabilities: PNG, iconv, MBCS, NLS Options enabled: shared BLAS, R profiling, Java Recommended packages: yes Do you have any suggestions?? Thanks, Vivek On 6/25/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: Is this ppc32 or ppc64? (What does uname -a say?) If the former, you might need to set CPICFLAGS and FPICFLAGS to -fPIC (rather than -fpic): please look these up in the R-admin.html file (which INSTALL points you to). For ppc64 configure should have found -fPIC. On Mon, 25 Jun 2007, Vivek Menon wrote: Hello everybody,I am having an error while compiling R-2.5.0 on Linux powerpc. This is what I see when I do a make: gcc -std=gnu99 -shared -L/usr/local/lib -o grDevices.so chull.o devNull.o devPicTeX.o devPS.o devQuartz.o init.o ../../../../library/grDevices/libs/grDevices.so is unchanged make[5]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0/src/library/grDevices/src' make[4]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0 /src/library/grDevices/src' Warning: unable to load shared library '/home/vivekv/sw_alg/R-2.5.0 /modules//lapack.so': /home/vivekv/sw_alg/R- 2.5.0/modules//lapack.so: R_PPC_REL24 relocation at 0x0e65d7e4 for symbol `strlen' out of range Error in solve.default(rgb) : lapack routines cannot be loaded Error: unable to load R code in package 'grDevices' Execution halted make[3]: *** [all] Error 1 make[3]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0 /src/library/grDevices' make[2]: *** [R] Error 1 make[2]: Leaving directory `/home/vivekv/sw_alg/R- 2.5.0/src/library' make[1]: *** [R] Error 1 make[1]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0/src' make: *** [R] Error 1 Please let me know what needs to be done for a successful installation. Thanks, Vivek [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. -- 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 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] transposing data.frames
Original Message Subject: [R] transposing data.frames From: Christoph Heibl [EMAIL PROTECTED] To: R-help@stat.math.ethz.ch Date: 25.06.2007 15:13 Hello, This must be simple... Thanks a lot - Christoph # Imagine you have a list, e.g: K - list(1:10, 2:11, 9:18) K # Transforming to dataframe... KK - as.data.frame(K) # ... one obtaines the list elements as column. KK # But I need the list elements as rows # How can I achieve this? Is there a simple way to transpose data.frames? yes: t(as.data.frame(K)) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] transposing data.frames
t(KK) will transpose your data frame On 25/06/07, Christoph Heibl [EMAIL PROTECTED] wrote: Hello, This must be simple... Thanks a lot - Christoph # Imagine you have a list, e.g: K - list(1:10, 2:11, 9:18) K # Transforming to dataframe... KK - as.data.frame(K) # ... one obtaines the list elements as column. KK # But I need the list elements as rows # How can I achieve this? Is there a simple way to transpose data.frames? __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-2.5.0 compilation problem on Linux powerpc
uname -a gives me this:== Linux 2.6.21.1-xserve #17 SMP Thu Jun 14 19:45:57 MDT 2007 ppc64 ppc64 ppc64 GNU/Linux === Also when I configure I see the foll. output: R is now configured for powerpc64-unknown-linux-gnu That might be the problem: 'powerpc64' not 'ppc64'. What Linux distro is this? I am using Yellow Dog Linux distro. Source directory: . Installation directory:/usr/local C compiler:gcc -std=gnu99 -g -O2 Fortran 77 compiler: gfortran -g -O2 C++ compiler: g++ -g -O2 Fortran 90/95 compiler:gfortran -g -O2 Obj-C compiler: Interfaces supported: External libraries:readline Additional capabilities: PNG, iconv, MBCS, NLS Options enabled: shared BLAS, R profiling, Java Recommended packages: yes Do you have any suggestions?? And what is the setting of the flags I mentioned? See the manual I pointed you to, or the Makeconf file? I checked the Makeconf file and found the following settings: CPICFLAGS = -fpic FPICFLAGS = -fpic Thanks, Vivek Thanks, Vivek On 6/25/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: Is this ppc32 or ppc64? (What does uname -a say?) If the former, you might need to set CPICFLAGS and FPICFLAGS to -fPIC (rather than -fpic): please look these up in the R-admin.html file (which INSTALL points you to). For ppc64 configure should have found -fPIC. On Mon, 25 Jun 2007, Vivek Menon wrote: Hello everybody,I am having an error while compiling R-2.5.0 on Linux powerpc. This is what I see when I do a make: gcc -std=gnu99 -shared -L/usr/local/lib -o grDevices.so chull.o devNull.o devPicTeX.o devPS.o devQuartz.o init.o ../../../../library/grDevices/libs/grDevices.so is unchanged make[5]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0/src/library/grDevices/src' make[4]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0 /src/library/grDevices/src' Warning: unable to load shared library '/home/vivekv/sw_alg/R-2.5.0 /modules//lapack.so': /home/vivekv/sw_alg/R- 2.5.0/modules//lapack.so: R_PPC_REL24 relocation at 0x0e65d7e4 for symbol `strlen' out of range Error in solve.default(rgb) : lapack routines cannot be loaded Error: unable to load R code in package 'grDevices' Execution halted make[3]: *** [all] Error 1 make[3]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0 /src/library/grDevices' make[2]: *** [R] Error 1 make[2]: Leaving directory `/home/vivekv/sw_alg/R- 2.5.0/src/library' make[1]: *** [R] Error 1 make[1]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0/src' make: *** [R] Error 1 Please let me know what needs to be done for a successful installation. Thanks, Vivek [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. -- 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 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-2.5.0 compilation problem on Linux powerpc
After setting the flags to -fPIC using ./configure --with-x=no --with-lapack=/apps/lib/LAPACK/lapack_LINUX.a CPICFLAGS=-fPIC FPICFLAGS=-fPIC I still get the following errors:cc -std=gnu99 -shared -L/usr/local/lib -o grDevices.so chull.o devNull.o devPicTeX.o devPS.o devQuartz.o init.o make[5]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0 /src/library/grDevices/src' make[4]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0 /src/library/grDevices/src' Warning: unable to load shared library '/home/vivekv/sw_alg/R-2.5.0 /modules//lapack.so': /home/vivekv/sw_alg/R-2.5.0/modules//lapack.so: R_PPC_REL24 relocation at 0x0e65d864 for symbol `strlen' out of range Error in solve.default(rgb) : lapack routines cannot be loaded Error: unable to load R code in package 'grDevices' Execution halted make[3]: *** [all] Error 1 make[3]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0 /src/library/grDevices' make[2]: *** [R] Error 1 make[2]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0/src/library' make[1]: *** [R] Error 1 make[1]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0/src' make: *** [R] Error 1 - Thanks, Vivek uname -a gives me this:== Linux 2.6.21.1-xserve #17 SMP Thu Jun 14 19:45:57 MDT 2007 ppc64 ppc64 ppc64 GNU/Linux === Also when I configure I see the foll. output: R is now configured for powerpc64-unknown-linux-gnu That might be the problem: 'powerpc64' not 'ppc64'. What Linux distro is this? I am using Yellow Dog Linux distro. Source directory: . Installation directory:/usr/local C compiler:gcc -std=gnu99 -g -O2 Fortran 77 compiler: gfortran -g -O2 C++ compiler: g++ -g -O2 Fortran 90/95 compiler:gfortran -g -O2 Obj-C compiler: Interfaces supported: External libraries:readline Additional capabilities: PNG, iconv, MBCS, NLS Options enabled: shared BLAS, R profiling, Java Recommended packages: yes Do you have any suggestions?? And what is the setting of the flags I mentioned? See the manual I pointed you to, or the Makeconf file? I checked the Makeconf file and found the following settings: CPICFLAGS = -fpic FPICFLAGS = -fpic Thanks, Vivek Thanks, Vivek On 6/25/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: Is this ppc32 or ppc64? (What does uname -a say?) If the former, you might need to set CPICFLAGS and FPICFLAGS to -fPIC (rather than -fpic): please look these up in the R-admin.html file (which INSTALL points you to). For ppc64 configure should have found -fPIC. On Mon, 25 Jun 2007, Vivek Menon wrote: Hello everybody,I am having an error while compiling R-2.5.0 on Linux powerpc. This is what I see when I do a make: gcc -std=gnu99 -shared -L/usr/local/lib -o grDevices.so chull.o devNull.o devPicTeX.o devPS.o devQuartz.o init.o ../../../../library/grDevices/libs/grDevices.so is unchanged make[5]: Leaving directory `/home/vivekv/sw_alg/R- 2.5.0/src/library/grDevices/src' make[4]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0 /src/library/grDevices/src' Warning: unable to load shared library '/home/vivekv/sw_alg/R- 2.5.0 /modules//lapack.so': /home/vivekv/sw_alg/R- 2.5.0/modules//lapack.so: R_PPC_REL24 relocation at 0x0e65d7e4 for symbol `strlen' out of range Error in solve.default(rgb) : lapack routines cannot be loaded Error: unable to load R code in package 'grDevices' Execution halted make[3]: *** [all] Error 1 make[3]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0 /src/library/grDevices' make[2]: *** [R] Error 1 make[2]: Leaving directory `/home/vivekv/sw_alg/R- 2.5.0 /src/library' make[1]: *** [R] Error 1 make[1]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0/src' make: *** [R] Error 1 Please let me know what needs to be done for a successful installation. Thanks, Vivek [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. -- 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 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list
Re: [R] fractional calculations
On Mon, 25 Jun 2007, Henrique Dallazuanna wrote: require(MASS) ?as.fractions as.fractions(1/2+1/8) I think Federico wanted 1/as.fractions(2) + 1/as.fractions(8) that is avoiding computing 1/8 in float (although it is exact). You might be better off with package gmp: 1/as.bigq(2) + 1/as.bigq(8) [1] 5/8 allows you to handle arbitrarily large fractions. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R behaviour related to user input (readline()) and run selection
When I run the below section of code I get the following error:
Error in if (co == A || co[1] == O) { :
missing value where TRUE/FALSE needed
When I run the code in two parts where I first get the user's input
then afterwards run the if/else section, there is no problem.
Is there a way to stop the run selection process until the user
has input a value?
-
calc_option - function(){
msg - cat(Please select an option:\n, 'O'ne or 'A'll':
)
co - readline(msg)
switch(co,
O = O, o = O,
A = A, a = A
)
}
co - calc_option()
if (co == A || co[1] == O) {
print(paste(calc_option = , co))
} else {
print(calc_option is not acceptable)
}
Thanks,
- Bruce
**
Please be aware that, notwithstanding the fact that the pers...{{dropped}}
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-2.5.0 compilation problem on Linux powerpc
On Mon, 25 Jun 2007, Vivek Menon wrote: uname -a gives me this:== Linux 2.6.21.1-xserve #17 SMP Thu Jun 14 19:45:57 MDT 2007 ppc64 ppc64 ppc64 GNU/Linux === Also when I configure I see the foll. output: R is now configured for powerpc64-unknown-linux-gnu That might be the problem: 'powerpc64' not 'ppc64'. What Linux distro is this? I am using Yellow Dog Linux distro. Source directory: . Installation directory:/usr/local C compiler:gcc -std=gnu99 -g -O2 Fortran 77 compiler: gfortran -g -O2 C++ compiler: g++ -g -O2 Fortran 90/95 compiler:gfortran -g -O2 Obj-C compiler: Interfaces supported: External libraries:readline Additional capabilities: PNG, iconv, MBCS, NLS Options enabled: shared BLAS, R profiling, Java Recommended packages: yes Do you have any suggestions?? And what is the setting of the flags I mentioned? See the manual I pointed you to, or the Makeconf file? I checked the Makeconf file and found the following settings: CPICFLAGS = -fpic FPICFLAGS = -fpic So my comment in the first reply applied, since it looks like your distro is using an unusual name. You need to change these (and in etc/Makeconf). Thanks, Vivek Thanks, Vivek On 6/25/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: Is this ppc32 or ppc64? (What does uname -a say?) If the former, you might need to set CPICFLAGS and FPICFLAGS to -fPIC (rather than -fpic): please look these up in the R-admin.html file (which INSTALL points you to). For ppc64 configure should have found -fPIC. On Mon, 25 Jun 2007, Vivek Menon wrote: Hello everybody,I am having an error while compiling R-2.5.0 on Linux powerpc. This is what I see when I do a make: gcc -std=gnu99 -shared -L/usr/local/lib -o grDevices.so chull.o devNull.o devPicTeX.o devPS.o devQuartz.o init.o ../../../../library/grDevices/libs/grDevices.so is unchanged make[5]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0/src/library/grDevices/src' make[4]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0 /src/library/grDevices/src' Warning: unable to load shared library '/home/vivekv/sw_alg/R-2.5.0 /modules//lapack.so': /home/vivekv/sw_alg/R- 2.5.0/modules//lapack.so: R_PPC_REL24 relocation at 0x0e65d7e4 for symbol `strlen' out of range Error in solve.default(rgb) : lapack routines cannot be loaded Error: unable to load R code in package 'grDevices' Execution halted make[3]: *** [all] Error 1 make[3]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0 /src/library/grDevices' make[2]: *** [R] Error 1 make[2]: Leaving directory `/home/vivekv/sw_alg/R- 2.5.0/src/library' make[1]: *** [R] Error 1 make[1]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0/src' make: *** [R] Error 1 Please let me know what needs to be done for a successful installation. Thanks, Vivek [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. -- 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 -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-2.5.0 compilation problem on Linux powerpc
I did not get what you replied in the previous email. I still get the same error with CPICFLAGS and FPICFLAGS set to -fPIC. Vivek On 6/25/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: On Mon, 25 Jun 2007, Vivek Menon wrote: uname -a gives me this:== Linux 2.6.21.1-xserve #17 SMP Thu Jun 14 19:45:57 MDT 2007 ppc64 ppc64 ppc64 GNU/Linux === Also when I configure I see the foll. output: R is now configured for powerpc64-unknown-linux-gnu That might be the problem: 'powerpc64' not 'ppc64'. What Linux distro is this? I am using Yellow Dog Linux distro. Source directory: . Installation directory:/usr/local C compiler:gcc -std=gnu99 -g -O2 Fortran 77 compiler: gfortran -g -O2 C++ compiler: g++ -g -O2 Fortran 90/95 compiler:gfortran -g -O2 Obj-C compiler: Interfaces supported: External libraries:readline Additional capabilities: PNG, iconv, MBCS, NLS Options enabled: shared BLAS, R profiling, Java Recommended packages: yes Do you have any suggestions?? And what is the setting of the flags I mentioned? See the manual I pointed you to, or the Makeconf file? I checked the Makeconf file and found the following settings: CPICFLAGS = -fpic FPICFLAGS = -fpic So my comment in the first reply applied, since it looks like your distro is using an unusual name. You need to change these (and in etc/Makeconf). Thanks, Vivek Thanks, Vivek On 6/25/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: Is this ppc32 or ppc64? (What does uname -a say?) If the former, you might need to set CPICFLAGS and FPICFLAGS to -fPIC (rather than -fpic): please look these up in the R-admin.html file (which INSTALL points you to). For ppc64 configure should have found -fPIC. On Mon, 25 Jun 2007, Vivek Menon wrote: Hello everybody,I am having an error while compiling R-2.5.0 on Linux powerpc. This is what I see when I do a make: gcc -std=gnu99 -shared -L/usr/local/lib -o grDevices.so chull.o devNull.o devPicTeX.o devPS.o devQuartz.o init.o ../../../../library/grDevices/libs/grDevices.so is unchanged make[5]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0/src/library/grDevices/src' make[4]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0 /src/library/grDevices/src' Warning: unable to load shared library '/home/vivekv/sw_alg/R- 2.5.0 /modules//lapack.so': /home/vivekv/sw_alg/R- 2.5.0/modules//lapack.so: R_PPC_REL24 relocation at 0x0e65d7e4 for symbol `strlen' out of range Error in solve.default(rgb) : lapack routines cannot be loaded Error: unable to load R code in package 'grDevices' Execution halted make[3]: *** [all] Error 1 make[3]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0 /src/library/grDevices' make[2]: *** [R] Error 1 make[2]: Leaving directory `/home/vivekv/sw_alg/R- 2.5.0 /src/library' make[1]: *** [R] Error 1 make[1]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0/src' make: *** [R] Error 1 Please let me know what needs to be done for a successful installation. Thanks, Vivek [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. -- 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 -- 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 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] how to plot this?
Hi, there: Suppose I have a couple of data.frames and each one has five columns (one for x-axis, two for y-axis and two for std of y's.) There is another dimensions (besides x and y) which is continuous. My question is, how to plot such series of data frames in one plot (thus, 3-dimensional plot) AND multiple 2-D plots. I am not familar with R's plotting utilities. Thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] eps in odfWeave
Dear Weavers, Does someone have an example of using eps or any other vector graphics with odfWeave? It tried the example below (and commented variants) with simple.odt in the examples directory, and got an error. Dieter #--- library(odfWeave) plotInfo - getImageDefs() plotInfo$type = eps #plotInfo$device = postscript setImageDefs(plotInfo) odfWeave(simple.odt, simpleOut.odt) #- # Writing to file content_1.xml # Processing code chunks ... #1 : term hide(label=loadLibs) #2 : term xml(label=showOutputList) #Error in check(options) : invalid value for 'type' : eps Version: 0.5.9 Date: 2007-20-06 platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 5.0 year 2007 month 04 day23 svn rev41293 language R version.string R version 2.5.0 (2007-04-23) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-2.5.0 compilation problem on Linux powerpc
On Mon, 25 Jun 2007, Vivek Menon wrote: I did not get what you replied in the previous email. I still get the same error with CPICFLAGS and FPICFLAGS set to -fPIC. And a completely fresh build? Vivek On 6/25/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: On Mon, 25 Jun 2007, Vivek Menon wrote: uname -a gives me this:== Linux 2.6.21.1-xserve #17 SMP Thu Jun 14 19:45:57 MDT 2007 ppc64 ppc64 ppc64 GNU/Linux === Also when I configure I see the foll. output: R is now configured for powerpc64-unknown-linux-gnu That might be the problem: 'powerpc64' not 'ppc64'. What Linux distro is this? I am using Yellow Dog Linux distro. Source directory: . Installation directory:/usr/local C compiler:gcc -std=gnu99 -g -O2 Fortran 77 compiler: gfortran -g -O2 C++ compiler: g++ -g -O2 Fortran 90/95 compiler:gfortran -g -O2 Obj-C compiler: Interfaces supported: External libraries:readline Additional capabilities: PNG, iconv, MBCS, NLS Options enabled: shared BLAS, R profiling, Java Recommended packages: yes Do you have any suggestions?? And what is the setting of the flags I mentioned? See the manual I pointed you to, or the Makeconf file? I checked the Makeconf file and found the following settings: CPICFLAGS = -fpic FPICFLAGS = -fpic So my comment in the first reply applied, since it looks like your distro is using an unusual name. You need to change these (and in etc/Makeconf). Thanks, Vivek Thanks, Vivek On 6/25/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: Is this ppc32 or ppc64? (What does uname -a say?) If the former, you might need to set CPICFLAGS and FPICFLAGS to -fPIC (rather than -fpic): please look these up in the R-admin.html file (which INSTALL points you to). For ppc64 configure should have found -fPIC. On Mon, 25 Jun 2007, Vivek Menon wrote: Hello everybody,I am having an error while compiling R-2.5.0 on Linux powerpc. This is what I see when I do a make: gcc -std=gnu99 -shared -L/usr/local/lib -o grDevices.so chull.o devNull.o devPicTeX.o devPS.o devQuartz.o init.o ../../../../library/grDevices/libs/grDevices.so is unchanged make[5]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0/src/library/grDevices/src' make[4]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0 /src/library/grDevices/src' Warning: unable to load shared library '/home/vivekv/sw_alg/R- 2.5.0 /modules//lapack.so': /home/vivekv/sw_alg/R- 2.5.0/modules//lapack.so: R_PPC_REL24 relocation at 0x0e65d7e4 for symbol `strlen' out of range Error in solve.default(rgb) : lapack routines cannot be loaded Error: unable to load R code in package 'grDevices' Execution halted make[3]: *** [all] Error 1 make[3]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0 /src/library/grDevices' make[2]: *** [R] Error 1 make[2]: Leaving directory `/home/vivekv/sw_alg/R- 2.5.0 /src/library' make[1]: *** [R] Error 1 make[1]: Leaving directory `/home/vivekv/sw_alg/R-2.5.0/src' make: *** [R] Error 1 Please let me know what needs to be done for a successful installation. Thanks, Vivek [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. -- 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 -- 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 -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented,
Re: [R] R-excel
Hi, Directly import from Excel files should be possible using the RODBC package. Yu may want to read the R data import/export manual about the RODBC package for further details. Another solution is to save each of your Excel sheets as *.csv file and import the data in R using the read.table command (see ?read.table). Sebastien Erika Frigo a écrit : Good morning to everybody, I have a problem : how can I import excel files in R??? thank you very much Dr.sa. Erika Frigo Università degli Studi di Milano Facoltà di Medicina Veterinaria Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare (VSA) Via Grasselli, 7 20137 Milano Tel. 02/50318515 Fax 02/50318501 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Imputing missing values in time series
On Fri, 22 Jun 2007, Horace Tso wrote: Thanks to Mark and Erik for different versions of locf, also Erik's pointer to archive where I found another function due to Simon Fear. I haven't tested the zoo locf function. Just as an addition to what Marc already wrote: zoo offers at least two advantages here: - it does not break if the first element is NA - if available it incorporates the corresponding time stamps When we wrote na.locf(), Gabor also tried to optimize it for speed. I haven't compared it to the solutions suggested here but would be surprised if any of them would substantially faster. As for your time series, I would recommend that you hold it as a zoo series with Date time stamps. See vignette(zoo-quickref, package = zoo) vignette(zoo, package = zoo) for some examples of zoo series in general and na.locf() in particular. Z __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] eps in odfWeave
Dieter,
What is the version of odfWeave? If you use those specifications in the
current version (0.5.9):
plotInfo - getImageDefs()
plotInfo$type = eps
plotInfo$device = postscript
setImageDefs(plotInfo)
you will probabiliy need to set
horizontal = FALSE, onefile = FALSE, and paper = special to generate
ps graphics for OpenOffice
an image size of 480 inches by 480 inches has been requested.
setImageDefs(plotInfo)
When I run somewhat altered options:
plotInfo - getImageDefs()
plotInfo$type = eps
plotInfo$plotWidth = 4
plotInfo$plotHeight = 4
plotInfo$device = postscript
plotInfo$args = list(
+horizontal = FALSE,
+onefile = FALSE,
+paper = special)
setImageDefs(plotInfo)
demoFile - system.file(examples, simple.odt, package =
odfWeave)
odfWeave(demoFile, c:/simpleOut.odt)
Copying C:/PROGRA~1/R/R250/library/odfWeave/examples/simple.odt
Setting wd to
C:\DOCUME~1\KuhnA03\LOCALS~1\Temp\Rtmpp4Zcsb/odfWeave25113622566
snip
Copying simple.odt
Resetting wd
Removing
C:\DOCUME~1\KuhnA03\LOCALS~1\Temp\Rtmpp4Zcsb/odfWeave25113622566
Done
There were some issues with eps and older versions of odfWeave, but I
don't recall that specific error.
[The only other issue with eps and odfWeave (on windows), is image
rendering. On my system, there is a windows system file called convert
(instead of imagemagick's convert) which messes up the image preview
within the document. Marc Schwartz and I have talked about this off-list
and he doesn't have the same issues.]
Max
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Dieter Menne
Sent: Monday, June 25, 2007 11:04 AM
To: R-Help
Subject: [R] eps in odfWeave
Dear Weavers,
Does someone have an example of using eps or any other vector graphics
with
odfWeave? It tried the example below (and commented variants) with
simple.odt in the examples directory, and got an error.
Dieter
#---
library(odfWeave)
plotInfo - getImageDefs()
plotInfo$type = eps
#plotInfo$device = postscript
setImageDefs(plotInfo)
odfWeave(simple.odt, simpleOut.odt)
#-
# Writing to file content_1.xml
# Processing code chunks ...
#1 : term hide(label=loadLibs)
#2 : term xml(label=showOutputList)
#Error in check(options) : invalid value for 'type' : eps
Version: 0.5.9
Date: 2007-20-06
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 5.0
year 2007
month 04
day23
svn rev41293
language R
version.string R version 2.5.0 (2007-04-23)
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] a string to enviroment or function
Hi, I am wondering how to make a function Fun to make the following work: t0 - (paste(hgu133a, ENTREZID, sep=)) xx - as.list(Fun(t0)) # make it work like xx-as.list(hgu133aENTREZID) thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] problem building first package
Hi, I am trying to build a package from source for the first time. I'm using Windows XP. After R CMD INSTALL or R CMD check I get an error message that I don't understand. I've tried to follow the instrucions provided in the R Installation and Administration .pdf and the text file that comes with Rtools, but most of this is new to me and clearly I'm missing something. Here's what I've done: -Downloaded perl and Rtools and put them in my c directory -Used package.skeleton() to set up the package structure and put the package-to-be removal in C:\toBuild -I edited my path to : C:\Rtools\bin;C:\perl\bin;C:\Rtools\MinGW\bin;C:\R-2.5.0\bin;... -I changed the following in the MkRules file: 1)HEADER=C:/Rtools/MinGW/include 2)HELPTYPES = -txt 3)WINHELP = NO 4)HEADER=C:/Rtools/MinGW/include 5)R_EXE=C:/R-2.5.0/bin/R.exe -Next, I opened up a command prompt and went to c:/toBuild -Then I ran: R CMD build removal. No problems. -Then I ran: R CMD INSTALL removal_1.0.tar.gz and got this: - installing to 'c:/R-2.5.0/library' latex: not found latex: not found latex: not found -- Making package removal latex: not found adding build stamp to DESCRIPTION latex: not found latex: not found latex: not found installing R files latex: not found installing data files latex: not found installing man source files installing indices latex: not found latex: not found not zipping data installing help Building/Updating help pages for package 'removal' Formats: text chm RemProbs text chm add.error text chm error.plottext chm firstDetect text chm funs text chm path text chm pll2 text chm remll2text chm removal-package text chm removal2 text chm var.d text chm hhc: not found cp: cannot stat `C:/toBuild/R.INSTALL.3064/removal/chm/removal.chm': No such fil e or directory make[1]: *** [chm-removal] Error 1 make: *** [pkg-removal] Error 2 *** Installation of removal failed *** Removing 'c:/R-2.5.0/library/removal' --- I don't know what hhc is. I'm guessing its trying to build the compiled help files even though I tried to ask for only text files. It also seems to want latex even though I read that it isn't necessary to build simple packages. Can someone please tell me what I'm doing wrong? Thanks. Richard -- Richard Chandler, PhD student Department of Natural Resources Conservation UMass Amherst (413)545-1237 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] eps in odfWeave
Kuhn, Max Max.Kuhn at pfizer.com writes: Thanks, Max. What is the version of odfWeave? If you use those specifications in the current version (0.5.9): Yes, version 0.5.9 (it was further below in my message, I forgot to put the odfWeave flag before it. I had tried your horizontal... suggestions before, because these came up nicely in the error message, but the error remained the same, so I removed them. Here another try for copy/paste, with a traceback. The convert problem is a well known Imagemagick problem; clashes with convert in the Windows directory. Workaround is to put the Imagemagick path before the Windows/system32 path. Dieter library(odfWeave) plotInfo - getImageDefs() plotInfo$type = eps plotInfo$plotWidth = 4 plotInfo$plotHeight = 4 plotInfo$device = postscript plotInfo$args = list( horizontal = FALSE, onefile = FALSE, paper = special) setImageDefs(plotInfo) demoFile - system.file(examples, simple.odt, package =odfWeave) odfWeave(demoFile, c:/simpleOut.odt) - Error in check(options) : invalid value for 'type' : eps traceback() 5: stop(gettextf(invalid value for '%s' : %s, opt, oldval), domain = NA) 4: check(options) 3: SweaveParseOptions(chunkopts, drobj$options, driver$checkopts) 2: Sweave(file = rnwFileName, output = content_1.xml, quiet = !control$verbose, driver = RweaveOdf(), control = control) 1: odfWeave(demoFile, c:/simpleOut.odt) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] simultaneous actions of grep ???
Hello R-users and developers, Once again, I'm asking for your help. There is other way to do the same more easily for applied simultaneous grep??? c-subset(c,!rownames(c) %in% grep(.1,rownames(c),value=T)) c-subset(c,!rownames(c) %in% grep(.5,rownames(c),value=T)) c-subset(c,!rownames(c) %in% grep(.6,rownames(c),value=T)) c-subset(c,!rownames(c) %in% grep(.9,rownames(c),value=T)) Thanks in advance for helping me. Atenciosamente, Ana Patricia Martins --- Serviço Métodos Estatísticos Departamento de Metodologia Estatística INE - Portugal Telef: 218 426 100 - Ext: 3210 E-mail: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] a string to enviroment or function
I think that you might want: t0 - (paste(hgu133a, ENTREZID, sep=)) xx - as.list(get(t0)) # make it work like xx-as.list(hgu133aENTREZID) On 6/25/07, Weiwei Shi [EMAIL PROTECTED] wrote: Hi, I am wondering how to make a function Fun to make the following work: t0 - (paste(hgu133a, ENTREZID, sep=)) xx - as.list(Fun(t0)) # make it work like xx-as.list(hgu133aENTREZID) thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] manipulate a matrix
I have read everything I can find on how to manipulate a results matrix in R and I have to admit I'm stumped. I have set up a process to extract a dataset from ArcGIS to compute a similarity index (Jaccards) in Vegan. The dataset is fairly simple, but large, and consists of rows = sample area, and columns = elements. I've been able to view the results in R, but I want to get the results out to a database and a matrix that is 6000-rows x 6000-columns can be very difficult to manipulate in Windows XP. I would to rotate the matrix so that the output would look like the old condensed format in programs like Conoco. Ideally, I would like format to look something like this; Site-row Site-col Jaccard 1 1 1 1 2 .9 1 3 .6 2 1 .9 2 2 1 2 3 .75 Thanks for any help, *** John Hak Senior GIS Analyst/Sr. Ecologist NatureServe 4001 Discovery Drive Boulder, CO 80303 (703) 797-4809 There is perhaps no better demonstration of the folly of human conceits than this distant image of our tiny world. To me, it underscores our responsibility to deal more kindly with one another, and to preserve and cherish the pale blue dot, the only home we've ever known. --Carl Sagan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Re : Half of a heatmap
I am trying to produce a heatmap of pairwise correlations, but since the matrix is symmetric, I only need either the upper or the lower triangle. I have scoured the web and R documentation, but I have not been able to find a way to produce such a figure. Is there a simple way to produce a heat map with only the part above or below the diagonal? Can you not just set the lower or upper triangle to NAs, and pass this on to heatmap - or am I misunderstanding you? tmp - matrix(rnorm(100),10,10) tmp[lower.tri(tmp)] - NA heatmap(tmp, Rowv=NA, Colv=NA) Regards - Gavin -- Gavin Kelly Senior Statistician, Bioinformatics Biostatistics Group Cancer Research UK __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R behaviour related to user input (readline()) and run selection
First of all you don't appear to be returning anything from your function,
so 'co' is NULL and your 'if' statement fails. You were also probably
cut/paste the code in, and the readline was reading from the statements you
pasted. Try sourcing in the code.
On 6/25/07, Bernzweig, Bruce (Consultant) [EMAIL PROTECTED] wrote:
When I run the below section of code I get the following error:
Error in if (co == A || co[1] == O) { :
missing value where TRUE/FALSE needed
When I run the code in two parts where I first get the user's input
then afterwards run the if/else section, there is no problem.
Is there a way to stop the run selection process until the user
has input a value?
-
calc_option - function(){
msg - cat(Please select an option:\n, 'O'ne or 'A'll':
)
co - readline(msg)
switch(co,
O = O, o = O,
A = A, a = A
)
}
co - calc_option()
if (co == A || co[1] == O) {
print(paste(calc_option = , co))
} else {
print(calc_option is not acceptable)
}
Thanks,
- Bruce
**
Please be aware that, notwithstanding the fact that the pers...{{dropped}}
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to plot this?
You might want to check out this link to the type of graphs that R can produce and find one you like; the code will be with it. http://addictedtor.free.fr/graphiques/allgraph.php On 6/25/07, Weiwei Shi [EMAIL PROTECTED] wrote: Hi, there: Suppose I have a couple of data.frames and each one has five columns (one for x-axis, two for y-axis and two for std of y's.) There is another dimensions (besides x and y) which is continuous. My question is, how to plot such series of data frames in one plot (thus, 3-dimensional plot) AND multiple 2-D plots. I am not familar with R's plotting utilities. Thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to plot this?
You might want to check out this link to the type of graphs that R can produce and find one you like; the code will be with it. http://addictedtor.free.fr/graphiques/allgraph.php On 6/25/07, Weiwei Shi [EMAIL PROTECTED] wrote: Hi, there: Suppose I have a couple of data.frames and each one has five columns (one for x-axis, two for y-axis and two for std of y's.) There is another dimensions (besides x and y) which is continuous. My question is, how to plot such series of data frames in one plot (thus, 3-dimensional plot) AND multiple 2-D plots. I am not familar with R's plotting utilities. Thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] degrees of freedom in lme
Dear all, I am starting to use the lme package (and plan to teach a course based on it next semester...). To understand what lme is doing precisely, I used balanced datasets described in Pinheiro and Bates and tried to compare the lme outputs to that of aov. Here is what I obtained: data(Machines) summary(aov(score~Machine+Error(Worker/Machine),data=Machines)) Error: Worker Df Sum Sq Mean Sq F value Pr(F) Residuals 5 1241.89 248.38 Error: Worker:Machine Df Sum Sq Mean Sq F valuePr(F) Machine2 1755.26 877.63 20.576 0.0002855 *** Residuals 10 426.53 42.65 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Error: Within Df Sum Sq Mean Sq F value Pr(F) Residuals 36 33.287 0.925 anova(lme(fixed=score~Machine,random=~1|Worker/Machine,data=Machines)) numDF denDF F-value p-value (Intercept) 136 773.5709 .0001 Machine 210 20.5762 3e-04 No problem here: the results are essentially the same, which is expected. Now I turn to an ANCOVA with a random grouping factor. data(Orthodont) OrthoFem - Orthodont[Orthodont$Sex==Female,]; summary(aov(distance~age+Error(Subject/age),data=OrthoFem)) Error: Subject Df Sum Sq Mean Sq F value Pr(F) Residuals 10 177.227 17.723 Error: Subject:age Df Sum Sq Mean Sq F valuePr(F) age1 50.592 50.592 52.452 2.783e-05 *** Residuals 10 9.645 0.965 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Error: Within Df Sum Sq Mean Sq F value Pr(F) Residuals 22 9.8250 0.4466 anova(lme(fixed=distance~age,random=~1+age|Subject,data=OrthoFem)) numDF denDF F-value p-value (Intercept) 132 1269.7764 .0001 age 132 52.4517 .0001 This time the F values are (almost) identical, the numerator degrees of freedom are the same, but the denominator degrees of freedom are very different (10 for aov vs. 32 for lme). I understand that there is an issue with the estimation of that number, but I would naively expect the number given by lme to be close to that provided by aov is the case of a balanced dataset. That's obviously not true in the case of an ANCOVA... But why?? And how should I interpret the F-test given by anova.lme? Thanks in advance for your help ! -- Jean-Baptiste Ferdy Institut des Sciences de l'Évolution de Montpellier CNRS UMR 5554 Université Montpellier 2 34 095 Montpellier cedex 05 tel. +33 (0)4 67 14 42 27 fax +33 (0)4 67 14 36 22 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] simultaneous actions of grep ???
On Mon, 2007-06-25 at 17:15 +0100, Ana Patricia Martins wrote:
Hello R-users and developers,
Once again, I'm asking for your help.
There is other way to do the same more easily for applied simultaneous
grep???
c-subset(c,!rownames(c) %in% grep(.1,rownames(c),value=T))
c-subset(c,!rownames(c) %in% grep(.5,rownames(c),value=T))
c-subset(c,!rownames(c) %in% grep(.6,rownames(c),value=T))
c-subset(c,!rownames(c) %in% grep(.9,rownames(c),value=T))
Thanks in advance for helping me.
One question might be what other possible values can the rownames take.
For example, if you want to check for '.9', but not for other values
containing a '9' after the decimal, something like the following should
work:
sub.c - subset(c,
!rownames(c) %in%
grep(\\.([156])|([9]{5}), rownames(c),
value = TRUE))
Otherwise, if you want to include anything with a '9' after a decimal,
the following would work:
sub.c - subset(c,
!rownames(c) %in%
grep(\\.[1569], rownames(c), value = TRUE))
See ?regex and the information there for some additional guidance. There
are also many regex references online, such as:
http://www.regular-expressions.info/
BTW, it would be preferable not to use 'c' to name an object in R, since
c() is a function. While conflicts should, in general, not occur, it
eliminates such risk and makes for more easily readable code to not use
function names for objects.
HTH,
Marc Schwartz
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem building first package
You can ignore the message about latex (and 2.5.1 RC does not give it). hhc is part of HTML Help Workshop: you either have not installed that or not put it in your path. The settings in MkRules affect the types of help for building R, not 'R CMD INSTALL'. If you only want text help you need to run R CMD INSTALL --docs=txt removal_1.0.tar.gz On Mon, 25 Jun 2007, Richard Chandler wrote: Hi, I am trying to build a package from source for the first time. I'm using Windows XP. After R CMD INSTALL or R CMD check I get an error message that I don't understand. I've tried to follow the instrucions provided in the R Installation and Administration .pdf and the text file that comes with Rtools, but most of this is new to me and clearly I'm missing something. Here's what I've done: -Downloaded perl and Rtools and put them in my c directory -Used package.skeleton() to set up the package structure and put the package-to-be removal in C:\toBuild -I edited my path to : C:\Rtools\bin;C:\perl\bin;C:\Rtools\MinGW\bin;C:\R-2.5.0\bin;... -I changed the following in the MkRules file: 1)HEADER=C:/Rtools/MinGW/include 2)HELPTYPES = -txt 3)WINHELP = NO 4)HEADER=C:/Rtools/MinGW/include 5)R_EXE=C:/R-2.5.0/bin/R.exe The last two are for cross-building, not what you are doing. -Next, I opened up a command prompt and went to c:/toBuild -Then I ran: R CMD build removal. No problems. -Then I ran: R CMD INSTALL removal_1.0.tar.gz and got this: - installing to 'c:/R-2.5.0/library' latex: not found latex: not found latex: not found -- Making package removal latex: not found adding build stamp to DESCRIPTION latex: not found latex: not found latex: not found installing R files latex: not found installing data files latex: not found installing man source files installing indices latex: not found latex: not found not zipping data installing help Building/Updating help pages for package 'removal' Formats: text chm RemProbs text chm add.error text chm error.plottext chm firstDetect text chm funs text chm path text chm pll2 text chm remll2text chm removal-package text chm removal2 text chm var.d text chm hhc: not found cp: cannot stat `C:/toBuild/R.INSTALL.3064/removal/chm/removal.chm': No such fil e or directory make[1]: *** [chm-removal] Error 1 make: *** [pkg-removal] Error 2 *** Installation of removal failed *** Removing 'c:/R-2.5.0/library/removal' --- I don't know what hhc is. I'm guessing its trying to build the compiled help files even though I tried to ask for only text files. It also seems to want latex even though I read that it isn't necessary to build simple packages. Can someone please tell me what I'm doing wrong? Thanks. Richard -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] LanguageR pvals.fnc error message
Hi. I get an error message about not converging when I try and use the pvals.fnc from the languageR library. The LMER analysis worked fine (See below). I am not an expert so I don't understand why the LMER worked but not the pvals.fnc Any help gratefully received. - Mike AIC BIC logLik MLdeviance REMLdeviance -7324 -7254 3673 -7451-7346 Random effects: Groups NameVariance Std.Dev. Item (Intercept) 5.3386e-05 0.0073066 Subj (Intercept) 1.8073e-03 0.0425128 Residual 1.0314e-02 0.1015578 number of obs: 4363, groups: Item, 294; Subj, 38 Fixed effects: Estimate Std. Error t value (Intercept) 5.848e+00 7.830e-03 746.9 PrevErr1 3.835e-03 3.808e-03 1.0 ExpOrd -3.708e-05 9.107e-06-4.1 pc4lex -4.630e-04 1.681e-03-0.3 pc4img -7.519e-04 1.642e-03-0.5 pc4nlen -4.413e-03 1.608e-03-2.7 pc4lsa8.118e-04 1.648e-03 0.5 pc4ng -5.183e-03 1.642e-03-3.2 I(pc4nlen^2) 2.999e-03 1.451e-03 2.1 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Re : Half of a heatmap
Just for the record, LDheatmap can display any upper-triangular matrix of measures between 0 and 1, not just LD measures. Users with their own matrix should pass it as the first argument (gdat) to the function. -b -- Brad McNeney Statistics and Actuarial Science Simon Fraser University Burnaby, BC, Canada On 6/25/07, Rosenfeld, Jeffrey [EMAIL PROTECTED] wrote: Thank you for your reply. I have looked at LDheatmap, but it does not seem to do what I want and seems to only work well for LD data. I was looking for something that would produce a figure identical to what heatmap.2 gives me, including the proper X and Y-axis labels and a dendogram, except that it would only have half of the map. Preferably, it would have the Color Key in the place where the other triangle of the heatmap would be, to save space. Jeff -Original Message- From: Neil Shephard [mailto:[EMAIL PROTECTED] Sent: Mon 6/25/2007 6:14 AM To: r-help@stat.math.ethz.ch Cc: Rosenfeld, Jeffrey Subject: Re : [R] Half of a heatmap I am trying to produce a heatmap of pairwise correlations, but since the matrix is symmetric, I only need either the upper or the lower triangle. I have scoured the web and R documentation, but I have not been able to find a way to produce such a figure. Is there a simple way to produce a heat map with only the part above or below the diagonal? You might want to check out the LDheatmap() package which can generate the plots you describe. The help indicates that it accepts a matrix of pair-wise linkage disequilibrium measures, one of which is R^2 (the correlation coefficient between loci), but I suspect you could simply pass it a matrix of correlation coefficents. Hope that helps, Neil -- In mathematics you don't understand things. You just get used to them. - Johann von Neumann Email - [EMAIL PROTECTED] / [EMAIL PROTECTED] Website - http://slack.ser.man.ac.uk/ Photos - http://www.flickr.com/photos/slackline/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] manipulate a matrix
Is this what you want? x [,1] [,2] [,3] [,4] [,5] [1,]16 11 16 21 [2,]27 12 17 22 [3,]38 13 18 23 [4,]49 14 19 24 [5,]5 10 15 20 25 cbind(row=as.vector(row(x)), col=as.vector(col(x)), value=as.vector(x)) row col value [1,] 1 1 1 [2,] 2 1 2 [3,] 3 1 3 [4,] 4 1 4 [5,] 5 1 5 [6,] 1 2 6 [7,] 2 2 7 [8,] 3 2 8 [9,] 4 2 9 [10,] 5 210 [11,] 1 311 [12,] 2 312 [13,] 3 313 [14,] 4 314 [15,] 5 315 [16,] 1 416 [17,] 2 417 [18,] 3 418 [19,] 4 419 [20,] 5 420 [21,] 1 521 [22,] 2 522 [23,] 3 523 [24,] 4 524 [25,] 5 525 On 6/25/07, Jon Hak [EMAIL PROTECTED] wrote: I have read everything I can find on how to manipulate a results matrix in R and I have to admit I'm stumped. I have set up a process to extract a dataset from ArcGIS to compute a similarity index (Jaccards) in Vegan. The dataset is fairly simple, but large, and consists of rows = sample area, and columns = elements. I've been able to view the results in R, but I want to get the results out to a database and a matrix that is 6000-rows x 6000-columns can be very difficult to manipulate in Windows XP. I would to rotate the matrix so that the output would look like the old condensed format in programs like Conoco. Ideally, I would like format to look something like this; Site-row Site-col Jaccard 1 1 1 1 2 .9 1 3 .6 2 1 .9 2 2 1 2 3 .75 Thanks for any help, *** John Hak Senior GIS Analyst/Sr. Ecologist NatureServe 4001 Discovery Drive Boulder, CO 80303 (703) 797-4809 There is perhaps no better demonstration of the folly of human conceits than this distant image of our tiny world. To me, it underscores our responsibility to deal more kindly with one another, and to preserve and cherish the pale blue dot, the only home we've ever known. --Carl Sagan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] degrees of freedom in lme
This is such a common question that it has a an FAQ-like response from Doug Bates. Google lmer p-values and all that to find the response. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jean-Baptiste Ferdy Sent: Monday, June 25, 2007 12:26 PM To: r-help@stat.math.ethz.ch Subject: [R] degrees of freedom in lme Dear all, I am starting to use the lme package (and plan to teach a course based on it next semester...). To understand what lme is doing precisely, I used balanced datasets described in Pinheiro and Bates and tried to compare the lme outputs to that of aov. Here is what I obtained: data(Machines) summary(aov(score~Machine+Error(Worker/Machine),data=Machines)) Error: Worker Df Sum Sq Mean Sq F value Pr(F) Residuals 5 1241.89 248.38 Error: Worker:Machine Df Sum Sq Mean Sq F valuePr(F) Machine2 1755.26 877.63 20.576 0.0002855 *** Residuals 10 426.53 42.65 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Error: Within Df Sum Sq Mean Sq F value Pr(F) Residuals 36 33.287 0.925 anova(lme(fixed=score~Machine,random=~1|Worker/Machine,data=Machines)) numDF denDF F-value p-value (Intercept) 136 773.5709 .0001 Machine 210 20.5762 3e-04 No problem here: the results are essentially the same, which is expected. Now I turn to an ANCOVA with a random grouping factor. data(Orthodont) OrthoFem - Orthodont[Orthodont$Sex==Female,]; summary(aov(distance~age+Error(Subject/age),data=OrthoFem)) Error: Subject Df Sum Sq Mean Sq F value Pr(F) Residuals 10 177.227 17.723 Error: Subject:age Df Sum Sq Mean Sq F valuePr(F) age1 50.592 50.592 52.452 2.783e-05 *** Residuals 10 9.645 0.965 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Error: Within Df Sum Sq Mean Sq F value Pr(F) Residuals 22 9.8250 0.4466 anova(lme(fixed=distance~age,random=~1+age|Subject,data=OrthoFem)) numDF denDF F-value p-value (Intercept) 132 1269.7764 .0001 age 132 52.4517 .0001 This time the F values are (almost) identical, the numerator degrees of freedom are the same, but the denominator degrees of freedom are very different (10 for aov vs. 32 for lme). I understand that there is an issue with the estimation of that number, but I would naively expect the number given by lme to be close to that provided by aov is the case of a balanced dataset. That's obviously not true in the case of an ANCOVA... But why?? And how should I interpret the F-test given by anova.lme? Thanks in advance for your help ! -- Jean-Baptiste Ferdy Institut des Sciences de l'Évolution de Montpellier CNRS UMR 5554 Université Montpellier 2 34 095 Montpellier cedex 05 tel. +33 (0)4 67 14 42 27 fax +33 (0)4 67 14 36 22 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] simultaneous actions of grep ???
On Mon, 2007-06-25 at 11:58 -0500, Marc Schwartz wrote:
On Mon, 2007-06-25 at 17:15 +0100, Ana Patricia Martins wrote:
Hello R-users and developers,
Once again, I'm asking for your help.
There is other way to do the same more easily for applied simultaneous
grep???
c-subset(c,!rownames(c) %in% grep(.1,rownames(c),value=T))
c-subset(c,!rownames(c) %in% grep(.5,rownames(c),value=T))
c-subset(c,!rownames(c) %in% grep(.6,rownames(c),value=T))
c-subset(c,!rownames(c) %in% grep(.9,rownames(c),value=T))
Thanks in advance for helping me.
One question might be what other possible values can the rownames take.
For example, if you want to check for '.9', but not for other values
containing a '9' after the decimal, something like the following should
work:
sub.c - subset(c,
!rownames(c) %in%
grep(\\.([156])|([9]{5}), rownames(c),
value = TRUE))
Otherwise, if you want to include anything with a '9' after a decimal,
the following would work:
sub.c - subset(c,
!rownames(c) %in%
grep(\\.[1569], rownames(c), value = TRUE))
See ?regex and the information there for some additional guidance. There
are also many regex references online, such as:
http://www.regular-expressions.info/
BTW, it would be preferable not to use 'c' to name an object in R, since
c() is a function. While conflicts should, in general, not occur, it
eliminates such risk and makes for more easily readable code to not use
function names for objects.
Quick possible correction:
I mis-read the regex as containing a decimal, which would need to be
escaped as I had.
If your use of the '.' is to refer to any character, then the following
would be correct:
sub.c - subset(c,
!rownames(c) %in%
grep(.([156])|([9]{5}), rownames(c),
value = TRUE))
or
sub.c - subset(c,
!rownames(c) %in%
grep(.[1569], rownames(c), value = TRUE))
Sorry for the confusion.
Marc
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] manipulate a matrix
On Mon, 2007-06-25 at 10:58 -0400, Jon Hak wrote: I have read everything I can find on how to manipulate a results matrix in R and I have to admit I'm stumped. I have set up a process to extract a dataset from ArcGIS to compute a similarity index (Jaccards) in Vegan. The dataset is fairly simple, but large, and consists of rows = sample area, and columns = elements. I've been able to view the results in R, but I want to get the results out to a database and a matrix that is 6000-rows x 6000-columns can be very difficult to manipulate in Windows XP. I would to rotate the matrix so that the output would look like the old condensed format in programs like Conoco. Ideally, I would like format to look something like this; Site-row Site-col Jaccard 1 1 1 1 2 .9 1 3 .6 2 1 .9 2 2 1 2 3 .75 Thanks for any help, Presuming that your source matrix for the above is: mat - matrix(c(1, .9, .6, .9, 1, .75), ncol = 3, byrow = TRUE) mat [,1] [,2] [,3] [1,] 1.0 0.9 0.60 [2,] 0.9 1.0 0.75 You can use the following: t.mat - t(mat) Res - cbind(Site-row = as.vector(col(t.mat)), Site-col = as.vector(row(t.mat)), Jaccard = as.vector(t.mat)) Res Site-row Site-col Jaccard [1,]111.00 [2,]120.90 [3,]130.60 [4,]210.90 [5,]221.00 [6,]230.75 See ?t and ?row HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to plot this?
On 6/25/07, jim holtman [EMAIL PROTECTED] wrote: You might want to check out this link to the type of graphs that R can produce and find one you like; the code will be with it. http://addictedtor.free.fr/graphiques/allgraph.php Or for examples using the ggplot2 package: http://had.co.nz/ggplot2 Hadley __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem building first package
Thanks so much. I was able to get it installed using: R CMD INSTALL --docs=normal removal_1.0.tar.gz However, setting --docs=txt gave me this error: ERROR: invalid --docs value `txt' The --help says it needs to be a list, but no matter, --docs=normal worked fine. Quoting Prof Brian Ripley [EMAIL PROTECTED]: You can ignore the message about latex (and 2.5.1 RC does not give it). hhc is part of HTML Help Workshop: you either have not installed that or not put it in your path. The settings in MkRules affect the types of help for building R, not 'R CMD INSTALL'. If you only want text help you need to run R CMD INSTALL --docs=txt removal_1.0.tar.gz On Mon, 25 Jun 2007, Richard Chandler wrote: Hi, I am trying to build a package from source for the first time. I'm using Windows XP. After R CMD INSTALL or R CMD check I get an error message that I don't understand. I've tried to follow the instrucions provided in the R Installation and Administration .pdf and the text file that comes with Rtools, but most of this is new to me and clearly I'm missing something. Here's what I've done: -Downloaded perl and Rtools and put them in my c directory -Used package.skeleton() to set up the package structure and put the package-to-be removal in C:\toBuild -I edited my path to : C:\Rtools\bin;C:\perl\bin;C:\Rtools\MinGW\bin;C:\R-2.5.0\bin;... -I changed the following in the MkRules file: 1)HEADER=C:/Rtools/MinGW/include 2)HELPTYPES = -txt 3)WINHELP = NO 4)HEADER=C:/Rtools/MinGW/include 5)R_EXE=C:/R-2.5.0/bin/R.exe The last two are for cross-building, not what you are doing. -Next, I opened up a command prompt and went to c:/toBuild -Then I ran: R CMD build removal. No problems. -Then I ran: R CMD INSTALL removal_1.0.tar.gz and got this: - installing to 'c:/R-2.5.0/library' latex: not found latex: not found latex: not found -- Making package removal latex: not found adding build stamp to DESCRIPTION latex: not found latex: not found latex: not found installing R files latex: not found installing data files latex: not found installing man source files installing indices latex: not found latex: not found not zipping data installing help Building/Updating help pages for package 'removal' Formats: text chm RemProbs text chm add.error text chm error.plottext chm firstDetect text chm funs text chm path text chm pll2 text chm remll2text chm removal-package text chm removal2 text chm var.d text chm hhc: not found cp: cannot stat `C:/toBuild/R.INSTALL.3064/removal/chm/removal.chm': No such fil e or directory make[1]: *** [chm-removal] Error 1 make: *** [pkg-removal] Error 2 *** Installation of removal failed *** Removing 'c:/R-2.5.0/library/removal' --- I don't know what hhc is. I'm guessing its trying to build the compiled help files even though I tried to ask for only text files. It also seems to want latex even though I read that it isn't necessary to build simple packages. Can someone please tell me what I'm doing wrong? Thanks. Richard -- 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 -- Richard Chandler, PhD student Department of Natural Resources Conservation UMass Amherst (413)545-1237 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Re : Half of a heatmap
I have correlation values between -1 and 1 and I need to keep the sign. Jeff -Original Message- From: Brad McNeney [mailto:[EMAIL PROTECTED] Sent: Mon 6/25/2007 1:01 PM To: Rosenfeld, Jeffrey Cc: Neil Shephard; r-help@stat.math.ethz.ch Subject: Re: [R] Re : Half of a heatmap Just for the record, LDheatmap can display any upper-triangular matrix of measures between 0 and 1, not just LD measures. Users with their own matrix should pass it as the first argument (gdat) to the function. -b -- Brad McNeney Statistics and Actuarial Science Simon Fraser University Burnaby, BC, Canada On 6/25/07, Rosenfeld, Jeffrey [EMAIL PROTECTED] wrote: Thank you for your reply. I have looked at LDheatmap, but it does not seem to do what I want and seems to only work well for LD data. I was looking for something that would produce a figure identical to what heatmap.2 gives me, including the proper X and Y-axis labels and a dendogram, except that it would only have half of the map. Preferably, it would have the Color Key in the place where the other triangle of the heatmap would be, to save space. Jeff -Original Message- From: Neil Shephard [mailto:[EMAIL PROTECTED] Sent: Mon 6/25/2007 6:14 AM To: r-help@stat.math.ethz.ch Cc: Rosenfeld, Jeffrey Subject: Re : [R] Half of a heatmap I am trying to produce a heatmap of pairwise correlations, but since the matrix is symmetric, I only need either the upper or the lower triangle. I have scoured the web and R documentation, but I have not been able to find a way to produce such a figure. Is there a simple way to produce a heat map with only the part above or below the diagonal? You might want to check out the LDheatmap() package which can generate the plots you describe. The help indicates that it accepts a matrix of pair-wise linkage disequilibrium measures, one of which is R^2 (the correlation coefficient between loci), but I suspect you could simply pass it a matrix of correlation coefficents. Hope that helps, Neil -- In mathematics you don't understand things. You just get used to them. - Johann von Neumann Email - [EMAIL PROTECTED] / [EMAIL PROTECTED] Website - http://slack.ser.man.ac.uk/ Photos - http://www.flickr.com/photos/slackline/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem building first package
It's a buglet: --docs=txt, works. On Mon, 25 Jun 2007, Richard Chandler wrote: Thanks so much. I was able to get it installed using: R CMD INSTALL --docs=normal removal_1.0.tar.gz However, setting --docs=txt gave me this error: ERROR: invalid --docs value `txt' The --help says it needs to be a list, but no matter, --docs=normal worked fine. Quoting Prof Brian Ripley [EMAIL PROTECTED]: You can ignore the message about latex (and 2.5.1 RC does not give it). hhc is part of HTML Help Workshop: you either have not installed that or not put it in your path. The settings in MkRules affect the types of help for building R, not 'R CMD INSTALL'. If you only want text help you need to run R CMD INSTALL --docs=txt removal_1.0.tar.gz On Mon, 25 Jun 2007, Richard Chandler wrote: Hi, I am trying to build a package from source for the first time. I'm using Windows XP. After R CMD INSTALL or R CMD check I get an error message that I don't understand. I've tried to follow the instrucions provided in the R Installation and Administration .pdf and the text file that comes with Rtools, but most of this is new to me and clearly I'm missing something. Here's what I've done: -Downloaded perl and Rtools and put them in my c directory -Used package.skeleton() to set up the package structure and put the package-to-be removal in C:\toBuild -I edited my path to : C:\Rtools\bin;C:\perl\bin;C:\Rtools\MinGW\bin;C:\R-2.5.0\bin;... -I changed the following in the MkRules file: 1)HEADER=C:/Rtools/MinGW/include 2)HELPTYPES = -txt 3)WINHELP = NO 4)HEADER=C:/Rtools/MinGW/include 5)R_EXE=C:/R-2.5.0/bin/R.exe The last two are for cross-building, not what you are doing. -Next, I opened up a command prompt and went to c:/toBuild -Then I ran: R CMD build removal. No problems. -Then I ran: R CMD INSTALL removal_1.0.tar.gz and got this: - installing to 'c:/R-2.5.0/library' latex: not found latex: not found latex: not found -- Making package removal latex: not found adding build stamp to DESCRIPTION latex: not found latex: not found latex: not found installing R files latex: not found installing data files latex: not found installing man source files installing indices latex: not found latex: not found not zipping data installing help Building/Updating help pages for package 'removal' Formats: text chm RemProbs text chm add.error text chm error.plottext chm firstDetect text chm funs text chm path text chm pll2 text chm remll2text chm removal-package text chm removal2 text chm var.d text chm hhc: not found cp: cannot stat `C:/toBuild/R.INSTALL.3064/removal/chm/removal.chm': No such fil e or directory make[1]: *** [chm-removal] Error 1 make: *** [pkg-removal] Error 2 *** Installation of removal failed *** Removing 'c:/R-2.5.0/library/removal' --- I don't know what hhc is. I'm guessing its trying to build the compiled help files even though I tried to ask for only text files. It also seems to want latex even though I read that it isn't necessary to build simple packages. Can someone please tell me what I'm doing wrong? Thanks. Richard -- 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 -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] complex contrasts and logistic regression
Hi, Sorry to take so long to reply, I was travelling last week. Thanks for your suggestions. Actually in this case contrast and predict gave the same result, and what I was looking at was the correct odds from the model. What is still confusing me is the 1st part of my question, looking for a trend in odds ratios. From what I understand testing the interaction: fit1-glmD(survived ~ as.numeric(Covariate)+Therapy + confounder,myDat,X=TRUE, Y=TRUE, family=binomial()) fit2-glmD(survived ~ as.numeric(Covariate)*Therapy + confounder,myDat,X=TRUE, Y=TRUE, family=binomial()) lrtest(fit1,fit2) Would be effectively testing for a trend in odds ratios? Do I have to fiddle with contrasts to make sure I am testing the correct parameter? Thanks Nicholas On Sat, 16 Jun 2007 11:14:12 -0500, Frank E Harrell Jr [EMAIL PROTECTED] said: Nicholas Lewin-Koh wrote: Hi, I am doing a retrospective analysis on a cohort from a designed trial, and I am fitting the model fit-glmD(survived ~ Covariate*Therapy + confounder,myDat,X=TRUE, Y=TRUE, family=binomial()) For logistic regression you can also use Design's lrm function which gives you more options. My covariate has three levels (A,B and C) and therapy has two (treated and control), confounder is a continuous variable. Also patients were randomized to treatment in the trial, but Covariate is something that is measured posthoc and can vary in the population. If by posthoc you mean that the covariate is measured after baseline, it is difficult to get an interpretable analysis. I am trying to wrap my head around how to calculate a few quantities from the model and get reasonable confidence intervals for them, namely I would like to test H0: gamma=0, where gamma is the regression coefficient of the odds ratios of surviving under treatment vs control at each level of Covariate (adjusted for the confounder) You mean regression coefficient on the log odds ratio scale. This is easy to do with the contrast( ) function in Design. Do ?contrast.Design for details and examples. and I would like to get the odds of surviving at each level of Covariate under treatment and control for each level of covariate adjusted for the confounder. I have looked at contrast in the Design library but I don't think it gives me the right quantity, for instance contrast(fit,list(covariate=A, Therapy=Treated, confounder=median(myDat$confounder), X=TRUE) ( A is the baseline level of Covariate) gives me beta0 + beta_Treated + beta_confounder*68 Is this correctly interpreted as the conditional odds of dying? As to the 1st contrast I am not sure how to get it, would it be using type = 'average' with some weights in contrast? The answers are probably staring me in the face, i am just not seeing them today. contrast( ) is for contrasts (differences). Sounds like you want predicted values. Do ?predict ?predict.lrm ?predict.Design. Also do ?gendata which will generate a data frame for getting predictors, with unspecified predictors set to reference values such as medians. Frank Nicholas -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] eps in odfWeave
Dieter Menne dieter.menne at menne-biomed.de writes: library(odfWeave) plotInfo - getImageDefs() plotInfo$type = eps plotInfo$plotWidth = 4 plotInfo$plotHeight = 4 plotInfo$device = postscript plotInfo$args = list( horizontal = FALSE,onefile = FALSE, paper = special) setImageDefs(plotInfo) demoFile - system.file(examples, simple.odt, package =odfWeave) odfWeave(demoFile, c:/simpleOut.odt) - Error in check(options) : invalid value for 'type' : eps Sorry, Max, my error (as you noted in private email). From an earlier attempt I had forgotten to remove the incorrect type=eps in the code. Dieter __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ANOVA non-sphericity test and corrections (eg, Greenhouse-Geisser)
Darren, Further to Peter Dalgaard's help; Take a look at the example in --- library(car) ?Anova # note upper case 'A' The example in the Anova help page following the --- ## a multivariate linear model for repeated-measures data ## See ?OBrienKaiser for a description of the data set used in this example gives a workings for -- ## Greenhouse-Geisser and Huynh-Feldt Corrections ## for Departure from Compound Symmetry You might find that example helpful. John __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Post-hoc tests for interactions of between- and within-subject factors
The glht function in package multcomp requires aov objects. As you discovered, it does not work with aovlist objects. See the documentation ?MMC in the HH package from CRAN. The maiz example is similar to your example. Come back to the list if you need further help. Rich __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] degrees of freedom in lme
On Mon, 2007-06-25 at 13:15 -0400, Doran, Harold wrote: This is such a common question that it has a an FAQ-like response from Doug Bates. Google lmer p-values and all that to find the response. Isn't this a different question, though, since Jean-Baptiste is using nlme. Details on the calculation of DF in nlme can be found in chapter 4 of the book by Pinheiro and Bates Mixed Effects Models in S and S-PLUS. Using the formula provided, I get denDF of 10 for level 1 and 32 for level 2. I'm not sure why lme is using the denDF estimated at level 2 in this example ... -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jean-Baptiste Ferdy Sent: Monday, June 25, 2007 12:26 PM To: r-help@stat.math.ethz.ch Subject: [R] degrees of freedom in lme Dear all, I am starting to use the lme package (and plan to teach a course based on it next semester...). To understand what lme is doing precisely, I used balanced datasets described in Pinheiro and Bates and tried to compare the lme outputs to that of aov. Here is what I obtained: data(Machines) summary(aov(score~Machine+Error(Worker/Machine),data=Machines)) Error: Worker Df Sum Sq Mean Sq F value Pr(F) Residuals 5 1241.89 248.38 Error: Worker:Machine Df Sum Sq Mean Sq F valuePr(F) Machine2 1755.26 877.63 20.576 0.0002855 *** Residuals 10 426.53 42.65 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Error: Within Df Sum Sq Mean Sq F value Pr(F) Residuals 36 33.287 0.925 anova(lme(fixed=score~Machine,random=~1|Worker/Machine,data=Machines)) numDF denDF F-value p-value (Intercept) 136 773.5709 .0001 Machine 210 20.5762 3e-04 No problem here: the results are essentially the same, which is expected. Now I turn to an ANCOVA with a random grouping factor. data(Orthodont) OrthoFem - Orthodont[Orthodont$Sex==Female,]; summary(aov(distance~age+Error(Subject/age),data=OrthoFem)) Error: Subject Df Sum Sq Mean Sq F value Pr(F) Residuals 10 177.227 17.723 Error: Subject:age Df Sum Sq Mean Sq F valuePr(F) age1 50.592 50.592 52.452 2.783e-05 *** Residuals 10 9.645 0.965 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Error: Within Df Sum Sq Mean Sq F value Pr(F) Residuals 22 9.8250 0.4466 anova(lme(fixed=distance~age,random=~1+age|Subject,data=OrthoFem)) numDF denDF F-value p-value (Intercept) 132 1269.7764 .0001 age 132 52.4517 .0001 This time the F values are (almost) identical, the numerator degrees of freedom are the same, but the denominator degrees of freedom are very different (10 for aov vs. 32 for lme). I understand that there is an issue with the estimation of that number, but I would naively expect the number given by lme to be close to that provided by aov is the case of a balanced dataset. That's obviously not true in the case of an ANCOVA... But why?? And how should I interpret the F-test given by anova.lme? Thanks in advance for your help ! -- Jean-Baptiste Ferdy Institut des Sciences de l'Évolution de Montpellier CNRS UMR 5554 Université Montpellier 2 34 095 Montpellier cedex 05 tel. +33 (0)4 67 14 42 27 fax +33 (0)4 67 14 36 22 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Manuel A. Morales http://mutualism.williams.edu __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] correlation structure
I have been using a nlme model and wish to specify the correlation structure. My data is grouped (bas), but I have no time component or adequate spatial description beyond the grouping variable. So I chose the simplest structure and updated my original nlme model by: update(model, corr=corCompSymm(~1|bas)) This is not significant. One of my variables measures area upstream of the sample. Area is a continuous variable, and there are some identical values of area. Can I model the dependence among residuals with in group (bas) and along area? Can the corCAR1 be used and the area used as a position variable? If so does the position variable need to be sorted when using the corCAR1 structure? Or could one use spatial classes and use area as one position and watershed as the other substituting numbers for the grouping variable? I have been trying, but R keeps crashing when I specify correlation structures other than compound symmetry. I assume this is because I am not specifying the form correctly. Any suggestions would be appreciated. Dan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] debug()
I am having problems using debug() when I am running R under linux. It works fine under the windows environment. Is there anything special that need to specify when running under linux. I would appreciate your help. Cheers../Murli [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] a string to enviroment or function
then how to do this
f1 - function(mylab){
library(mylab)
...
}
it seems that if you call
library(hgu133a) # which is file
# but
library(mylab) # even you pass hgu133a as parameter, it still
complains about mylab does not exist. It seems that it consider
mylab as package instead of its value.
On 6/25/07, jim holtman [EMAIL PROTECTED] wrote:
I think that you might want:
t0 - (paste(hgu133a, ENTREZID, sep=))
xx - as.list(get(t0)) # make it work like xx-as.list(hgu133aENTREZID)
On 6/25/07, Weiwei Shi [EMAIL PROTECTED] wrote:
Hi,
I am wondering how to make a function Fun to make the following work:
t0 - (paste(hgu133a, ENTREZID, sep=))
xx - as.list(Fun(t0)) # make it work like xx-as.list(hgu133aENTREZID)
thanks,
--
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.
Did you always know?
No, I did not. But I believed...
---Matrix III
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
--
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.
Did you always know?
No, I did not. But I believed...
---Matrix III
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] How to shadow 'power' area?
Dear all, Suppose I plot two normal distributions (A and B) side by side and add vertical line which hipotheticaly represent alpha value; e.g.: x - seq(-3.5,5, length=1000) y - dnorm(x) # Plot distribution A plot(y~x, type='l',axes=F,xlab=,ylab=,lwd=2) # Plot distribution B y2 - dnorm(x-1.5) lines(y2~x,lwd=2) # Plot vertical line for alpha value abline(h=0) segments(qnorm(.5)+1.5,0,qnorm(.5)+1.5,dnorm(qnorm(.5))) text(2,0.2,Power) Now I want to shadow area labeled as Power. Any suggestion how to do that using 'polygon' function? Thanks in advance for any suggestion. Andrej __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to shadow 'power' area?
Look at the following link: http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=88 This should be pretty close to what you want. HTH -Christos -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Andrej Kastrin Sent: Monday, June 25, 2007 4:51 PM To: R-help Subject: [R] How to shadow 'power' area? Dear all, Suppose I plot two normal distributions (A and B) side by side and add vertical line which hipotheticaly represent alpha value; e.g.: x - seq(-3.5,5, length=1000) y - dnorm(x) # Plot distribution A plot(y~x, type='l',axes=F,xlab=,ylab=,lwd=2) # Plot distribution B y2 - dnorm(x-1.5) lines(y2~x,lwd=2) # Plot vertical line for alpha value abline(h=0) segments(qnorm(.5)+1.5,0,qnorm(.5)+1.5,dnorm(qnorm(.5))) text(2,0.2,Power) Now I want to shadow area labeled as Power. Any suggestion how to do that using 'polygon' function? Thanks in advance for any suggestion. Andrej __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to shadow 'power' area?
On Mon, 2007-06-25 at 22:50 +0200, Andrej Kastrin wrote: Dear all, Suppose I plot two normal distributions (A and B) side by side and add vertical line which hipotheticaly represent alpha value; e.g.: x - seq(-3.5,5, length=1000) y - dnorm(x) # Plot distribution A plot(y~x, type='l',axes=F,xlab=,ylab=,lwd=2) # Plot distribution B y2 - dnorm(x-1.5) lines(y2~x,lwd=2) # Plot vertical line for alpha value abline(h=0) segments(qnorm(.5)+1.5,0,qnorm(.5)+1.5,dnorm(qnorm(.5))) text(2,0.2,Power) Now I want to shadow area labeled as Power. Any suggestion how to do that using 'polygon' function? Thanks in advance for any suggestion. Andrej See the latter section of this post: http://tolstoy.newcastle.edu.au/R/help/03b/2475.html and in turn, ?polygon HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] LanguageR pvals.fnc error message
Mike Ford mford at csl.psychol.cam.ac.uk writes: Hi. I get an error message about not converging when I try and use the pvals.fnc from the languageR library. The LMER analysis worked fine (See below). I am not an expert so I don't understand why the LMER worked but not the pvals.fnc Any help gratefully received. - Mike results of traceback() after the error? precise wording of the error message? any chance of sending to the list, or posting, a data set that produces the error? (see the posting guide ...) on the face of it is puzzling because pvals.fnc doesn't seem to do any fitting, just post-processing of the lmer object ... (by the way, that's the languageR package -- library(fortunes); fortune(Maechler.*package)) Ben Bolker __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problem installing MCMCpack
I am having a problem installing MCMCpack on a Linux ppc64 machine. Has someone had this problem??This is what I see when I do an install package: install.packages(c(MCMCpack)) trying URL ' http://www.sourcekeg.co.uk/cran/src/contrib/MCMCpack_0.8-2.tar.gz' Content type 'application/x-tar' length 310117 bytes opened URL == downloaded 302Kb * Installing *source* package 'MCMCpack' ... checking for C++ compiler default output file name... configure: error: C++ compiler cannot create executables See `config.log' for more details. ERROR: configuration failed for package 'MCMCpack' ** Removing '/home/vivekv/sw_alg/R-2.5.0/library/MCMCpack' --- Thanks, Vivek [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] fft and the derivative
Can one take f(t) and transform to F(omega) in the frequency domain using fft(), and use the properties of the fft and find the derivative of f(t)? For example, f(t) - F(omega) = f(t)^n - (i*omega)^n * F(omega) Use this and get, f(t)^n = F^(-) [ (i*omega)^n * F(omega) ] to get the nth derivative of f(t)? Todd Remund __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Quiver in 1d
Dear all R-users, I am try to plot quiver in one dimension, but there is only code for two dimension in different R web pages. Somebody know same code that can help me in plot quiver in one dimension. Any help gratefully received . Thanks for all Fernando __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] a string to enviroment or function
Weiwei
See ?library and the character.only argument.
f - function(x) library(x)
f(hgu95av2)
Error in library(x) : there is no package called 'x'
f - function(x) library(x, character.only=TRUE)
f(hgu95av2)
search()
[1] .GlobalEnvpackage:hgu95av2 package:stats
[4] package:graphics package:grDevices package:utils
[7] package:datasets package:methods Autoloads
[10] package:base
Also
g - function(x) as.list(get(paste(x, ENTREZID, sep=)))
ll - g(hgu95av2)
length(ll)
[1] 12625
and finally reverseSplit in Biobase and revmap in AnnotationDbi might
be helpful (though AnnotationDbi is only available with R-devel and
revmap seems not to be documented).
res - revmap(hgu95av2ENTREZID)
hgu95av2ENTREZID[[1190_at]]
[1] 5800
res[[5800]]
[1] 1190_at 32199_at
Martin
Weiwei Shi [EMAIL PROTECTED] writes:
then how to do this
f1 - function(mylab){
library(mylab)
...
}
it seems that if you call
library(hgu133a) # which is file
# but
library(mylab) # even you pass hgu133a as parameter, it still
complains about mylab does not exist. It seems that it consider
mylab as package instead of its value.
On 6/25/07, jim holtman [EMAIL PROTECTED] wrote:
I think that you might want:
t0 - (paste(hgu133a, ENTREZID, sep=))
xx - as.list(get(t0)) # make it work like xx-as.list(hgu133aENTREZID)
On 6/25/07, Weiwei Shi [EMAIL PROTECTED] wrote:
Hi,
I am wondering how to make a function Fun to make the following work:
t0 - (paste(hgu133a, ENTREZID, sep=))
xx - as.list(Fun(t0)) # make it work like xx-as.list(hgu133aENTREZID)
thanks,
--
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.
Did you always know?
No, I did not. But I believed...
---Matrix III
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
--
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.
Did you always know?
No, I did not. But I believed...
---Matrix III
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] a string to enviroment or function
On 25/06/2007 4:19 PM, Weiwei Shi wrote:
then how to do this
f1 - function(mylab){
library(mylab)
...
}
it seems that if you call
library(hgu133a) # which is file
# but
library(mylab) # even you pass hgu133a as parameter, it still
complains about mylab does not exist. It seems that it consider
mylab as package instead of its value.
One of the examples in ?library shows how to do what you want.
pkg - splines
library(pkg, character.only = TRUE)
Duncan Murdoch
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.
P.S. If you think this was helpful, one of the ways to contribute back
to the R project would be to ask your employer to become an
institutional member: see
http://www.r-project.org/foundation/membership.html
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] changing the position of the y label (ylab)
How can I change the position of the ylab, after
enlarging the margins with par(mar=...)?
Here is the relevant code snippet
par(mar=c(5.1,5.1,4.1,2.1))
plot(c(1979,2003),c(40,50),ylim=c(1,73),lab=c(20,10,1),pch=21,col='blue',bg='blue',axes=FALSE,xlab=Years,ylab=Onset/Withdrawl
Date,font.lab=2)
box()
axis(1,las=2)
axis(2,las=2,labels=c('JAN','FEB','MAR','APR','MAY','JUN','JUL','AUG','SEP','OCT','NOV','DEC','JAN'),at=seq(from=1,to=73,by=6))
axis(3,labels=FALSE)
axis(4,labels=FALSE,at=seq(from=1,to=73,by=6))
Thanks
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to shadow 'power' area?
You can look at the power.examp function in the TeachingDemos package to see if it gives you the graph you want, or look at the code to see how you could modify it to give you the plot you want. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Andrej Kastrin Sent: Monday, June 25, 2007 2:51 PM To: R-help Subject: [R] How to shadow 'power' area? Dear all, Suppose I plot two normal distributions (A and B) side by side and add vertical line which hipotheticaly represent alpha value; e.g.: x - seq(-3.5,5, length=1000) y - dnorm(x) # Plot distribution A plot(y~x, type='l',axes=F,xlab=,ylab=,lwd=2) # Plot distribution B y2 - dnorm(x-1.5) lines(y2~x,lwd=2) # Plot vertical line for alpha value abline(h=0) segments(qnorm(.5)+1.5,0,qnorm(.5)+1.5,dnorm(qnorm(.5))) text(2,0.2,Power) Now I want to shadow area labeled as Power. Any suggestion how to do that using 'polygon' function? Thanks in advance for any suggestion. Andrej __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] degrees of freedom in lme
I don't believe the issue is different. In some respects, lme and lmer essentially accomplish the same thing for mixed linear models. lmer differs in many ways than lme in how estimates are computed and in the type of models it can handle. It is probably best to read the new vignettes in the lme4 package to see inside lmer a bit more. However, if you estimate the same model with lme and lmer to the same data you'll get the same results. But, lme gives DF and p-values but lmer does not. -Original Message- From: Manuel Morales [mailto:[EMAIL PROTECTED] Sent: Mon 6/25/2007 3:32 PM To: Doran, Harold Cc: Jean-Baptiste Ferdy; r-help@stat.math.ethz.ch Subject: Re: [R] degrees of freedom in lme On Mon, 2007-06-25 at 13:15 -0400, Doran, Harold wrote: This is such a common question that it has a an FAQ-like response from Doug Bates. Google lmer p-values and all that to find the response. Isn't this a different question, though, since Jean-Baptiste is using nlme. Details on the calculation of DF in nlme can be found in chapter 4 of the book by Pinheiro and Bates Mixed Effects Models in S and S-PLUS. Using the formula provided, I get denDF of 10 for level 1 and 32 for level 2. I'm not sure why lme is using the denDF estimated at level 2 in this example ... -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jean-Baptiste Ferdy Sent: Monday, June 25, 2007 12:26 PM To: r-help@stat.math.ethz.ch Subject: [R] degrees of freedom in lme Dear all, I am starting to use the lme package (and plan to teach a course based on it next semester...). To understand what lme is doing precisely, I used balanced datasets described in Pinheiro and Bates and tried to compare the lme outputs to that of aov. Here is what I obtained: data(Machines) summary(aov(score~Machine+Error(Worker/Machine),data=Machines)) Error: Worker Df Sum Sq Mean Sq F value Pr(F) Residuals 5 1241.89 248.38 Error: Worker:Machine Df Sum Sq Mean Sq F valuePr(F) Machine2 1755.26 877.63 20.576 0.0002855 *** Residuals 10 426.53 42.65 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Error: Within Df Sum Sq Mean Sq F value Pr(F) Residuals 36 33.287 0.925 anova(lme(fixed=score~Machine,random=~1|Worker/Machine,data=Machines)) numDF denDF F-value p-value (Intercept) 136 773.5709 .0001 Machine 210 20.5762 3e-04 No problem here: the results are essentially the same, which is expected. Now I turn to an ANCOVA with a random grouping factor. data(Orthodont) OrthoFem - Orthodont[Orthodont$Sex==Female,]; summary(aov(distance~age+Error(Subject/age),data=OrthoFem)) Error: Subject Df Sum Sq Mean Sq F value Pr(F) Residuals 10 177.227 17.723 Error: Subject:age Df Sum Sq Mean Sq F valuePr(F) age1 50.592 50.592 52.452 2.783e-05 *** Residuals 10 9.645 0.965 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Error: Within Df Sum Sq Mean Sq F value Pr(F) Residuals 22 9.8250 0.4466 anova(lme(fixed=distance~age,random=~1+age|Subject,data=OrthoFem)) numDF denDF F-value p-value (Intercept) 132 1269.7764 .0001 age 132 52.4517 .0001 This time the F values are (almost) identical, the numerator degrees of freedom are the same, but the denominator degrees of freedom are very different (10 for aov vs. 32 for lme). I understand that there is an issue with the estimation of that number, but I would naively expect the number given by lme to be close to that provided by aov is the case of a balanced dataset. That's obviously not true in the case of an ANCOVA... But why?? And how should I interpret the F-test given by anova.lme? Thanks in advance for your help ! -- Jean-Baptiste Ferdy Institut des Sciences de l'Évolution de Montpellier CNRS UMR 5554 Université Montpellier 2 34 095 Montpellier cedex 05 tel. +33 (0)4 67 14 42 27 fax +33 (0)4 67 14 36 22 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Manuel A. Morales http://mutualism.williams.edu [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help
Re: [R] fft and the derivative
Todd, Your idea is correct for continuous Fourier transform, but I am not sure how one could apply that to fft, which corresponds to the discrete Fourier transform. For instance, what values of omega would you use for the term i*omega to get the discrete fourier transform of the derivative of f(t)? Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: [EMAIL PROTECTED] Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Todd Remund Sent: Monday, June 25, 2007 5:16 PM To: r-help@stat.math.ethz.ch Subject: [R] fft and the derivative Can one take f(t) and transform to F(omega) in the frequency domain using fft(), and use the properties of the fft and find the derivative of f(t)? For example, f(t) - F(omega) = f(t)^n - (i*omega)^n * F(omega) Use this and get, f(t)^n = F^(-) [ (i*omega)^n * F(omega) ] to get the nth derivative of f(t)? Todd Remund __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] changing the position of the y label (ylab)
Thanks (Merci) Christophe!
that did it
--- Christophe Bonenfant
[EMAIL PROTECTED] wrote:
Hi Etienne - consider to use the mtext function:
par(mar=c(5.1,5.1,4.1,2.1))
plot(c(1979,2003),c(40,50),ylim=c(1,73),lab=c(20,10,1),
pch=21,col='blue',bg='blue',axes=FALSE,xlab=,ylab=,font.lab=2)
box()
axis(1,las=2)
axis(2,las=2,labels=c('JAN','FEB','MAR','APR','MAY','JUN','JUL',
'AUG','SEP','OCT','NOV','DEC','JAN'),at=seq(from=1,to=73,by=6))
axis(3,labels=FALSE)
axis(4,labels=FALSE,at=seq(from=1,to=73,by=6))
mtext(Years, 1, 3.5, cex = 1.7)
# first interger is the axis number, second number
is the distance to
the axis
mtext(Onset/Withdrawl Date, 2, 4, cex = 1.7)
see ?mtext
Christophe
Etienne a écrit :
How can I change the position of the ylab, after
enlarging the margins with par(mar=...)?
Here is the relevant code snippet
par(mar=c(5.1,5.1,4.1,2.1))
plot(c(1979,2003),c(40,50),ylim=c(1,73),lab=c(20,10,1),pch=21,col='blue',bg='blue',axes=FALSE,xlab=Years,ylab=Onset/Withdrawl
Date,font.lab=2)
box()
axis(1,las=2)
axis(2,las=2,labels=c('JAN','FEB','MAR','APR','MAY','JUN','JUL','AUG','SEP','OCT','NOV','DEC','JAN'),at=seq(from=1,to=73,by=6))
axis(3,labels=FALSE)
axis(4,labels=FALSE,at=seq(from=1,to=73,by=6))
Thanks
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained,
reproducible code.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] running Rcmdr
Thanks for your answer, but i think i dont do correctly my question. I need the command line to run Rmdr, like that: R Rcmdr or R loadRcmdr.R where loadRcmdr has library(Rcmdr). or something like that. I tried the last example, but when Rcmdr is executed, later it is closed. About RProfile.site, i dont know what i have to change. If you think its useful to me, please explain me. Thanks. Felipe Carrillo escribió: First, you need to install the Rcmdr packages and then in the R Command window or Tinn-R window type library(Rcmdr) without the quotation marks. In addition, if you want Rcmdr to start automatically everytime you start R, go to the following path C:\Program Files\R\R-2.5.0\etc\RProfile.site if you installed R in program files, otherwise follow your own path and type the same command library(Rcmdr) and the R commander window should pop up everytime you start R */Manuel [EMAIL PROTECTED]/* wrote: Hi to all, i want to know how can run Rcmdr automatically , or how to load a library in the call of R greetings __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Choose the right car based on your needs. Check out Yahoo! Autos new Car Finder tool. http://us.rd.yahoo.com/evt=48518/*http://autos.yahoo.com/carfinder/;_ylc=X3oDMTE3NWsyMDd2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDY2FyLWZpbmRlcg--%20 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-excel
Also try xlsReadWrite package on CRAN. --- Erika Frigo [EMAIL PROTECTED] wrote: Good morning to everybody, I have a problem : how can I import excel files in R??? thank you very much Dr.sa. Erika Frigo Università degli Studi di Milano Facoltà di Medicina Veterinaria Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare (VSA) Via Grasselli, 7 20137 Milano Tel. 02/50318515 Fax 02/50318501 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Has anyone tryed out my software?
Hello all, Has anyone ( who uses a Linux desktop ) tryed out my stuff I mentioned a few weeks ago? Perhaps installed it and run a couple of example programs? If you have, tell me what you think. Robert ( it's the tarball in the download section at http://code.google.com/p/vilno , discussed briefly in comparison to Awk a couple of weeks ago ) PS Of R users: how many use Windows XP, how many use an Apple, and how many use a Linux desktop? Are there a lot of Linux users out there? Is R more popular in Europe than North America? I'll need to do a statistical analysis of the mailing list. I notice a ton of Europeans. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] a-priori orthogonal contrasts
Dear R-helpers, I have some stacked data with which I want to generate orthogonal contrasts - with the caveat that I determine what means comparisons are taking place a-priori. Does it matter for e.g. 'contr.SUM' that the data are stacked, and does 'contr.SUM' allow me to set the contrasts efficiently even if the data are unballanced? Is there an alternative in R I should consider? Sincerely, KeithC. Psych Undergrad, CU Boulder (US) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-excel
The R(D)COM server (contaiong the RExcel Excel addin) and/or the rcom package allow (among other things) to select a range in Excel and directly transfer it to R as an array or as a dataframe. It only works on Windows with Excel and R installed. More information on these packages is available at http://rcom.univie.ac.at Erika Frigo wrote: Good morning to everybody, I have a problem : how can I import excel files in R??? thank you very much Dr.sa. Erika Frigo Università degli Studi di Milano Facoltà di Medicina Veterinaria Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare (VSA) Via Grasselli, 7 20137 Milano Tel. 02/50318515 Fax 02/50318501 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Erich Neuwirth, Didactic Center for Computer Science University of Vienna Visit our SunSITE at http://sunsite.univie.ac.at Phone: +43-1-4277-39464 Fax: +43-1-4277-9394 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Howto fix colors in colorRampPalette?
Hi All, I am plotting a correlation matrix using the heatmap function. I create my color palette as follows (say, for red-green palette): colorRampPalette( c(green, black, red), space=rgb)(10) But I want to fix colors for a specific range of values, i.e. green=-1, black=0, red=+1. The purpose of doing this is I can then quickly compare two different correlation matrices visually, i.e., one matrix has values in the range -1 to +1, whereas the other has from -0.5 to +0.5. Then the two heatmaps differ in color levels. I searched in the help archives to find any hints but didn't. Is there an easy way of doing this? Any help is greatly appreciated. Thanks. Ashoka. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-excel
There are also some notes about this in the R Data Import/Export manual: http://cran.r-project.org/doc/manuals/R-data.html#Reading-Excel-spreadsheets But I've gathered the following examples from the R-help mailing list archives [in addition to the option of saving the spreadsheet as a .csv file and reading it in with read.csv()]. Personally, I use option 4 regularly (I happened to have Perl installed on my Windows XP machine already) and have had good luck with it. Hope this helps. = Option 1 = # SIMPLEST OPTION install.packages(xlsReadWrite) library(xlsReadWrite) data = read.xls(sampledata.xls,sheet=1) = Option 2 = # ALSO SIMPLE BUT MORE MANUAL WORK EACH TIME # (1) highlight region in Excel you want to import and data = read.delim(file=clipboard,header=TRUE) # or, if you don't have a header, data = read.delim(file=clipboard,header=FALSE) = Option 3 = # RODBC IS A BIG APPLICATION, FOR INTERFACING # WITH MANY TYPES OF FILES/SERVERS install.packages(RODBC) library(RODBC) fid - odbcConnectExcel(sampledata.xls) data - sqlFetch(fid,Sheet1) close(fid) = Option 4 = # REQUIRES CONCURRENT INSTALLATION OF PERL install.packages(gdata) library(gdata) data = read.xls(sampledata.xls,sheet=1) --- Erika Frigo [EMAIL PROTECTED] wrote: Good morning to everybody, I have a problem : how can I import excel files in R??? thank you very much Dr.sa. Erika Frigo Università degli Studi di Milano Facoltà di Medicina Veterinaria Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare (VSA) Via Grasselli, 7 20137 Milano Tel. 02/50318515 Fax 02/50318501 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Comedy with an Edge to see what's on, when. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
