[R] I need your help.

Hi, I need your help, so I send letter to you. I have a problem about plsr in pls package. I want to show how classfied or related each ohter samples, so I tried to use plsr and biplot. But, I failed. Because, I had to change data type of my sample. Unfortunately, I didn't know

[R] Duplicating meta-regression results from PROC MIXED with lmer

R-experts: In 2002, Hans Van Houwelingen et al. published a tutorial on how to do meta-regression in Statistics in Medicine. They used the classic BCG dataset of Colditz to demonstrate correct methodology and computed the results using PROC MIXED in SAS. In trying to duplicate the results

Re: [R] Heatmap without levelplot

Hi Uwe, thanks a lot for your answer! And thanks a lot to all others helping me with this issue! Uwe Ligges schrieb: Antje wrote: Hi Uwe, I tried to explain my problem with the given example. I don't see any documentation which tells me that the length of "col.regions" should be one less

[R] Call R from Perl

Hi, I am trying to call R in my perl program but is not working. It does not give an error but my program gets stuck indefinitely. I am using the following command to call R from Perl `R BATCH regressExpr.spl temp`; Any suggestions? Best, Daniel F. [[alternative HTML version deleted]]

Re: [R] problem with ggplot2 boxplot, groups and facets

On Tue, May 05, 2009 at 09:21:49PM -0400, stephen sefick wrote: > > If you would provide a reproducible example I could tinker. > The code I posted is real. I attach here the relevant part of the data-set as CSV. Best regards, Zeljko. "","sp","wg","n","v.realtime" "9968","GP","1","1",28.924 "

Re: [R] subset data

Or somewhat more readibly selected.data <- subset(data, id %in% selected.id) Bill Venables http://www.cmis.csiro.au/bill.venables/ -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Kushantha Perera Sent: Wednesday, 6 May 2009 3:

Re: [R] Do you use R for data manipulation?

I also put my 2cents on sqldf :-) milton On Wed, May 6, 2009 at 12:30 AM, Wensui Liu wrote: > take a look at sqldf package(http://code.google.com/p/sqldf/), you > will be amazed. > > On Wed, May 6, 2009 at 12:22 AM, Farrel Buchinsky > wrote: > > Is R an appropriate tool for data manipulation a

Re: [R] subset data

Try, data[data$id%in%selected.id,] Good day! Kushantha -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of abdul kudus Sent: Wednesday, May 06, 2009 10:12 AM To: r-help@r-project.org Subject: [R] subset data Dear all, > data <- data.

Re: [R] subset data

just a small adjusts... data[data$id %in% selected.id, ] --- so elegant! :-) On Wed, May 6, 2009 at 1:15 AM, milton ruser wrote: > Like this? > > > > data<-read.table(stdin(), head=T, sep=",") > id,x > 1,0.3604464 > 2,0.4813987 > 3,0.0160058 > 4,0.7165909 > 5,0.6092248 > 6,0.2413049 > 7,0.79815

Re: [R] subset data

Like this? data<-read.table(stdin(), head=T, sep=",") id,x 1,0.3604464 2,0.4813987 3,0.0160058 4,0.7165909 5,0.6092248 6,0.2413049 7,0.7981568 8,0.6093960 9,0.2887064 10,0.3485780 selected.id <- sample(data$id,3,replace=F) selected.id data.subset<-subset(data, id %in% selected.id) data.subset

Re: [R] subset data

data[data$id==selected$id, ] - cuncta stricte discussurus - -Ursprüngliche Nachricht- Von: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Im Auftrag von abdul kudus Gesendet: Wednesday, May 06, 2009 12:42 AM An: r-help@

[R] bivariate normal and rho

Hi, Let f(rho) = E[F_1(x) F_2(y)], i.e f(rho) is the expectation of F(x) * F(y) with respect to the bivariate Gaussian density with mean 0 and covariance matrix [1 rho; rho 1]. Moreover, assume F_1(x) and F_2(y) to be increasing functions of x and y respectively. I was wondering if it was true th

[R] subset data

Dear all, > data <- data.frame(id=seq(1:10),x=runif(10)) > data id x 1 1 0.3604464 2 2 0.4813987 3 3 0.0160058 4 4 0.7165909 5 5 0.6092248 6 6 0.2413049 7 7 0.7981568 8 8 0.6093960 9 9 0.2887064 10 10 0.3485780 > selected.id <- sample(data$id,3,replace=F) > selected.id

Re: [R] Do you use R for data manipulation?

take a look at sqldf package(http://code.google.com/p/sqldf/), you will be amazed. On Wed, May 6, 2009 at 12:22 AM, Farrel Buchinsky wrote: > Is R an appropriate tool for data manipulation and data reshaping and data > organizing? I think so but someone who recently joined our group thinks not. >

[R] Do you use R for data manipulation?

Is R an appropriate tool for data manipulation and data reshaping and data organizing? I think so but someone who recently joined our group thinks not. The new recruit believes that python or another language is a far better tool for developing data manipulation scripts that can be then used by sev

[R] Problem with update.packages on repo with a single package

I've set up a CRAN-style repository to distribute a single package. The repository contains several versions of the package, I was hoping that update.packages pointed at this repository would grab the highest version number. In fact it returns an error: Error in available[, "Bundle"] : incor

Re: [R] [R-sig-ME] Duplicating meta-regression results from PROC MIXED with lmer

On 6/05/2009, at 3:00 PM, Brant Inman wrote: R-experts: In 2002, Hans Van Houwelingen et al. published a tutorial on how to do meta-regression in Statistics in Medicine. They used the classic BCG dataset of Colditz to demonstrate correct methodology and computed the results using PROC MIXED i

[R] RW: smoothing spline in package gam

Dear jianghua and all R professor: I use the suggestion that jianghua gives. But the problem is still there. Use "summary(m1)" or "summary.gam(m1)" is the same result and it doesn't show the significance results of parametric terms. Should I choose another smoother to get significa

Re: [R] re shape package - use one cast() instead of many

On Tue, May 5, 2009 at 3:55 PM, jwg20 wrote: > > Thanks for your help! I wasn't sure what the margins variable did, but I'm > beginning to understand. I'm almost there, but with my data (and with ff_d) > I tried to margin over two variable names, however it only does one of them. > So with ff_d I

Re: [R] Stepwise logistic regression with significance testing - stepAIC

David Freedman wrote: Didn't a 2008 paper by Austin in J Clin Epidemiol show that bootstrapping was just as bad as backward stepwise regression for finding the true predictors? Yes Any variable selection without shrinkage is problematic. Frank http://xrl.in/26em Dimitris Rizopoulos-4 wro

Re: [R] dotplot: labeling coordinates for each point

Hi Deepayan, Thanks for the hint. I spent some time on the research but haven't got any luck in writing the custom panel function for the conditional labeling of points in a graph. Could you please provide some more thoughts and probably some pseudo code? Thank you so much for your time! Best,

Re: [R] RMySQL insert statements?

Have you tried dbSendQuery() ? That is, construct an SQL insert statement and use it in dbSendQuery. Might have to follow it with dbCommit(). You could also use break your data up into smaller pieces and use dbWriteTable to write it a piece at a time, if really is too much to do all at once.

Re: [R] xYplot() produces empty pdf

print() fixed it. Thank you! sp --- On Tue, 5/5/09, Rolf Turner wrote: > From: Rolf Turner > Subject: Re: [R] xYplot() produces empty pdf > To: "to_rent_2...@yahoo.com" > Cc: "r-help@r-project.org" > Date: Tuesday, May 5, 2009, 9:26 PM > On 6/05/2009, at 12:50 PM, x wrote: > > > > > Hi,

Re: [R] xYplot() produces empty pdf

On 6/05/2009, at 12:50 PM, x wrote: Hi, While xYplot(...) below produces an empty pdf file, plot(...) works fine. The same xYplot(...) produces correct output if tried directly in R console. Any suggestions? RTFFAQ (7.22) cheers, Rolf Turner ##

[R] R readline customization with rl_application_name

I tried to customize R completion in my .inputrc like this: $if RCustomCompletion Control-q: "q(save=\"no\")\n" $endif I looked in the R source to find about RCustomCompletion BUBBA$ grep -r 'rl_readline_name' * src/unix/sys-std.c:rl_readline_name = "RCustomCompletion"

Re: [R] problem with ggplot2 boxplot, groups and facets

If you would provide a reproducible example I could tinker. Stephen Sefick On Tue, May 5, 2009 at 4:59 PM, Zeljko Vrba wrote: > I have a following problem: > > The call > > qplot(wg, v.realtime, data=df.best.medians$gv1, colour=sp,  geom="boxplot") > > works nice: for each value of the wg factor

[R] xYplot() produces empty pdf

Hi, While xYplot(...) below produces an empty pdf file, plot(...) works fine. The same xYplot(...) produces correct output if tried directly in R console. Any suggestions? Thanks, sp # empty pdf trellis.device("pdf", file="./resid1_lat.pdf"); xYplot(resid(f) ~ fitted(f), method='quantile', nx

Re: [R] ellipse

On 05/05/2009 6:28 PM, Antonio Lucadamo wrote: Dear all, I'm using the ellipse package and I would like to verify if the confidence region that I build with this package can be equivalent to an Union Intersection Test. I used different value for the t-statistic but I can not find the right eq

Re: [R] Stepwise logistic regression with significance testing - stepAIC

Didn't a 2008 paper by Austin in J Clin Epidemiol show that bootstrapping was just as bad as backward stepwise regression for finding the true predictors? http://xrl.in/26em Dimitris Rizopoulos-4 wrote: > > Greg Snow wrote: >> There is not a meaningful alternative way since the way you propos

Re: [R] novice question regarding R archives

http://cran.r-project.org/web/packages/ On Tue, May 5, 2009 at 8:28 PM, Xao Ping wrote: > Dear All: > I am new here. Please, advise how can I reach the R-archives to look through > the libraries available for download. > > Thanks > > Xao Ping > R&R Pharmakinetics > Taiwan > > > >        [[altern

[R] novice question regarding R archives

Dear All: I am new here. Please, advise how can I reach the R-archives to look through the libraries available for download.   Thanks   Xao Ping R&R Pharmakinetics Taiwan [[alternative HTML version deleted]] __ R-help@r-project.org mail

Re: [R] Way to handle variable length and numbers of columns using read.table(...)

You can read in your data with 'readLines' and then edit out the offending lines. Here is something that works with the data you posted. You will have to tailor to your real data and add error checks: > # read in the data with 'readLines' to get all the lines x <- readLines('clipboard') > cat(x,

Re: [R] Relative subscripts?

?diff > x ID LENGTH DIFF 1 1 10 NA 2 2 155 3 3 205 4 4 12 -8 5 5 186 > x <- x[,-3] > x ID LENGTH 1 1 10 2 2 15 3 3 20 4 4 12 5 5 18 > x$DIFF <- c(NA, diff(x$LENGTH) ) > x ID LENGTH DIFF 1 1 10 NA 2 2 155 3 3

[R] Relative subscripts?

Dear R-helpers, I have a dataframe with several columns, one of which is called LENGTH. I would like to make a new column called DIFF containing the value of LENGTH minus LENGTH in the previous row, like this: ID LENGTH DIFF 1 1 10 NA 2 2 155 3 3 205 4 4 12 -8 5

Re: [R] yacas

You haven't provided any code so we have no idea what the problem is. Make sure you have read the troubleshooting sections on the home page? http://ryacas.googlecode.com Here is an example: > library(Ryacas) Loading required package: XML > x <- Sym("x") > Factor(x^2-1) [1] "Starting Yacas!" exp

Re: [R] FOURIER INTEGRALS IN R

Isn't it possible to write this as the real part of a fourier transform? You could then use the fft to calculate it for all the values of x, all at once. The Madan and Carr paper offers some pointers on how to do this: http://www.imub.ub.es/events/sssf/vgfrier7.pdf On May 6, 1:06 am, "Ravi Varad

[R] yacas

Hi, as I find problems with yacas package... is there any R function equivalent to the yacas function "Factor" ? the factor function which i found in the R help is not the same. it doesn't factor an algebraic expression.. thanks hassan [[alternative HTML version deleted]] ___

[R] illegal levels in yaImpute() / AsciiGridImpute()

I'm using randomForest in yaImpute to create a yai-type object which associates "L" with landscape features. Then I use the sp() package to impute L to a landscape consisting of four ascii files) I keep getting the message "NA's generated due to illegal level(s)" when I do the imputation. It's

[R] ellipse

Dear all, I'm using the ellipse package and I would like to verify if the confidence region that I build with this package can be equivalent to an Union Intersection Test. I used different value for the t-statistic but I can not find the right equivalence. Does someone know how to choose the

Re: [R] self organizing map advice for categorical data

George Chen schrieb: Hello, Could anybody offer any advice about implementing a Kohonen self organizing map for categorical data? Specifically I am wondering if there are any pre-existent packages that can deal with categorical data and/or how one would compare the input vector of categorica

[R] problem with ggplot2 boxplot, groups and facets

I have a following problem: The call qplot(wg, v.realtime, data=df.best.medians$gv1, colour=sp, geom="boxplot") works nice: for each value of the wg factor I get two box-plots (two levels in the sp factor) in different colours, side-by-side, centered at the wg x-axis. However, I want to separat

Re: [R] re shape package - use one cast() instead of many

Thanks for your help! I wasn't sure what the margins variable did, but I'm beginning to understand. I'm almost there, but with my data (and with ff_d) I tried to margin over two variable names, however it only does one of them. So with ff_d I set margins=c("treatment","variable"); however I only e

Re: [R] re shape package - use one cast() instead of many

On Tue, May 5, 2009 at 3:03 PM, jwg20 wrote: > > I have a data set that I'm trying to melt and cast in a specific way using > the reshape package. (I'll use the ff_d dataset from reshape so I don't have > to post a toy data set here. ) > > Lets say I'm looking for the interaction of treatment with

Re: [R] documenting quirky behavior of as.POSIXct, as.POSIX.lt regarding AM/PM, possibly other cases

Seems to work fine for me on R 2.9.0: > as.POSIXct("2009/03/26 01:00:00 AM" , format="%Y/%m/%d %I:%M:%S %p" ) [1] "2009-03-26 01:00:00 GMT" > as.POSIXct("2009/03/26 01:00:00 PM" , format="%Y/%m/%d %I:%M:%S %p" ) [1] "2009-03-26 13:00:00 GMT" > On Tue, May 5, 2009 at 2:55 PM, Galkowski, Jan wrot

[R] re shape package - use one cast() instead of many

I have a data set that I'm trying to melt and cast in a specific way using the reshape package. (I'll use the ff_d dataset from reshape so I don't have to post a toy data set here. ) Lets say I'm looking for the interaction of treatment with each type of "variable" in ff_d. Using the command belo

Re: [R] R 2.9 and XML

> After I installed R 2.9.0 my XML package cannot load; I get an error "This > application has failed to start because iconv.dll was not found. > Re-installing the application may fix this problem". I already re-installed > both but the problem persists. Does anyone know what is going on? I would

Re: [R] Error building package: LaTeX error when creating PDF version

I recently came across the same problem reported here: http://tolstoy.newcastle.edu.au/R/e6/help/09/04/12383.html The fix was to edit "$R_HOME/etc/Renviron" and change R_PDFLATEXCMD=${R_PDFLATEXCMD-${PDFLATEX-'/usr/texbin/pdflatex'}} to R_PDFLATEXCMD=${R_PDFLATEXCMD-${PDFLATEX-'pdflatex'}} w

[R] documenting quirky behavior of as.POSIXct, as.POSIX.lt regarding AM/PM, possibly other cases

I wanted to put this on the R Wiki, but found the suitable pages were read-only. I wanted to get it out in public to save people work. I was converting dates like "2009/03/26 01:00:00 AM" using as.POSIXct. I found that using a format of "%Y/%m/%d %I:%M:%S %p" did not work correctly to disti

Re: [R] quick square root axes

> If you do write your own, the hardest part will be picking the nice tick > marks.  They should be approximately evenly spaced, but at nice round values > of the original variable:  that's hard to do in general.  R has the pretty() > function for the linear scale, and doesn't do too badly on log a

Re: [R] quick square root axes

On 5 May 2009, at 19:28, Duncan Murdoch wrote: On 5/5/2009 1:05 PM, Markus Loecher wrote: Dear R users, while I enjoy the built-in log argument to the plot() function, I wished it would be as easy to create more general custom transformed axes such as sqrt(), logit, etc... for example, i

Re: [R] Heatmap without levelplot

Antje wrote: Hi Uwe, I tried to explain my problem with the given example. I don't see any documentation which tells me that the length of "col.regions" should be one less than "at". (At least I assume now that it should be this way...) If it's equal or longer some colors (in the middle of t

Re: [R] quick square root axes

On 5/5/2009 1:05 PM, Markus Loecher wrote: Dear R users, while I enjoy the built-in log argument to the plot() function, I wished it would be as easy to create more general custom transformed axes such as sqrt(), logit, etc... for example, instead of plot(x=exp(rnorm(10)), y=(1:10)^4, log = "xy

Re: [R] Sampling a matrix with different probability distributions

Greg Snow-2 wrote: > > The sample function has a prob argument that can be used to sample with > unequal probabilities. It sounds like you can just pass in the species > abundance vector to prob and it will do what you want. > > It might be that my question is even more basic than it sounds:

[R] big databases

Dear all, I have a .dta database which is about 400 MB. I cannot open it though I have no problem to import smaller ones (80 MB or even 174 MB). I tried to modify some options with --max-mem-size=2047M --max-vsize=2047M. But it does not seem to be enough. I do not know the exact meaning of these

[R] quick square root axes

Dear R users, while I enjoy the built-in log argument to the plot() function, I wished it would be as easy to create more general custom transformed axes such as sqrt(), logit, etc... for example, instead of plot(x=exp(rnorm(10)), y=(1:10)^4, log = "xy"), sth. along the lines of plot(x=exp(rnorm

Re: [R] Sampling a matrix with different probability distributions

The sample function has a prob argument that can be used to sample with unequal probabilities. It sounds like you can just pass in the species abundance vector to prob and it will do what you want. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail

Re: [R] Hierarchical Diagram of Networks in sna or otherwise?

No worries. I've actually switched to using Rgraphviz from bioconductor, and the results are pretty great (after the initial head-pounding to get it setup). Gábor Csárdi-2 wrote: > > On Mon, May 4, 2009 at 8:31 PM, jebyrnes wrote: >> >> Nearly.  The algorithm turns up slightly different graph

Re: [R] setting trellis auto.key color values

Sundar, Thanks for the assistance. Much appreciated. Steve Steve Friedman Ph. D. Spatial Statistical Analyst Everglades and Dry Tortugas National Park 950 N Krome Ave (3rd Floor) Homestead, Florida 33034 steve_fried...@nps.gov Office (305) 224 - 4282 Fax (305) 224 - 4147

Re: [R] Plotting pairs of bars

Look at the beside argument to the barplot function. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- > project.org] On Behalf Of Steve Mu

Re: [R] Stepwise logistic regression with significance testing - stepAIC

Greg Snow wrote: There is not a meaningful alternative way since the way you propose is not meaningful. The Wald tests have some know problems even in the well defined cases. Both types of tests are designed to test a predefined hypothesis, not a conditional hypothesis on the stepwise procedure.

Re: [R] smoothing spline in package gam

Strangely, summary.gam(m1) should give you significance results of parametric terms such as ost, wst, park10, sch50, comm, build and suite. These results should be located above the summary results for smooth terms. Please using summary.gam(m1) to have a look if there is the information you need.

[R] method for calculating grey level occurrence matrices (GLCM) with R

hello, does anybody know a method for calculating grey-level co-occurrence matrices (GLCM) for RGB-pictures with R? (unfortunately i haven't found a solution for this problem neither via (scholar)google nor via r-project helplist) thank you very much! best regards Hans-Joachim Klemmt -- --

[R] Re : Re : Support Vector Machines

Of course SVM is for supervise learning method (classification or regression). You cannot use a boat to fly man !   Justin BEM BP 1917 Yaoundé Tél (237) 99597295 (237) 22040246 Envoyé le : Mardi, 5 Mai 2009, 16h07mn 10s Objet : Re : [R] Support Vector Machin

Re: [R] Stepwise logistic regression with significance testing - stepAIC

There is not a meaningful alternative way since the way you propose is not meaningful. The Wald tests have some know problems even in the well defined cases. Both types of tests are designed to test a predefined hypothesis, not a conditional hypothesis on the stepwise procedure. It is best to

[R] A question about using “by” in GAM model fitting of interaction between smooth terms and factor

I am a little bit confusing about the following help message on how to fit a GAM model with interaction between factor and smooth terms from http://rss.acs.unt.edu/Rdoc/library/mgcv/html/gam.models.html: “Sometimes models of the form: E(y)=b0+f(x)z need to be estimated (where f is a smooth functi

[R] how to modify a function in a R package calling other (invisible?) functions

Hey hey kids! I'm facing this rough problem: I have to modify a function in a R package (namely, homals) but I'm not able to do it from the R interface, since this function recalls other functions which looks like invisible... I downloaded the source package from CRAN, http://cran.r-project.org/sr

Re: [R] Heatmap without levelplot

The image function in base graphics does the same type of plot, just different names and structure of the data (and the documentation says that the number of breaks should be 1 more than the number of colors). Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermounta

Re: [R] Create Pie chart from .csv file

Sorry for mailing to you personally... for types read.csv(file.choose()) freqTable = table(types) pie(freqTable) ##example for some data temp = data.frame(types = 1:10) pie(table(temp)) Thomas Roth PS: use barplot instead of pie DonkeyRhubarb schrieb: Hi all, I am looking to create a pie

Re: [R] setting trellis auto.key color values

Set the colors in graph.sets and not auto.key. graph.sets <- list(axis.text = list(cex = 0.65), par.ylab.text = list(cex = 1.25), par.xlab.text = list(cex = 1.25), superpose.polygon = list(col = 3:5)) Then remove the "col = 3:5" from auto.key and barchart

Re: [R] levelplot question

The function that is doing the color assignments is level.colors in the lattice package. Looking at the code confirms that the number of colors should be 1 less than the length of the at variable (the documentation implies that it should be 1 more, looks like a documentation bug to me). It is

[R] Sampling a matrix with different probability distributions

I need to sample a matrix according to different distributions, instead of just randomly. Here is some code that will hopefully clarify what I need: I have a matrix M of 1287 interactions between species in rows and species in columns, according to their abundance: pla<- c(10, 9, 6, 5, 3) #abun

[R] Plotting pairs of bars

Dear all, I have a matrix called combine86 which looks as follows: > combine86 Sim Mean Obs Mean Sim Sum Obs Sum AMAZON 1172.0424 1394.44604 553204 659573 NILE 262.4440 164.23921 67973 41881 CONGO682.8007 722.63971 205523 214624 MISSISSIPPI 363.

[R] setting trellis auto.key color values

I'm working with Lattice graphics and I would like very much to color code the auto.key fill color with the same corresponding colors that I use in the panels. I've looked on the web for clues, and on the CRAN-R help sites searching on "trellis auto.key color" and variations, unfortunately the r

[R] Bristol mirror GPG problem ubuntu repository

Hello, I am getting a GPG error with the ubuntu repository at the bristol UK mirror. When my source.list has this line: deb http://www.stats.bris.ac.uk/R/bin/linux/ubuntu/ intrepid/ On an "apt-get update" you get this: W: GPG error: http://www.stats.bris.ac.uk intrepid/ Release: The following

Re: [R] Cox Proportional Hazard with missing covariate data

(1) Makes sense. Another approach is to use the time since study entry and include the age of the part in the model. A related discussion here: http://tolstoy.newcastle.edu.au/R/e2/help/07/02/9831.html (2) It is left-truncation. A part is observed only if it has survived until study entry. Of co

Re: [R] FOURIER INTEGRALS IN R

Your integrand is smooth. What are the limits of integration: 0 to 1 or 0 to infinity? Main challenge is that it is increasingly oscillatory as x and/or t increase. You can find the zeros of the cosine function and add up the integrals between successive zeros. In what context does this intteg

[R] Stepwise logistic regression with significance testing - stepAIC

Hello R-Users,   I have one binary dependent variable and a set of independent variables (glm(formula,…,family=”binomial”) ) and I am using the function stepAIC (“MASS”) for choosing an optimal model. However I am not sure if stepAIC considers significance properties like Likelihood r

[R] Re : Support Vector Machines

there is a SVM function in svmpath by Trevor Hastie. Before use it take time to read this http://www-stat.stanford.edu/~hastie/Papers/svmpath.pdf If you install then svmpath library ! run the attach source file. Justin BEM BP 1917 Yaoundé Tél (237) 99597295 (237) 22040246 ___

[R] Stepwise logistic Regression with significance testing - stepAIC

Hello R-Users,   I have one binary dependent variable and a set of independent variables (glm(formula,…,family=”binomial”) ) and I am using the function stepAIC (“MASS”) for choosing an optimal model. However I am not sure if stepAIC considers significance properties like Likelihood r

Re: [R] FOURIER INTEGRALS IN R

Ok thanks.. No, my function is not smooth. Actually, I am dealing with an integral having the following form, for example: \int cos(tx) (1-t^2)^3 \exp(0.5*t^2) dt I want to estimate this Fourier Cosine integral for a given value of x. Thanks for the help. AA On Tue, May 5, 2009 2:34 am,

[R] Stepwise logistic regression with significance testing - stepAIC

Hello R-Users,   I have one binary dependent variable and a set of independent variables (glm(formula,…,family=”binomial”) ) and I am using the function stepAIC (“MASS”) for choosing an optimal model. However I am not sure if stepAIC considers significance properties like Likelihood r

Re: [R] Create Pie chart from .csv file

> I am looking to create a pie chart from a given column in a .csv file. > > My class variables are as follows: > > entry_type, uniquekey, types, title,url, abstract, journal, > author, month, > year, howpublished > > So say I want to export a pie chart that groups together all entrie

Re: [R] calibration plot

I believe something like: scatter.smooth(est.prob, as.numeric(y == "level of interest")) would be close. You may want to use a larger span than default. Andy From: abbas tavassoli > > Hi, > I have a binary variable and corresponding predicted > probability (using > logistic regression on

Re: [R] calibration plot

Dear Abbas, Take a look at the results of require(Hmisc) require(Design) apropos("calibrate") ?calibrate ?plot.calibrate HTH, Jorge On Tue, May 5, 2009 at 9:41 AM, abbas tavassoli wrote: > Hi, > I have a binary variable and corresponding predicted probability (using > logistic regression on s

Re: [R] Heatmap without levelplot

Hi Uwe, I tried to explain my problem with the given example. I don't see any documentation which tells me that the length of "col.regions" should be one less than "at". (At least I assume now that it should be this way...) If it's equal or longer some colors (in the middle of the color-vector)

[R] View cluster results of large data sets

Hi all, I am trying to run a cluster analysis with a relatively large data set (545 samples) and obviously am having trouble viewing the results using standard plot() method. Is there a way to plot the results of a large cluster analysis in a window with a scroll bar. Any recommendations would b

[R] text mining in italian

Hello everybody, I'm trying to do text mining on a serie of texts in italian. I would like to know if it is possible to find the italian synonyms and/or if something like WordNet database for English exists also for italian. Thank you very much in advance. Regards, Laura _

[R] ERPs analysis

Good morning to Everyone, I'm an Italian PhD student that is working on ERPs experiment (cognitive psychology) and I would like to know if there are R packages for this kind of analysis. I'm using BrainAmp to record the data and this program gives me t

[R] calibration plot

Hi, I have a binary variable and corresponding predicted probability (using logistic regression on some explanatoey variables); I want to check that the model is well-calibrated using a calibration plot. how can I have the calibration plot for my data? thanks. [[alternative HTM

Re: [R] Support Vector Machines

I see that index is giving me the group for the classification problem. But my problem is not the same. I had a sample X<-rnorm(1000) for example. I don't want to make classification (i have only one group in fact) but i want to estimate the density which generates my sample (like i can do with

[R] Find cyclically identical binary sequences (corrected)

Dear R-helpers, I need to generate all the binary sequences of length n (here n = 8) that start with 1 and have no fewer than two of each digit, and are not cyclic permutations of each other. Here is what I have done: len <- 8 df <- as.data.frame(numeric(2^(len - 1)) %o% numeric(len)) require(wl

Re: [R] problem with rgl package

(off list) On 5 May 2009 at 05:15, Erin Hodgess wrote: | I also needed libglu1-mesa-dev, but now all is well. a) You still haven't explained why you need to rebuild it when sudo apt-get install r-cran-rgl gets you a binary b) Yes, as sudo apt-get build-dep r-cran-rgl wo

Re: [R] Cox Proportional Hazard with missing covariate data

Hi, In fact, you have left-truncated observations. What timescale do you use, time 0 is the study entry, or when the wear-part has been used for the first time? If it is the latter, you can specify the "age" of the wear part at study entry in Surv(). For example, if a wear part has been used fo

Re: [R] Cox Proportional Hazard with missing covariate data

Hi, Arthur, thanks a lot for your super-fast reply! In fact I am using the time when the part has been used for the first time, so your example should work in my case. Moreover, as I have time-variant covariates, the example should look like this in my specific case: start stopstatus te

Re: [R] Create Pie chart from .csv file

Hi, I used ggplot2 for plotting recently, you should give it a try - it's excellent. http://had.co.nz/ggplot2/ All the best Philipp DonkeyRhubarb wrote: > Hi all, > > I am looking to create a pie chart from a given column in a .csv file. > > My class variables are as follows: > > entry_type

Re: [R] Create Pie chart from .csv file

You could go to rseek.org and search for pie chart; that will give you lots of ideas and examples, including discussion of why pie charts are a bad idea. Sarah On Tue, May 5, 2009 at 9:02 AM, DonkeyRhubarb wrote: > > Hi all, > > I am looking to create a pie chart from a given column in a .csv fi

Re: [R] problem with rgl package

I also needed libglu1-mesa-dev, but now all is well. thanks for the help! Sincerely, Erin On Tue, May 5, 2009 at 5:07 AM, Barry Rowlingson wrote: > On Tue, May 5, 2009 at 10:55 AM, Erin Hodgess wrote: >> Dear R People: >> >> Here is something strange.  I'm using Ubuntu 9.04 with R 2.9.0. >> >>

Re: [R] JGR

The point is that one Cpu stays at 100% for all time JGR is up. Any ideas? Andrea Uwe Ligges wrote: r...@quantide.com wrote: Dear R User I am using JGR on a Linux Ubuntu Computer with 2 Cpus When Opening JGR, one Cpu goes up to 100% even if no calculation is yet started Did any of you alrea

[R] Create Pie chart from .csv file

Hi all, I am looking to create a pie chart from a given column in a .csv file. My class variables are as follows: entry_type, uniquekey, types, title,url, abstract, journal, author, month, year, howpublished So say I want to export a pie chart that groups together all entries u

Re: [R] Can't build termstrc package from source

Thanks, Uwe. I've managed to get it done with R CMD BUILD -binary. 2009/5/5 Uwe Ligges > I guess you asked R to: > > R CMD build ... > > which builds the source package, but you need > > R CMD INSTALL ... > > in order to install the package or > > R CMD INSTALL --build ... > > in order to i

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