[R] error in arules package

Hi, we noticed there was a error in the "arules" package. After reading the source code, we saw that the Dice similarity index was "miscalculated" in "dissimilarity" function : an copy-paste from Jaccard Index was not corrected (2* a_b_c, ie 2*(a+b+c) in the code instead of 2*a +b + c !!!). A

Re: [R] D'Agostino test

Am Montag, 22. Januar 2007 12:33 schrieb Matthieu Mourroux: > Hello, > > I'd like to know if the D'Agostino test of normality is reliable, The test is not consistent. The test statistic can be used for testing the hypothesis of uniformity. See the paper Baringhaus, L.; Henze, N. A test for u

Re: [R] Loess with more than 4 predictors / offsets

On Mon, 22 Jan 2007, Louisell, Paul wrote: > Hello, > > Does anyone know of an R version of loess that allows more than 4 > predictors and/or allows the specification of offsets? For that matter, > does anyone know of _any_ version of loess that does either of the > things I mention? Why would yo

Re: [R] Question about rpart and regression trees

On Mon, 22 Jan 2007, Paul Smith wrote: > Dear All > > I would like to use rpart to obtain a regression tree for a dataset > like the following: > > Y X1 X2 X3 X4 > 5.500033 B A 3 2 > 0.35625148D B 6 5 > 0.8062546 E C 4

Re: [R] factor()

> TeamInfo TEAMNAME LEVEL WORKTIME BONUS 1 batch sunan B 135 9,818 2 batch Chenqi E 121 6,050 3 batch jiangxu F 97 4,189 4 online zhouxi F 63 2,720 5 online chenhe H 36 1,064 ## try: > factor(TeamInfo$TEAM) [1] batch batch batch o

Re: [R] Query about using try block

Usually (that is, not limited in R language), when error occurs in try, stacks are rollbacked, so the variables defined in try no longer exists after calling try. One non-elegant solution is: fit<-NULL try ( (fit = lm(y~x, data = data_fitting)), silent =T) if(!is.null(fit)){ coeffs = as.list(coef

[R] Questions about xtable and print.xtable

I have been using the wonderful xtable package lately, in combination with Sweave, and I have a couple of general questions along with a more particular one. I'll start with the particular question. I basically have a 1x3 array with column names but no row names. I want to create a latex tab

[R] Loess with more than 4 predictors / offsets

Hello, Does anyone know of an R version of loess that allows more than 4 predictors and/or allows the specification of offsets? For that matter, does anyone know of _any_ version of loess that does either of the things I mention? Thanks, Paul Louisell 650-833-6254 [EMAIL PROTECTED] Research Asso

Re: [R] logistic regression model + Cross-Validation

why not use lda{MASS} and it has cv=T option; it does "loo", though. Or use randomForest. if you have to use lrm, then the following code might help: n.fold <- 5 # 5-fold cv n.sample <- 50 # assumed 50 samples s <- sample(1:n.fold, size=n.sample, replace=T) for (i in 1:n.fold){ # create your tr

Re: [R] lattice: put key where unused panel would have been

Benjamin Tyner said the following on 1/22/2007 3:18 PM: > Hi, > > Say I have > > z<-data.frame(y=runif(190), >x=runif(190), >f=gl(5,38), >g=gl(19,10)) > > plot<-xyplot(y~x|g, > data=z, >

Re: [R] sequential processing

So, I take it, given that the use of a pipe is suggested for sequential reading, that the standard approach to processing a data frame is to load the entire file? Please correct if wrong. BTW, I am not interested in finding direct translations of SAS data step statements to R, but instead in f

[R] Question about rpart and regression trees

Dear All I would like to use rpart to obtain a regression tree for a dataset like the following: Y X1 X2 X3 X4 5.500033B A 3 2 0.35625148 D B 6 5 0.8062546 E C 4 3 5.100014C A 3

[R] lattice: put key where unused panel would have been

Hi, Say I have z<-data.frame(y=runif(190), x=runif(190), f=gl(5,38), g=gl(19,10)) plot<-xyplot(y~x|g, data=z, layout=c(5,4), groups=f, auto.key

Re: [R] sequential processing

One option for processing very large files with R is split: ## split a large file into pieces #--parameters: the folder, file and number of parts FLD=/home/user/data F=very_large_file.dat parts=50 #---split cd $FLD fn=`echo $F | awk -F\. '{print $1}'` #file name without extension

Re: [R] Query about using optimizers in R without causing program to crash

Hi Lalitha, Use try() or tryCatch() Cheers Andrew On Mon, Jan 22, 2007 at 12:43:28PM -0800, lalitha viswanath wrote: > Hi > I am a newbie to R and am using the lm function to > fit my data. > This optimization is to be performed for around 45000 > files not all of which lend themselves to

Re: [R] Query about using try block

Hi Thanks for your response. However I seem to be doing something wrong regarding the try block resulting in yet another error described below. I have a function that takes in a file name and does the fit for the data in that file. Hence based on your input, I tried try ( (fit = lm(y~x, data = da

Re: [R] Query about using optimizers in R without causing program to crash

This is answered in the FAQ list. -thomas On Mon, 22 Jan 2007, lalitha viswanath wrote: > Hi > I am a newbie to R and am using the lm function to > fit my data. > This optimization is to be performed for around 45000 > files not all of which lend themselves to > optimization. Some of t

[R] Recursive-SVM (R-SVM)

I am trying to implement a simple r-svm example using the iris data (only two of the classes are taken and data is within the code). I am running into some errors. I am not an expert on svm's. If any one has used it, I would appreciate their help. I am appending the code below. Thanks../Murli

[R] Query about using optimizers in R without causing program to crash

Hi I am a newbie to R and am using the lm function to fit my data. This optimization is to be performed for around 45000 files not all of which lend themselves to optimization. Some of these will and do crash. However, How do I ensure that the program simply goes to the next file in line without

Re: [R] Repeated measures

In the two solutions for the repeated measures problem given in the original reply below, the F and p values given by aov() with the error strata defined by Error() are different from those given by lme(). However, when one does the problem "by hand" using the standard split plot model, the results

[R] R interpretation

Hi, I am new to R (and not really a stats expert) and am having trouble interpreting its output. I am running a human learning experiment, with 6 scores per subject in both the pretest and the posttest. I believe I have fitted the correct model for my data- a mixed-effects design, with subject

Re: [R] Integration + Normal Distribution + Directory Browsing Processing Questions

Nils Hoeller wrote: > > for example. > > BUT what can I do for dynamic m and sd? > I want something like integrate(dnorm(,0.6,0.15),0,1), with the first > dnorm parameter open for the > integration but fixed m and sd. integrate(function(x)dnorm(x,0.1,1.2), 0, 1) is a way of "fixing" additional

Re: [R] How to get correct integration in C for step function?

On Mon, 22 Jan 2007, Lynette wrote: > Dear all, especially to Thomas, > > I have figured out the problem. For the step function, something wrong with > my C codes. I should use the expression ((x>=0.25)&&(x<=0.75)) ? 2:1 instead > of ((x>=1/4)&&(x<=3/4)) ? 2:1 ). Have no idea why 0.25 makes diff

Re: [R] How to get correct integration in C for step function?

Dear all, especially to Thomas, I have figured out the problem. For the step function, something wrong with my C codes. I should use the expression ((x>=0.25)&&(x<=0.75)) ? 2:1 instead of ((x>=1/4)&&(x<=3/4)) ? 2:1 ). Have no idea why 0.25 makes difference from 1/4 in C. But now I can go ahead

[R] Example function for bigglm (biglm) data input from file

This is to submit a commented example function for use in the data argument to the bigglm(biglm) function, when you want to read the data from a file (instead of a URL), or rescale or modify the data before fitting the model. In the hope that this may be of help to someone out there. make.data <

Re: [R] [ESS] How to get correct integration in C for step function?

On Mon, 22 Jan 2007, Lynette wrote: > Well, > > I have no idea either. I can get correct answers for continous functions but > incorrect for step functions. > I have just tried using Rdqags from C for the function x>0 and it worked fine (once I had declared all the arguments correctly). The code

Re: [R] Problem with C extension

On Mon, 22 Jan 2007, Markus Schmidberger wrote: > Hello, > thanks for help and code. > We did a lot of work to speedup our function in R. We have a nested loop, > vectorizing is the fastest way. But there we got a very big matrix and > problems with memory. So we want to stay by loops an speedup

Re: [R] efficient code. how to reduce running time?

On Jan 22, 2007, at 10:39 AM, John Fox wrote: > One thing that seems particularly > striking in your results is the large difference between elapsed > time and > user CPU time, making me wonder what else was going on when you ran > these > examples. Yes, indeed there were a lot of other thin

[R] lnme convergence

Dear R-user, I am trying to use the R "nlme" function to fit a non linear mixed effects model. The method has some problem to reach the convergence. I am trying to understand causes of the problem by following step by step evolution of the iterative algorithm (verbose=TRUE command). However, I

Re: [R] How to get correct integration in C for step function?

Well, I have no idea either. I can get correct answers for continous functions but incorrect for step functions. Sign, I have been trying to realize the integration in C for long time. Thank you for your answering. Best, Lynette - Original Message - From: "Thomas Lumley" <[EMAIL PROT

Re: [R] Problem with C extension

Hello, thanks for help and code. We did a lot of work to speedup our function in R. We have a nested loop, vectorizing is the fastest way. But there we got a very big matrix and problems with memory. So we want to stay by loops an speedup with C. My code is similar to this. (my_c is code from Br

Re: [R] efficient code. how to reduce running time?

Dear Brian, > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Prof > Brian Ripley > Sent: Monday, January 22, 2007 11:06 AM > To: Charilaos Skiadas > Cc: John Fox; r-help@stat.math.ethz.ch > Subject: Re: [R] efficient code. how to reduce running tim

Re: [R] Compare effects between lm-models

Thank you Alain and Max for your swift responses. It might be that I'm misunderstanding your responses, but aren't you testing if there is a difference between the two full models? What I want to know, os whether the effect of a specific predictor (x) differs between model1 and model2. I'm n

[R] Latin hyper cube sampling from expand.grid()

Dear R experts I am looking for a package which gives me latin hyper cube samples from the grid of values produced from the command "expand.grid". Any pointers to this issue might be very useful. Basically, I am doing the following: > a<-(1:10) > b<-(20:30) > dataGrid<-expand.grid(a,b) Now, is t

Re: [R] efficient code. how to reduce running time?

Dear Haris, My timings were on a 3 GHz Pentium 4 system with 1 GB of memory running Win XP SP2 and R 2.4.1. I'm no expert on these matters, and I wouldn't have been surprised by qualitatively different results on different systems, but this difference is larger than I would have expected. One thi

Re: [R] efficient code. how to reduce running time?

On Mon, 22 Jan 2007, Charilaos Skiadas wrote: > On Jan 21, 2007, at 8:11 PM, John Fox wrote: > >> Dear Haris, >> >> Using lapply() et al. may produce cleaner code, but it won't >> necessarily >> speed up a computation. For example: >> >>> X <- data.frame(matrix(rnorm(1000*1000), 1000, 1000)) >>> y

Re: [R] Finding the effect of Box-Cox transformation using "vis.boxcoxu"

?box.cox ?boxcox On Jan 22, 2007, at 2:25 AM, Arun Kumar Saha wrote: > I have a dataset 'data' and I want to see the effect of Box-Cox > transformation on it Interactively for different lambda values. I > already > got a look on function "vis.boxcoxu" in package "TeachingDemos". But I > didn't

Re: [R] predict.survreg() with frailty term and newdata

It can't be done with the current code. In a nutshell, you are trying to use a feature that I never got around to coding. It's been on my "to do" list, but may never make it to the top. Terry __ R-help@stat.math.ethz.ch mailing list http

Re: [R] How to get correct integration in C for step function?

On Sun, 21 Jan 2007, Lynette wrote: > Dear all, > > I am using Rdqags in C to realize the integration. It seems for the > continous C function I can get correct results. However, for step functions, > the results are not correct. For example, the following one, when integrated > from 0 to 1 gives

Re: [R] Compare effects between lm-models

You can use the anova function a la: > anova(model1, model2) Analysis of Variance Table Model 1: y ~ x Model 2: y ~ x + z Res.DfRSS Df Sum of Sq F Pr(>F) 1 13 4.4947 2 12 4.4228 10.0720 0.1952 0.6665 I would suggest getti

[R] naiveBayes question

Aimin: The problem is that the columns you choose for training (only 4 variables) do not match the ones used for prediction (all except y). David I try to use naiveBayes > p.nb.90<-naiveBayes(y~aa_three+bas+bcu+aa_ss,data=training) > pr.nb.90<-table(predict(p.nb.90,training[,-13],ty

[R] Compare effects between lm-models

Dear helpeRs, I'm estimating a series of linear models (using lm) in which in every new model variables are added. I want to test to what degree the new variables can explain the effects of the variables already present in the models. In order to do that, I simply observe wether these effe

Re: [R] efficient code. how to reduce running time?

On Jan 21, 2007, at 8:11 PM, John Fox wrote: > Dear Haris, > > Using lapply() et al. may produce cleaner code, but it won't > necessarily > speed up a computation. For example: > >> X <- data.frame(matrix(rnorm(1000*1000), 1000, 1000)) >> y <- rnorm(1000) >> >> mods <- as.list(1:1000) >> system.

[R] Time-varying correlation calculation

Dear R useres, I'm interested in getting a series of time-varying correlation, simply between two random variables. Could you please introduce a package to do this task? Thank you so much for any help. Amir - Don't pick lemons.

Re: [R] Combination of variables

You might find the following code useful. It's part of a package I'm developing for interactive model exploration. Hadley # Generate all models # Fit all combinations of x variables ($2^p$) # # This technique generalises \code{\link{fitbest}}. While it is much # slower it will work for any type

Re: [R] Combination of variables

You don't say what model you want to do. It isn't necessary to store each combination of predictors in a separate matrix unless you really need to do this for some other reason, in which case I imagine you could adopt this idea. I dare say there are better ways, but this should work (assuming you

[R] Fwd: Re: aov y lme

Dear Prof. Ripley and Christoph, thank you very much for your comments. You have helped me a lot. Thanks, Tomas Goicoa >Dear Prof. Ripley > >Thank you for your email. Yes, this is of course the correct >syntax to save us the extra calculation. And I forgot the >"lower.tail = FALSE" fo

[R] D'Agostino test

Hello, I'd like to know if the D'Agostino test of normality is reliable, because somme of our results are not really coherent. This test seems to be very sensitive. Even compared to a normal distribution generated by R, the results are not very clear. thanks for any help Matthieu. __

[R] Combination of variables

Hi, List , i have 6 predictor variables and i want to make possible combinations of these 6 predictors ,all the data is in matrix form , if i am having 6 predictors than possible combination of sets are 64 2 power 6, or 63 ,whatever it may be i want to store the result in another variable to

Re: [R] Unusual behaviour get.hist.quote

Jerry Pressnell wrote: > I have been running this script regularly for some time. This morning the > following error message appeared. > EWL<-get.hist.quote("EWL",start=(today <- Sys.Date())-350,quote="Cl") > Error in if (dat[n] != start) cat(format(dat[n], "time series starts > %Y-%m-%d\n")) :

Re: [R] ECB/Sidebar/R (Emacs) was: Re: kate editor for R

On 1/22/07, Dirk Eddelbuettel <[EMAIL PROTECTED]> wrote: > > On 22 January 2007 at 00:05, Ramon Diaz-Uriarte wrote: > | On 1/20/07, Dirk Eddelbuettel <[EMAIL PROTECTED]> wrote: > | > Just confirms my suspicion that even after all these years, I barely > | > scratched the surface of ess. That '2+ y

[R] Unusual behaviour get.hist.quote

I have been running this script regularly for some time. This morning the following error message appeared. Any suggestions to correct this change would be appreciated. EWL<-get.hist.quote("EWL",start=(today <- Sys.Date())-350,quote="Cl") trying URL 'http://chart.yahoo.com/table.csv?s=EWL&a=1

Re: [R] How to disable existing menus in tcltk?

play below after your code and look at tk window: tkentryconfigure(editMenu,0,state="disable") tkentryconfigure(editMenu,0,state="active") tkentryconfigure(topMenu,1,state="disable") tkentryconfigure(topMenu,1,state="active") HTH On 1/22/07, Jarno Tuimala <[EMAIL PROTECTED]> wrote: > Hi! > > I'

Re: [R] Scatterplot help

The following three lines will do what you want. You will probably want to change some of the default behaviour; just look at the relevant help pages. plot(x,y) text(x,y,ID) grid(2) On 21/01/07, gnv shqp <[EMAIL PROTECTED]> wrote: > Hi my friends, > > I'm trying to make a scatterplot like this.

Re: [R] aov y lme

Dear Tomas You can produce the results in Montgomery Montgomery with lme. Please remark that you should indicate the nesting with the levels in your nested factor. Therefore I recreated your data, but used 1,...,12 for the levels of batch instead of 1,...,4. purity<-c(1,-2,-2,1,-1,-3,0,4, 0,-4, 1

[R] How to disable existing menus in tcltk?

Hi! I've constructed a small menu-driven interface to a couple of R functions using the possibilities offered by the tcltk package. When user runs some specific analyses, I would then like to disable some of the menus (or menu choises) that are not applicable after the performed analysis. I tri

[R] Combination diffrent variables ,how to calculates

Hi, List , i have 6 predictor variables and i want to make possible combinations of these 6 predictors ,all the data is in matrix form , if i am having 6 predictors than possible combination of sets are 64 2 power 6, or 63 ,whatever it may be i want to store the result in another variable to

Re: [R] Integration + Normal Distribution + Directory Browsing Processing Questions

the reason is that is more natural to use pnorm(), which also should a more efficient approximation of the Normal integral than intgrate(), you may even use diff(pnorm(0:1, mean = 0.5, sd = 1.2)) however, the point I meant to make was to use the '...' argument that can found in many R function

Re: [R] command-line arguments in R

see: ?commandArgs or more detail for R startup mechanisms: ?Startup On 1/22/07, Deepak Chandra <[EMAIL PROTECTED]> wrote: > Hi All, > > A simple and naive question from a newbie. How can one access command-line > arguments in R i.e. equivalent of argv in C? > Have spent a lot of time on findin

Re: [R] Integration + Normal Distribution + Directory Browsing Processing Questions

Hi Nils, I would say, pnorm is faster and has a higher precision. Best, Matthias - original message Subject: Re: [R] Integration + Normal Distribution + Directory Browsing Processing Questions Sent: Mon, 22 Jan 2007 From: Nils Hoeller<[EMAIL PROTECTED]> > Thank you, > > both wor