similar to: stepAIC and coxph objects with cluster(id)

Dear All, With a colleague we are writing a paper where we show how R is a very nice tool to deal with some issues in the analyses of data in evolutionary biology. For the intro, I wonder if 1) Anybody has any rough idea of how many people might be using R or how many people have downloaded R, or similar (I am aware answering this question might require divinatory powers...). 2) Have/are any

Dear All, In the title of a plot, I would like to mix greek letters with numbers, where the numbers are obtained from a particular function to a vector (e.g., max(x)); in each call, the value of this vector can change. Without greek symbols I use something like: title(sub=paste("x1=", deparse(x[1]),"beta = ",deparse(max(x)), "rho = ", deparse(min(x)))) but I'd

Dear All, When generating pdf documentation for a package (using R CMD Rd2dvi --pdf), is there a way to get the date to use the typical international standard of day month year instead of the US one of month day, year? Thanks, Ramon -- Ramón Díaz-Uriarte Dept. Zoology and Statistics University of Wisconsin-Madison Madison, WI 53706-1381 email: rdiazuri at students.wisc.edu (NOTE: starting

Dear All, The help for prcomp, under "Value" says: sdev: the standard deviation of the principal components (i.e., the eigenvalues of the cov matrix, though the calculation is actually done with the singular values of the data matrix). The way I read it, it implies that the sdev are the eigenvalues, but I think that sdev is actually the square root of the

Hi, I am new to Linux. I recently installed R (0.64.1 using rpm for Red Hat 6.0); then I installed several libraries. When following the steps in VR complements to R, everything worked fine but I got the following messages (this happened for every single one of the libraries installed): make: *** Warning: File /usr/lib/R/etc/Makeconf' has modification time in the future

I noticed this error in my demo from previous versions as well as R 0.99.0. Is there a way around this one also? Thanks in advance... > demo(dyn.load) demo(dyn.load) ---- ~~~~~~~~ Type <Return> to start : > dyn.load(file.path(R.home(), "demos", "dynload", paste("zero", .Platform$dynlib.ext, sep = ""))) Error in

Dear All, For logistic regression models: is it possible to use validate (rms package) to compute bias-corrected AUC, but have variable selection with AIC use step (or stepAIC, from MASS), instead of fastbw? More details: I've been using the validate function (in the rms package, by Frank Harrell) to obtain, among other things, bootstrap bias-corrected estimates of the AUC, when variable

Hello, My question concerns model selection, stepAIC(), add1(), and coxph(). In Venables and Ripley (3rd Ed) pp389-390 there is an example of using stepAIC() for the automated selection of a coxph model for VA lung cancer data. A statistics question: Can partial likelihoods be interpreted in the same manner as likelihoods with respect to information based criterion and likelihood ratio tests?

Hi, i'm trying to apply StepAIC with coxph...but i have the same error: stepAIC(fitBMT) Start: AIC=327.77 Surv(TEMPO,morto==1) ˜ VOD + SESSO + ETA + ........ Error in dropterm.default(fit,scope$drop, scale=scale,trace=max(0, : number of rows in use has changed: remove missing values? anybody know this error?? Thanks. Michele [[alternative HTML version deleted]]

Hi, I'm having a bit of trouble with using StepAIC with a coxph model. Can anybody tell me if there is anything wrong with what I am doing here (I've removed a few of the variables for the purpose of this email, I had about 20 before): start<- coxph(Surv(entryage2,age_at_death_yr,death)~finih5+prev+magegp+zpluralgp ,data=project_model1) fmAIC1 <-

Dear R-Help, I am trying to perform forward selection on the following coxph model: >my.bpfs <- Surv(bcox$pfsdays, bcox$pfscensor) > b.cox <- coxph(my.bpfs ~ Cbase + Abase + Cbave + CbSD + KPS + gender + as.factor(eor) + Age)>stepAIC(b.cox, scope=list(upper =~ Cbase + Abase + Cbave + CbSD + KPS + gender + as.factor(eor) + Age, lower=~1), direction= c("forward")) However

On Wed, 30-12-2015, at 12:44, Dirk Eddelbuettel <edd at debian.org> wrote: > On 30 December 2015 at 05:00, Dario Strbenac wrote: > | Good day, > | > | In section A.2, the manual advises "Linux users will want the urw-fonts package". However, this package only seems to be available for RedHat Linux and Fedora Linux. What about for Debian or Ubuntu ? There is no

Dear all, I am trying to prepare some figures where I'd like the color of the plot region (i.e., the area bounded by the axes) to be different from the margin area (i.e., the area of the figure not within the axes region). I can use "bg" but that changes the background of everything? How can I accomplish what I want? Thanks, Ramon -- Ramón Díaz-Uriarte Triana 47 28016 Madrid

Dear All, I think I am confused about how I'd be able to use zlib starting with R 2.7.0. I just downloaded the latest development version, built it, etc, but I am not able to find the zlib.h that, I believe, R should place somewhere under "where/you/want/R/to/go" (from --prefix=/where/you/want/R/to/go). There seem to be entry points for zlib in the binary (e.g., grep -r gzopen ./

Dear All, I just apt-get source r-base-core and noticed that file "rules" under ./r-base-3.2.4-revised/debian contains (lines 277 to 279) --with-system-bzlib \ --with-system-pcre \ --with-system-zlib \ I wonder if these are still necessary and, in fact, when building R alpha (specifically, R-alpha_2016-03-21_r70361.tar.gz) I get a warning saying that those options are not

On Wed, 30-12-2015, at 21:08, Dirk Eddelbuettel <edd at debian.org> wrote: > On 30 December 2015 at 20:07, Ramon Diaz-Uriarte wrote: > | > | > | > | On Wed, 30-12-2015, at 12:44, Dirk Eddelbuettel <edd at debian.org> wrote: > | > On 30 December 2015 at 05:00, Dario Strbenac wrote: > | > | Good day, > | > | > | > | In section A.2, the manual

On Mon, 03-07-2017, at 12:18:36, Dirk Eddelbuettel <edd at debian.org> wrote: > On 3 July 2017 at 13:05, Ramon Diaz-Uriarte wrote: > | If I might chime in, I'd like to add my vote to the "users should be able > | to use install.packages and should be able to install bioconductor > | packages with biocLite". > | > | Longer story > | ============ > | >

On 30 December 2023 at 23:49, Ramon Diaz-Uriarte wrote: | All is good. (Just for the sake of curiosity, and if you have the time: why did you find those incantations suspicious?) Memory is fuzzy and no ECC in my wetware :) but as I seem to recall it had to do with my fears over filenames not being standardized enough / this interfering with the update-alternatives mechanism. May well have been

On Mon, 03-07-2017, at 07:58:41, Dirk Eddelbuettel <edd at debian.org> wrote: > On 2 July 2017 at 23:24, Kirill M?ller wrote: > | On 02.07.2017 22:01, Dirk Eddelbuettel wrote: > | > On 2 July 2017 at 21:39, Kirill M?ller wrote: > | > | Hi > | > | > | > | An upgrade to R 3.4.1 on Ubuntu removed the default setting of > | > | R_LIBS_USER in /etc/R/Renviron.

Dear All, Summary: ======== To test some packages, I want to build R-3.1.0 (current R devel). However, when I use the default libblas, make check fails with running code in 'reg-BLAS.R' ...make[3]: *** [reg-BLAS.Rout] Error 1 It does not fail, however, if I use libatlas3 or libopenblas. The same thing happens with the current R patched. I've google around and cannot find