[R] [R-pkgs] new package benchden 1.0.0 : benchmark densities for nonparametric density estimation

The new package benchden 1.0.0 implements 28 benchmark densities for nonparametric density estimation that were introduced by A. Berlinet and L. Devroye (A Comparison of Kernel Density Estimates, Pub. Inst. Stat. Univ. Paris, XXXVIII, fasc. 3, 1994, 3-59, http://cg.scs.carleton.ca/~luc/devs.html

[R] How to install R 2.5 with Synaptic in Ubuntu?

Dear R-users, I'm using Ubuntu dapper, which only have R of Version 2.2.1. Would anybody tell me how to install the latest version of R with Synaptic in Ubuntu dapper system. Thanks! __ R-help@stat.math.ethz.ch mailing list

Re: [R] exaustive subgrouping or combination

David Duffy wrote: Waverley [EMAIL PROTECTED] asked: Dear Colleagues, I am looking for a package or previous implemented R to subgroup and exaustively divide a vector of squence into 2 groups. -- Waverley @ Palo Alto Google [R] Generating all possible partitions and you will find

Re: [R] using self-written functions

I use something like Gavin's solution for functions which are not used too often. The problem with using 'source' is that the user environment gets cluttered. I 'save' the most useful functions to a single file (MMmisc.Rda), put it in the HOMEPATH directory (use Sys.getenv(HOMEPATH) to find

Re: [R] align() function missing in R ?

Hi Markus, You can't assume that a typical R users knows much about S+. R has been beyond S+ for a long time {{ :-) :-) please Insightful staff, don't start to jump at me !}} Even I, as a very long time S and Splus user (of the past: 1987--~1997), have never, I think, used align(). Can you

[R] Comparison: glm() vs. bigglm()

Hi, Until now, I thought that the results of glm() and bigglm() would coincide. Probably a naive assumption? Anyways, I've been using bigglm() on some datasets I have available. One of the sets has 15M observations. I have 3 continuous predictors (A, B, C) and a binary outcome (Y). And

Re: [R] How to install R 2.5 with Synaptic in Ubuntu?

I'm using Ubuntu dapper, which only have R of Version 2.2.1. Would anybody tell me how to install the latest version of R with from the CRAN Ubuntu readme- works for synaptic as well: * UBUNTU R packages for Ubuntu on i386 are available. The plans are to support at least the latest Ubuntu

Re: [R] using self-written functions

One of your home directories on Windows is %HOMEDRIVE%%HOMEPATH% (you do need to give the drive), but only one: see the rw-FAQ. Reading ?file.path will help you not reinvent the wheel. So I think attach(path.expand(~/MMmisc.rda) is far more portable (as well as much more readable). On Thu, 28

Re: [R] align() function missing in R ?

On Fri, 29 Jun 2007, Martin Maechler wrote: Hi Markus, You can't assume that a typical R users knows much about S+. R has been beyond S+ for a long time {{ :-) :-) please Insightful staff, don't start to jump at me !}} Even I, as a very long time S and Splus user (of the past:

Re: [R] embedFonts() and bounding box

As embedFonts creates a new file, the bounding box of the original one is not relevant. (Yes, outfile = file by default, but it is still a new file.) I guess the switches -dDEVICEWIDTHPOINTS=w -dDEVICEHEIGHTPOINTS=h might help to create the new file with the bounding box you want. On

[R] acf and na.pass

Hello, I would like to have some information about acf with missing values. Let us consider this example: x=rnorm(100) x2=x x2[sample(100,10)]=NA acf1=acf(x) acf2=acf(x2,na.action=na.pass) The computation of the acf is different for the two data sets. Looking at the the code reveals that with

[R] How to add elements to a table

Hi, I've been using R for a few weeks now, but consider myself still a newbie, especially in what concerns the basics of data handling in R. My situation is this: I read in data from a database using RODBC, and then use table to produce a table of counts per years, table which I give to

[R] Warning message in Design ...

Hello! There were some questions regarding warning messages in Design library, but no answer how to fix them. What about: use of storage.mode(x) - single is deprecated: use mode- instead What does it mean? How to use properly simple model like: m1 = ols(Y ~ A + B + C, data = someData) After

Re: [R] How to add elements to a table

z - read.table(clipboard) z V1 V2 1 1990 20 2 1991 15 3 1995 17 4 1997 9 5 1998 10 6 1999 11 7 2000 5 zz - merge(data.frame(V1=1990:2000), z, by=V1, all.x=T) plot(zz, type=l) Jacques VESLOT INRA - Biostatistique Processus Spatiaux Site Agroparc 84914 Avignon Cedex 9, France Tel:

Re: [R] no applicable method

Hi From help page A data frame is a list of variables of the same length with unique row names, given class data.frame. so something completely different from matrix (which is AFAIK a vector with dimensions attribute). Therefore matrix needs to have all its values of the same type

Re: [R] How to add elements to a table

Thanks a lot! Wow, I know why I love R, things are so incredibly easy with R (once you know how ;-) ) Moreover I've found messages in the archive showing how to make plot draw as many ticks as I've got years, so everything is OK. Thanks for the help, Anne-Marie Quoting Jacques VESLOT

[R] Problem with library(CarbonEL) in .Rprofile

Hello, I am a Mac user and prefer the quartz device. So far, I have always typed the following in manually after starting R via ESS: library(CarbonEL) options(device=quartz) That works without problems, and allows me to use the quartz device instead of X11. I put this into my .Rprofile,

Re: [R] \include-mechanism in Sweave?

Dietrich Trenkler wrote: Dear HelpeRs, I'm very fond of Sweave and I use it as often as possible. It'a a pity I can't use it for larger projects or can I? For instance suppose I have three files file1.rnw, file2.rnw and file3.rnw with Sweave code. Working on file2.rnw I whould like to

[R] \include-mechanism in Sweave?

Dear HelpeRs, I'm very fond of Sweave and I use it as often as possible. It'a a pity I can't use it for larger projects or can I? For instance suppose I have three files file1.rnw, file2.rnw and file3.rnw with Sweave code. Working on file2.rnw I whould like to exclude file1.rnw and file3.rnw

Re: [R] \include-mechanism in Sweave?

Tobias Verbeke wrote: Dietrich Trenkler wrote: Dear HelpeRs, I'm very fond of Sweave and I use it as often as possible. It'a a pity I can't use it for larger projects or can I? For instance suppose I have three files file1.rnw, file2.rnw and file3.rnw with Sweave code. Working on

Re: [R] Repeat if

Birgit Lemcke wrote: Hello, (Power Book G4, Mac OS X, R 2.5.0) I would like to repeat the function range for 85 Vectors (V1-V85). I tried with this code: i-0 repeat { + i-i+1 + if (i85) next + range (Vi, na.rm = TRUE) + if (i==85) break + } I presume that the Vi is wrong,

Re: [R] Another loop avoidance question.

Sorry folks I posted the code with a bug in approach 2. aarrrhh. it should have been... ## Approach 2: loop on k2 output2 = matrix(0,nrow=n,ncol=k2) pt2 = proc.time(for (i in 1:k2) output2[,i] = rowSums( m1*(m2[,rep(i,3)]) )) I haven't seen any other response yet (after 8 hours!) but doesn't:

Re: [R] Function call within a function.

--- Stephen Tucker [EMAIL PROTECTED] wrote: Dear John, Perhaps I am mistaken in what you are trying to accomplish but it seems like what is required is that you call lstfun() outside of ukn(). [and remove the call to lstfun() in ukn()]. nts - lstfun(myfile, aa, bb) results - ukn(dd1,

Re: [R] Repeat if

Hello Jim, thanks for your answer. At the moment I am using this code: Range0-sapply(1:85, function(i) eval(parse(text=paste(range(V, i, , na.rm=T), sep= and it works really fine. The code you sent me is also fine but how can I implement, that missing values are TRUE? Thanks a lot for

Re: [R] Function call within a function.

--- Jason Barnhart [EMAIL PROTECTED] wrote: The problem isn't the function call. First, list1 returned by lstfun does not name its elements so nts$cda won't work. See code change in lstfun. Oh, I see. I missed this completely. I clearly was a bit groggy yesterday afternoon.

Re: [R] extracting df and MS values from aov

Hi, model1-aov(dv~iv.1*iv.2*iv.3) mod.av - anova(model1) names(mod.av) mod.av$Df mod.av$Mean On 29/06/07, Taka Matzmoto [EMAIL PROTECTED] wrote: Dear R users, I would like to extract df and Mean Sq values. I tried several things (e.g ., str(model1), names(model1)) but I can't find a way to

[R] Fat tails

I have a process that generates distributions that look like normal, but with fat tails. I would like to model them as if they were a mix of two normals (with zero mean). Is there any function that recovers the standard deviations and the probability based on a sample? I would like to generate

Re: [R] Repeat if

On 6/29/07, Birgit Lemcke [EMAIL PROTECTED] wrote: Hello Jim, thanks for your answer. At the moment I am using this code: Range0-sapply(1:85, function(i) eval(parse(text=paste(range(V, i, , na.rm=T), sep= It is a matter of taste, but I tend to prefer: a - list() for (i in 1:85)

[R] Spectral Decomposition

All of my resources for numerical analysis show that the spectral decomposition is A = CBC' Where C are the eigenvectors and B is a diagonal matrix of eigen values. Now, using the eigen function in R # Original matrix aa - matrix(c(1,-1,-1,1), ncol=2) ss - eigen(aa) # This results yields back

Re: [R] : regular expressions: escaping a dot

EOF from a keyboard on Windows is often Ctrl+Z. But you're right; it's platform dependent. CtrlZ in Unix has less desirable effects on readLines(). And on your running R process... Drat. Peter Dalgaard [EMAIL PROTECTED] 29/06/2007 12:42:41 S Ellison wrote: Wouldn't it be nice if the Help

Re: [R] Function call within a function.

Thanks very much. A very nice solution. The environment problem was the result of one last deperate try when the actual problem as Jason pointed out was that I was not naming my list elements and thought that I had. This looks like it will work quite nicely. I am pretty sure that there is a

Re: [R] Function call within a function.

--- Jason Barnhart [EMAIL PROTECTED] wrote: The problem isn't the function call. First, list1 returned by lstfun does not name its elements so nts$cda won't work. See code change in lstfun. I missed that entirely. I was groggier than I realised yesterday afternoon. I had at least once

Re: [R] logistic regression and dummy variable coding

Bingshan Li wrote: Hi All, Now it works. Thanks for all your answers and the explanations are very clear. Bingshan But note that you are not using R correctly unless you are doing a simulation and have some special speed issues. Let the model functions do all this for you. Frank

Re: [R] Warning message in Design ...

Petar Milin wrote: Hello! There were some questions regarding warning messages in Design library, but no answer how to fix them. What about: use of storage.mode(x) - single is deprecated: use mode- instead What does it mean? How to use properly simple model like: m1 = ols(Y ~ A + B +

Re: [R] align() function missing in R ?

Thank you for your responses, I should have given an example of the functionality I am looking for, here are three typical scenarios that I deal with a lot in my work: - a regular timeseries with lots of missing values that I want to convert to the corresponding regular time series with mssing

Re: [R] Spectral Decomposition

For a general square matrix A, the eigenvalue decomposition is A = CBC^{-1} For the special case of symmetric A, C^{-1} = C' __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

[R] cbind

Hi, I have a series of return data, a and b are factors. I would like to build a matrix which contains each vector of returns. I am thinking about something as following, but I guess there should be a sensible way of doing this. returns - split(return, list(regimef, assetf)) cbind(returns[[1]],

Re: [R] Spectral Decomposition [OOPS]

On 29-Jun-07 13:23:05, Ted Harding wrote: [Sorry -- a silly typo in my previous]: If A is not symmetric, you have left eigenvectors: x'*A = lambda*x' and right eigenvectors: A*x = lambda*x and the left eigenvectors are not the same as the right eigenvectors, though you have the

Re: [R] Spectral Decomposition

On 29-Jun-07 12:29:31, Doran, Harold wrote: All of my resources for numerical analysis show that the spectral decomposition is A = CBC' Where C are the eigenvectors and B is a diagonal matrix of eigen values. Now, using the eigen function in R # Original matrix aa -

Re: [R] cbind

livia wrote: Hi, I have a series of return data, a and b are factors. I would like to build a matrix which contains each vector of returns. I am thinking about something as following, but I guess there should be a sensible way of doing this. returns - split(return, list(regimef, assetf))

Re: [R] cbind

why don't you use a 'list' as the return value. The 'cbind' is going to assume that each of the 'return[[..]]' have the same length or you are going to get error messages: cbind(1:3,4:10) [,1] [,2] [1,]14 [2,]25 [3,]36 [4,]17 [5,]28 [6,]39

Re: [R] align() function missing in R ?

On Fri, 29 Jun 2007, Markus Loecher wrote: Thank you for your responses, I should have given an example of the functionality I am looking for, here are three typical scenarios that I deal with a lot in my work: - a regular timeseries with lots of missing values that I want to convert to

[R] shading bar charts

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi alls, i have to code a family of bar charts. After reading the doc, i cannot understand if it is possible to shade the bar colors and how. With shading i don't mean `density`. I mean something like that:

[R] GAMS and interactions

Dear all, I am fitting a generalized additive model with several discrete and continuous predictors, using the library mgcv. Basically, I have two questions: 1. If I model the response variable y with f(x), z and f(x):z, where f(x) has 1 edf and f(x):z has 4 edf, can I model x parametrically,

Re: [R] Comparison: glm() vs. bigglm()

Benilton Carvalho wrote: Hi, Until now, I thought that the results of glm() and bigglm() would coincide. Probably a naive assumption? Anyways, I've been using bigglm() on some datasets I have available. One of the sets has 15M observations. I have 3 continuous predictors (A, B, C) and

Re: [R] Comparison: glm() vs. bigglm()

Hi Peter, thank you very much for your feedback. As for your observations, I do realize that I'm using 1.5 chunks for this particular case (10e6 gives around 8 chunks on other sets). I just noticed that I didn't add the difference in the deviances that I observed: m1$deviance-m2$deviance

Re: [R] unequal variance assumption for lme (mixed effect model)

comments in line shirley zhang wrote: Hi Simon, Thanks for your reply. Your reply reminds me that book. I've read it long time ago, but haven't try the weights option in my projects yet:) Is the heteroscedastic test always less powerful because we have to estimate the within group

[R] regexpr

Hi, I 'd like to match each member of a list to a target string, e.g. -- mylist=c(MN,NY,FL) g=regexpr(mylist[1], Those from MN:) if (g0) { On list } -- My question is: How to add an end-of-string symbol '$' to the to-match string? so that

Re: [R] logistic regression and dummy variable coding

Hi Frank, I do not quite get you. What do you mean by simulation and speed issues? I do not see why they have to be considered in logistic regression. Thanks. Bingshan From: Frank E Harrell Jr [mailto:[EMAIL PROTECTED] Sent: Fri 6/29/2007 7:40 AM To: Li,

Re: [R] \include-mechanism in Sweave?

Hi Dietrich, I am writing my thesis, made up of several papers that have been expanded into chapters. Each chapter was a .tex file until I started using Sweave. Now each chapter is an .Rnw file. My master LaTeX document has this: \include{introduction} \include{epidemiology} \include{report}

Re: [R] regexpr

mylist=c(MN,NY,FL) g=regexpr(paste(mylist[1], $, sep=), Those from MN:) if (g0) { On list } or in a loop for (i in mylist){ if (regexpr(paste(mylist[i], $, sep=)) 0){ .code for those from } } On 6/29/07, runner [EMAIL PROTECTED] wrote: Hi, I 'd like to match each

Re: [R] logistic regression and dummy variable coding

Li, Bingshan wrote: Hi Frank, I do not quite get you. What do you mean by simulation and speed issues? I do not see why they have to be considered in logistic regression. Exactly. So don't use techniques that are only needed when such issues do have to be considered. Thanks.

[R] modify tick labels in 3D GAM plot

Hello, I have a GAM plot in 3D which was generated from the mgcv package (plot.gam) which seems to call the persp( ) function from graphics. This plot is one of three being plotted in the graphics window to copy to a manuscript. The plot's rotation has been set to clearly show the response

[R] Installing packages.

Dear, I'm not getting Installing packages: install.packages(c(exactRankTests)) trying URL `http://cran.r-project.org/bin/windows/contrib/2.0/PACKAGES' Content type `text/plain' length 26129 bytes opened URL downloaded 25Kb trying URL `http://cran.r-

Re: [R] shading bar charts

The first question you should ask yourself (and really think about the answer) is Why do I want to do this? Fancy colors and shadings can detract from a plot rather than enhance it. The wrong choice of colors can make bars look bigger or smaller than they really are. Reading Tufte's The visual

Re: [R] Installing packages.

require(exactRankTests) -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O On 29/06/07, Marcus Vinicius [EMAIL PROTECTED] wrote: Dear, I'm not getting Installing packages: install.packages(c(exactRankTests)) trying URL

Re: [R] regexpr

I think you are looking for paste(). And you can replace your for loop with lapply(), which will apply regexpr to every element of 'mylist' (as the first argument, which is 'pattern'). 'text' can be a vector also: mylist - c(MN,NY,FL) lapply(paste(mylist,$,sep=),regexpr,text=Those from MN:)

[R] GAM for censored data? (survival analysis)

First let me admit that I am no statistician... rather, an ecologist with just enough statistical knowledge to be dangerous. I've got a dataset with percent ground cover values for species and other entities. The data are left censored at zero, in that percent ground cover cannot be negative.

[R] Print grid/ggplot to a metafile

Dear UseRs called Hadley, or Paul, I am trying to print an edited ggplot2/grid graphics to a metafile. With the commented line below it works, but when I edit the plot by uncommenting the line, it fails, because it's illegal to have 2 graphics in a metafile. It works with pdf, but even then I get

[R] R-2.5.1 problem listing dataframe in GUI/CMDLINE

I have a dataframe called hawk. Source file looks ok. read.table seems ok. Can view using R editor. Again looks fine. Now, I am new to windows version of R. When I type in 'hawk' under Linux, I expect to see the rows listed. That isn't happening, as shown below. attach(hawk) hawk Error in

Re: [R] Installing packages.

Marcus Vinicius wrote: Dear, I'm not getting Installing packages: install.packages(c(exactRankTests)) trying URL `http://cran.r-project.org/bin/windows/contrib/2.0/PACKAGES' Content type `text/plain' length 26129 bytes opened URL downloaded 25Kb This means you are using R-2.0.x?

Re: [R] R-2.5.1 problem listing dataframe in GUI/CMDLINE

Roy Wilson wrote: I have a dataframe called hawk. Source file looks ok. read.table seems ok. Can view using R editor. Again looks fine. Now, I am new to windows version of R. When I type in 'hawk' under Linux, I expect to see the rows listed. That isn't happening, as shown below.

[R] Dominant eigenvector displayed as third (Marco Visser)

Dear R users Experts, This is just a curiousity, I was wondering why the dominant eigenvetor and eigenvalue of the following matrix is given as the third. I guess this could complicate automatic selection procedures. 000005 100000 0100

Re: [R] Dominant eigenvector displayed as third (Marco Visser)

There is no dominant eigenvalue: The eigenvalues of that matrix are the 6 different roots of 5. All have modulus (or absolute value) = 1.307660. When I raised them all to the 6th power, all 6 were 5+0i. Someone else can tell us why this is, but this should suffice as an initial

Re: [R] Dominant eigenvector displayed as third (Marco Visser)

Marco Visser wrote: Dear R users Experts, This is just a curiousity, I was wondering why the dominant eigenvetor and eigenvalue of the following matrix is given as the third. I guess this could complicate automatic selection procedures. 000005 1000

Re: [R] exaustive subgrouping or combination

On Fri, 29 Jun 2007, Peter Dalgaard wrote: David Duffy wrote: Waverley [EMAIL PROTECTED] asked: Dear Colleagues, I am looking for a package or previous implemented R to subgroup and exaustively divide a vector of squence into 2 groups. -- Waverley @ Palo Alto Google [R]

Re: [R] Function call within a function.

[SNIP] This has been very helpful though I still do not understand why one must call nts$cda using the eval(parse()) command. Is it because nts is created within the ukn environment? You don't *have* to use the eval(parse()). This works just as well: mysum - nts$cda. However, it

Re: [R] Dominant eigenvector displayed as third (Marco Visser)

On 29-Jun-07 21:09:37, Peter Dalgaard wrote: Marco Visser wrote: This is just a curiousity, I was wondering why the dominant eigenvetor and eigenvalue of the following matrix is given as the third. I guess this could complicate automatic selection procedures. 000005 1

Re: [R] exaustive subgrouping or combination

David Duffy wrote: On Fri, 29 Jun 2007, Peter Dalgaard wrote: David Duffy wrote: Waverley [EMAIL PROTECTED] asked: Dear Colleagues, I am looking for a package or previous implemented R to subgroup and exaustively divide a vector of squence into 2 groups. -- Waverley @ Palo

Re: [R] Dominant eigenvector displayed as third (Marco Visser)

Marco Visser wrote: Dear R users Experts, This is just a curiousity, I was wondering why the dominant eigenvetor and eigenvalue of the following matrix is given as the third. I guess this could complicate automatic selection procedures. Comment: In Matlab the the

[R] Assign name to a name

I would like to know how I can assign a name to a name. I have a dataset that has different years in it. I am writing scripts using R and I would like to give a month a generic name and then use the generic name to do different analysis. The reason for the generic name would be so that I only

[R] PCA + xValidation

Dear R users; Is there any package or function that I can use to perform LOOCV with prcomp? Basically I want to use that approach to get an idea of the optimal number of PC. Thanks for any idea PM __ R-help@stat.math.ethz.ch mailing list

[R] Gamma scale parameter in GEE?

Hi, Is there a way to get the scale parameter for the gamma link in the gee package? I know that object$scale gives the dispersion parameter, but I'm looking for the scale parameter, similar to what gamma.shape() or gamma.dispersion() gives in glm(). Thanks Patrick [[alternative HTML

[R] Problem installing RGTK2 on ubuntu 7.04

Hello, all I am trying to install RGTK2 on my Ubuntu 7.04 system. The installation fails with a message that RGtk2 requires GTK 2.8. As far as I can tell I have GTK+ 2.10.11 installed. Can anyone suggest a way to proceed? Thanks very much. Here is the failed installation:

Re: [R] Problem installing RGTK2 on ubuntu 7.04

On Fri, 2007-06-29 at 23:11 -0400, Andrew Muller wrote: Hello, all I am trying to install RGTK2 on my Ubuntu 7.04 system. The installation fails with a message that RGtk2 requires GTK 2.8. As far as I can tell I have GTK+ 2.10.11 installed. Can anyone suggest a way to proceed? Thanks

Re: [R] Problem installing RGTK2 on ubuntu 7.04

On 29 June 2007 at 23:11, Andrew Muller wrote: | I am trying to install RGTK2 on my Ubuntu 7.04 system. The installation | fails with a message that RGtk2 requires GTK 2.8. As far as I can tell I | have GTK+ 2.10.11 installed. Can anyone suggest a way to proceed? Something is not right in your

[R] How can i compute error?

Hi I work with package rpart for draw trees,for example: library(rpart) fit - rpart(Price ~ Mileage + Type + Country, cu.summary) plot(fit, compress=TRUE) text(fit, use.n=TRUE) and then i want compute error of each tree with t.test.(with package ROCR comparison two trees). and i

Re: [R] Assign name to a name

You can just create another variable which contains the names you want: ## let Year - c(rep(1999,2),rep(2000,2),rep(2001,3)) ## one alternative getYearCode1 - function(yr) { # yr can be a vector ifelse(yr==1999,Year1, ifelse(yr==2000,Year2, ifelse(yr==2001,Year3)))