Re: [R] Error message: The following object(s) are masked

Ettinger, Nicholas wrote: Hello! First time posting here: Here is my code: x - c(1:22) finaloutput=cidrm=NULL finaldiversityoutput=diversitym=NULL diversityinfo=read.table(Diversity_info.txt, header=T, sep=\t, row.names=NULL) attach(diversityinfo) diversitynr=nrow(diversityinfo)

[R] t test on data frame

Hi, I have constructed a dataframe as follows: Oil - rep(c(Oil1,Oil2,Oil3),8) Comp - rep(rep(c(C1,C2),c(4,4)),3) Mth - rep(c(M1,M1,M2,M2),6) Meas - rep(c(1,2),12) Result - rnorm(24,mean=100, sd=5) df - data.frame(Oil, Comp, Mth, Meas, Result) The same compound (Comp) is found in different

[R] Simplify iterative programming

Dear, I am looking for the simplification of a formula to improve the calculation speed of my program. Therefore I want to simplify the following formula: H = sum{i=0..n-1 , [ sum {j=0..m-1 , sqrt ( (Ai - Bj)^2 + (Ci - Dj)^2) } ] } where: A, C = two vectors (with numerical data) of length n

Re: [R] Simplify iterative programming

Hello Stefaan, I'm not an expert, but maybe something like this is quite straightforward withourtusing for-loops? (It is an idea I wrote down, but check of course if this is correct!) term1 =(matrix(A,ncol=m,nrow=n)-matrix(B,ncol=m,nrow=n,byrow=TRUE))^2 term2

[R] residual variance in lmer

Hi, when running lmer with family set to quasibinomial, is the residual variance reported among the random effects, the dispersion parameter as in glm, or something else? Thanks, Tom __ R-help@stat.math.ethz.ch mailing list

[R] How to load a workspace, which was created in Windows, in Unix

Hi all I can't seem to load a workspace created in Windows, when I try to load it in R on a Unix machine. How can I do it? Thanks! regards, Jens Johansen __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do

Re: [R] t test on data frame

Bart Joosen bartjoosen at hotmail.com writes: I have constructed a dataframe as follows: Oil - rep(c(Oil1,Oil2,Oil3),8) Comp - rep(rep(c(C1,C2),c(4,4)),3) Mth - rep(c(M1,M1,M2,M2),6) Meas - rep(c(1,2),12) Result - rnorm(24,mean=100, sd=5) df - data.frame(Oil, Comp, Mth, Meas, Result)

Re: [R] How to load a workspace, which was created in Windows, in Unix

Jens Vilstrup Johansen [EMAIL PROTECTED] writes: Hi all I can't seem to load a workspace created in Windows, when I try to load it in R on a Unix machine. How can I do it? load(myfile) should work... -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ ---

[R] plot of mice.mids objects

Hello... how can I plot mice.mids objects as described by Buuren (2000) http://web.inter.nl.net/users/S.van.Buuren/mi/docs/Manual.pdf page 17, if there are many variables (~80) with NAs included? mice runs well, but the plot is not possible because it seems that there are too many variables.

Re: [R] plot of mice.mids objects

Hi, it is impossible to plot a subset of the variables at the moment, but we could add it. p.s. The latest version of mice is v1.14, which can be downloaded from CRAN. Roel de Jong. Leo Gürtler wrote: Hello... how can I plot mice.mids objects as described by Buuren (2000)

Re: [R] How to load a workspace, which was created in Windows, in Unix

On Fri, 4 Nov 2005, Jens Vilstrup Johansen wrote: Hi all I can't seem to load a workspace created in Windows, when I try to load it in R on a Unix machine. How can I do it? What error message do you get? It normally works (and is widely used in R packages for the .rda format), so did you

Re: [R] Simplify iterative programming

you could consider something like: H - sum(sqrt(outer(A, B, -)^2 + outer(C, D, -)^2)) I hope it helps. Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel:

[R] Background only white when using rgl.postscript()

Hello! I use scatter3D() to produce my graphics. This works as expected, and I am able to set my background color to black. But when I write to file using rgl.postscript(), the background color changes to white. Can anyone tell me how I can avoid this problem? Example code: # Produces 3D

[R] R graphics help

Halo friends, I have a problem to solve in R graphics.. I have a matrix like A= 2 3 4 5 6 7 8 9 4 and I like to generate the same matrix in terms of shaded circles in which the density of shading depends on the value... for eg in the above matrix A the value 2 is a

Re: [R] R graphics help

Probably you can get some ideas from the balloonplot function in package gplots. Best, Matthias Halo friends, I have a problem to solve in R graphics.. I have a matrix like A= 2 3 4 5 6 7 8 9 4 and I like to generate the same matrix in terms of shaded circles

[R] Graphics question on putting axes in the margins

Hello I am writing an article demonstrating how quantile plots work. In one figure, I generate 3 sets of normal data, and add different sorts of outliers to each. I then make 9 qqnorm plots, in a 3x3 array: Outlier1 Outler2 Outlier3 Dataset1 Dataset2 Dataset3 which

[R] exponential convolution (different lembdas)?

Anyone knows how to realize multiple exponential(different lembdas) convolutons in R or where I can find the final equation? Thanks. Best, Lynette __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the

Re: [R] encrypted RData file?

May I suggest that further discussion of this issue be directed to R-Devel. -- Bert Gunter Genentech Non-Clinical Statistics South San Francisco, CA The business of the statistician is to catalyze the scientific learning process. - George E. P. Box -Original Message- From:

[R] Lars/lasso help

Hi, I tried with lars, but for a 29(n)x4662(p) dataset, I kept getting error. One is the program failed,giving out a message:if (zmin gamhat) {missing value where TRUE/FALSE needed, another problem, for leave one out cross validation with cv.lars, the program sometimes gives very large ridiculous

[R] [R-pkgs] New version of RQuantLib

A new version of RQuantLib has been uploaded to CRAN a few days ago (and should be available at http://cran.r-project.org and all mirrors). Debian binaries are also available. Among the new features in version 0.2.0, all of which are due to excellent contributions by Dominick Samperi, are - new

[R] Daily Time serie

I am working with a daily series of time of financial and not character like defining the frequency in R. In addition gustaria me who R took into account the worked Days. Nobody orientacion well is received Thanks __ R-help@stat.math.ethz.ch mailing

[R] question about precision, floor, and powers of two.

At the risk of being beaten about the face and body, can somebody explain why the middle example: log2(2^3); floor(log2(2^3)) is different than examples 1 and 3? log2(2^2); floor(log2(2^2)) [1] 2 [1] 2 log2(2^3); floor(log2(2^3)) [1] 3 [1] 2 log2(2^4); floor(log2(2^4)) [1] 4 [1] 4 DrC

[R] Help for MDS !!

Hi All, I am trying to apply MDS for 4 groups in my data. The groups are: groups = list( Day1C=c(9), Day1T=c(7,8,10), Day2C=c(1,2,3,6,11,13,14,15), Day2T=c(4,5,12,16,17,18) ) When I do the MDS plot the group1 appears twice instead of one time in the plot. I don't know why this is happening.

[R] Real FFT

The book Numerical Recipes in Fortran77 by Press, Teukolsky, Vetterling and Flannery describes a way to pack the even and odd coordinates of a real vector R into a complex vector C of half the length. Then using various FFT symmetries, they extract the FFT of R from the FFT of C which is half

Re: [R] residual variance in lmer

On 11/4/05, Tom Van Dooren [EMAIL PROTECTED] wrote: when running lmer with family set to quasibinomial, is the residual variance reported among the random effects, the dispersion parameter as in glm, or something else? It should be the dispersion parameter. I say should be because I am not

[R] Optim function

Hello, Is there a general procedure when using the the optim function(BFGS) to only output the converging value (i.e. final par value) rather than all the other output? Thank you. __ R-help@stat.math.ethz.ch mailing list

Re: [R] How can I test temporal autocorrelation of binary data?

Since the data is dichotomous already, the nonparametric 'runs test' might be appropriate, though I am ignorant as to its properties (power in particular). help(runs.test,package=tseries) Regards, Andreas - Original Message - From: Patrick Burns [EMAIL PROTECTED] To: [EMAIL

[R] Can I do content analysis by R?

Can R conduct content analysis? I search content analysis in mail archives and only find the concord package can compute Krippendorff's alpha. If R cannot cope with content analysis, does anyone can tell me some other softwares? Thank you very much!

[R] model.matrix for non-hierarchical models

Dear R-users, Using the function model.matrix I noticed the following behaviour (example below): Using the formula ~ a + a:b will give a matrix of the same dimension as using ~ a * b. In the first case there are additional columns for the interaction (to compensate for the missing main-effect).

Re: [R] question about precision, floor, and powers of two.

Dr Carbon wrote: At the risk of being beaten about the face and body, can somebody explain why the middle example: log2(2^3); floor(log2(2^3)) is different than examples 1 and 3? Because log2(2^3) - 3 [1] -4.440892e-16 see the R FAQ Why doesn't R think these numbers are equal?. Uwe

Re: [R] Graphics question on putting axes in the margins

Peter Flom wrote: which I did using mfrow = c(3,3). I'd like to use the space on the page as efficiently as possible,so I made the margins small, but that leaves no space for axes. Is there a way to put axes only along the bottom and left side, so that a) The individual qqplots maintain

Re: [R] Help for MDS !!

On 11/2/05 6:42 AM, A Ezhil [EMAIL PROTECTED] wrote: Hi All, I am trying to apply MDS for 4 groups in my data. The groups are: groups = list( Day1C=c(9), Day1T=c(7,8,10), Day2C=c(1,2,3,6,11,13,14,15), Day2T=c(4,5,12,16,17,18) ) When I do the MDS plot the group1 appears twice

Re: [R] Optim function

Hi, is this what you meant? myfun - function(x) { return(x^2) } optim(par=0.5, fn=myfun, method=BFGS)$par Best, Roland -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Friday, October 28, 2005 1:23 AM To:

Re: [R] Optim function

Try: optim(.)$par Bye Elio [EMAIL PROTECTED] wrote: Hello, Is there a general procedure when using the the optim function(BFGS) to only output the converging value (i.e. final par value) rather than all the other output? Thank you. __

Re: [R] Can I do content analysis by R?

What, in particular, do you want to do? Content analysis is a mode of research, not a statistical technique. -- Andrew J Perrin - http://www.unc.edu/~aperrin Assistant Professor of Sociology, U of North Carolina, Chapel Hill

Re: [R] Help for MDS !!

Hi Sean, I am sorry for that. I am using the following code for doing MDS: groups = list( Day1C=c(1), Day1T=c(2,3,4), Day2C=c(5,6,7,8,9,10,11,12), Day2T=c(14,15,16,17,18)) len = length(groups) dist = dist(data, method=euclidean) data.mds=isoMDS(dist) plot(data.mds$points,type = n,main=MDS plot)

Re: [R] Can I do content analysis by R?

Look for in http://egsh.enst.fr/lebart/ Campo Elías PARDO Profesor Asociado Universidad Nacional de Colombia Facultad de Ciencias Departamento de Estadística Emails: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list

Re: [R] residual variance in lmer

On Fri, 4 Nov 2005, Douglas Bates wrote: On 11/4/05, Tom Van Dooren [EMAIL PROTECTED] wrote: when running lmer with family set to quasibinomial, is the residual variance reported among the random effects, the dispersion parameter as in glm, or something else? It should be the dispersion

Re: [R] residual variance in lmer

On Fri, 4 Nov 2005, Prof Brian Ripley wrote: On Fri, 4 Nov 2005, Douglas Bates wrote: On 11/4/05, Tom Van Dooren [EMAIL PROTECTED] wrote: when running lmer with family set to quasibinomial, is the residual variance reported among the random effects, the dispersion parameter as in glm, or

Re: [R] Search within a file

Thanks for a great suggestions. I guess the code you suggested would look something like this: fregexpr = function(pattern, filename) { # same as gregexpr but operating on files not strings # Only single string 'pattern's allowed buf.size=1024 n = file.info(filename)$size

Re: [R] question about precision, floor, and powers of two.

Uwe Ligges [EMAIL PROTECTED] writes: Dr Carbon wrote: At the risk of being beaten about the face and body, can somebody explain why the middle example: log2(2^3); floor(log2(2^3)) is different than examples 1 and 3? Because log2(2^3) - 3 [1] -4.440892e-16 see the R FAQ Why

Re: [R] Real FFT

How about 'fft' function. It is a little higher level than Fortran function you mention, since array can be any length and you do not need to pack complex numbers into a vector of floats. Jarek Tuszynski -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of

Re: [R] model.matrix for non-hierarchical models

Lukas Meier [EMAIL PROTECTED] writes: Dear R-users, Using the function model.matrix I noticed the following behaviour (example below): Using the formula ~ a + a:b will give a matrix of the same dimension as using ~ a * b. In the first case there are additional columns for the interaction

Re: [R] question about precision, floor, and powers of two.

On Fri, 4 Nov 2005, Peter Dalgaard wrote: Uwe Ligges [EMAIL PROTECTED] writes: Dr Carbon wrote: At the risk of being beaten about the face and body, can somebody explain why the middle example: log2(2^3); floor(log2(2^3)) is different than examples 1 and 3? Because log2(2^3) - 3 [1]

Re: [R] model.matrix for non-hierarchical models

Peter Dalgaard writes: Lukas Meier [EMAIL PROTECTED] writes: Dear R-users, Using the function model.matrix I noticed the following behaviour (example below): Using the formula ~ a + a:b will give a matrix of the same dimension as using ~ a * b. In the first case there are

Re: [R] question about precision, floor, and powers of two.

In this particular case, it is slightly odd that we can't get an exact answer for operations that could in principle be carried out using integer arithmetic, but we're actually calculating log(8)/log(2). (Curiously, the same effect is not seen on Linux or Solaris until log2(2^29)-29

Re: [R] question about precision, floor, and powers of two.

On 11/4/2005 10:58 AM, Peter Dalgaard wrote: Uwe Ligges [EMAIL PROTECTED] writes: Dr Carbon wrote: At the risk of being beaten about the face and body, can somebody explain why the middle example: log2(2^3); floor(log2(2^3)) is different than examples 1 and 3? Because

[R] random forests and memory allocation

Dear all, I am trying to run a random forest on a 4-class dataset with 10 215 variables. Whatever the number of trees (I was thinking of combining the trees), I first got the error on Windows: Error: cannot allocate vector of size 407562 Kb In addition: Warning messages: 1: Reached total

Re: [R] Plotting Factorial GLMs

Thanks to all who replied (although next time, reply to the list!) The simplest answer is to replace A in the curve statement with the following: rep(A, times=length(x)) Now if I could just figure out the workaround to plotting multiple sets of points onto my graph in the first place (i.e.

Re: [R] question about precision, floor, and powers of two.

On Fri, 4 Nov 2005, Uwe Ligges wrote: Dr Carbon wrote: At the risk of being beaten about the face and body, can somebody explain why the middle example: log2(2^3); floor(log2(2^3)) is different than examples 1 and 3? Because log2(2^3) - 3 [1] -4.440892e-16 This is a less

Re: [R] random forests and memory allocation

Please give more info on your problem, as the Posting Guide asked. How exactly did you call randomForest? How many cases are in the data? What options did you request in randomForest? People have run randomForest on data with more variables than that on lesser machines without problem. You

Re: [R] question about precision, floor, and powers of two.

On Fri, 4 Nov 2005, Thomas Lumley wrote: On Fri, 4 Nov 2005, Uwe Ligges wrote: Dr Carbon wrote: At the risk of being beaten about the face and body, can somebody explain why the middle example: log2(2^3); floor(log2(2^3)) is different than examples 1 and 3? Because log2(2^3) - 3 [1]

[R] Stress in multidimensional scaling

Hello, We are trying to find a function to compute stress in our multidimensional scaling analysis of a dissimilarity matrix. We've used dist() to create the matrix and cmdscale() for the scaling. In order to determine the number of dimensions we would like to plot stress vs. dimensions. However,

[R] Default keyboard shortcuts in JGR

Hi R List, A very minor item, but I was just wondering if there is a way to change the default keyboard shortcuts in the JGR GUI. By default, the Run command is CTRL-R which requires more finger gymnastics than the F-10 in S-PLUS. Any suggestions? Thank you, Zev --

[R] problem in waveslim library?

This code consistenly segfaults for me. Can someone please take a look and tell me if the problem is due to something I am doing or is there a problems with the dwt (idwt) functions in the waveslim library. Thanks tom library(waveslim)

Re: [R] RODBC and Excel: Wrong Data Type Assumed on Import

Gabor Grothendieck [EMAIL PROTECTED] wrote in message news:[EMAIL PROTECTED] You could try using the COM interface rather than the ODBC interface. Try code such as this: library(RDCOMClient) xls - COMCreate(Excel.Application) xls[[Workbooks]]$Open(MySpreadsheet.xls) sheet -

Re: [R] Stress in multidimensional scaling

cmdscale calculates an eigenanalysis of the dissimilarity matrix, and does not employ stress per se. Rather, it attempts to maximize variability along axes. If you call the the cmdscale() function with eig=TRUE it returns a list object with the coordinates called points and the eigenvalues

Re: [R] Problem installing ROracle package under R

In gmane.comp.lang.r.general Vittorio [EMAIL PROTECTED] wrote: configuration warning: Oracle pre-compiler proc not in /usr/local/oracle8-client/bin/proc you may not be able to compile ROracle You don't have the Oracle Pro*C precompiler installed. You can't build ROracle without that.

Re: [R] RODBC error

Hi Tom, Thanks for this suggestion. It now works perfectly. You have been a great help Cheers Evan Sergeant At 10:00 PM 02/11/2005, tom wright wrote: On Wed, 2005-02-11 at 07:55 +1000, Evan Sergeant wrote: Hi, I hope that someone can help me with the following problem with RODBC

[R] [OTAnn] Groups:New Developments at Roomity

I was interested in getting feedback from current communities of Roomity.com and let you know the recent improvements we are working on for better interface. Roomity.com v 1.5 is a web 2.01/RiA poster child community webapp. This new version adds broadcast video, social networking such as

[R] problem with the assignment function

Hello, I run into the most weird problem I have ever met. I wrote a function rhopair, which calls a .C function. I cannot assign its value to a variable using either = nor -. After I did the assignment, rhopair cannot reproduce the same result as before with the same argument. Here is the code

Re: [R] AR(1) with NLME

Have you plotted the residuals (without the AR(1))? Lack of fit can masquerade as highly autocorrelated residuals. Alternatively, can you still estimate your model using the first differences of your data? If yes, do you have a problem? Have you studied the

Re: [R] RODBC and Excel: Wrong Data Type Assumed on Import

On 11/4/05, Earl F. Glynn [EMAIL PROTECTED] wrote: Gabor Grothendieck [EMAIL PROTECTED] wrote in message news:[EMAIL PROTECTED] You could try using the COM interface rather than the ODBC interface. Try code such as this: library(RDCOMClient) xls - COMCreate(Excel.Application)

Re: [R] problem with the assignment function

Wang, Yan [EMAIL PROTECTED] wrote: I run into the most weird problem I have ever met. I wrote a function rhopair, which calls a .C function. I cannot assign its value to a variable using either = nor -. After I did the assignment, rhopair cannot reproduce the same result as before with the