similar to: command option for R CMD BATCH

Hi All, Another newbie question. I want to write an R script that takes argument from command line and runs and produces output to stdin. For example if there is file foo.R with following in it. args = commandArgs() print(args) then, when I run it like $ R foo.R hello it should print 'hello' on the terminal. I searched the mainling list and found a very old post that said said that

I got Rmpi to compile with little difficulty, but had a tricky time setting the LD_LIBRARY_PATH to use the OpenMPI libs. I now get a different error when I try to load Rmpi > require(Rmpi) Loading required package: Rmpi librdmacm: couldn't read ABI version. librdmacm: assuming: 4 libibverbs: Fatal: couldn't read uverbs ABI version. CMA: unable to open

I'm attempting to modify how biplot draws its red vectors (among other things). This is how I've started: Biplot <- function(xx, comps = c(1, 2), cex = c(.6, .4)) { ## Purpose: Makes a biplot with princomp() object to not show arrows ## ---------------------------------------------------------------------- ## Arguments: xx is an object made using princomp() ##

> version _ platform x86_64-unknown-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 2.1 year 2005 month 12 day 20 svn rev

I wish to set up a simple function using boxplot so that it will be available to someone using R for Windows. (I myself use Linux.) The way the data is organised makes it convenient to use the boxplot function in a manner similar to this example given in the help. > mat <- cbind(Uni05 = (1:100)/21, Norm = rnorm(100), + T5 = rt(100, df = 5), Gam2 = rgamma(100, shape

Dear R experts: I am a bit stymied by how the argument picking-off works in R batch file usage. $ cat commandArgs.R cat(" Command Line Arguments were ", commandArgs(), "\n"); $ /usr/bin/R CMD BATCH commandArgs.R --args 1 2 3 $ /usr/bin/R --args 1 CMD BATCH commandArgs.R ... I am now getting into interactive mode ?! I guess it really is skipping the rest of the command line

Is there a way to append to the outfile when using R CMD BATCH? My code, right now, is: R CMD BATCH --slave --vanilla '--args place .2 -.1 .9 .6' StratificationSimulation example.output Everything else is working the way I'd like it. The first few lines of code of my script file are: options(echo=FALSE) cmd_args = commandArgs() print (cmd_args) #d <-

Hello and sorry to bother. Please help. I searched the archives but could not find out why --args is being ignored on Windows 2000. I try R CMD BATCH --slave 11.R 11.Rout --args "12" and 11.R has x=commandArgs(trail=T) print(x) a=x[length(x)] write.csv(a,file="13.out") q("no") the argument is not passed to the R process. 11.Rout only shows processing time and

Hello, I'm actually trying to fit a gee model with 2 nesting levels since I expect a correlation between all members of a litter at a first level and between all individuals sharing a mother at a second superior level with an exchangeable matrix. I order my dataframe by both mother and litter I try several syntaxes: id= mother*litter which give the same correlation matrix as id=

Windows 2000 (v.5.00.2195), R 1.5.1 I have an lme object, fm0, which I examine with anova() and intervals(). The anova output indicates one of the interaction terms is significant, but the intervals output shows that the single parameter for that term includes 0.0 in its 95% CI. I believe that the anova is a conditional (sequential) test; is intervals marginal or approximate? Which should I

Dear List, Can anyone please explain the difference between cluster() and frailty() in a coxph? I am a bit puzzled about it. Would appreciate any useful reference or direction. cheers, Ehsan > marginal.model <- coxph(Surv(time, status) ~ rx + cluster(litter), rats) > frailty.model <- coxph(Surv(time, status) ~ rx + frailty(litter), rats) > marginal.model Call: coxph(formula =

Hello useRs, I`m running structural equation models with R, but for one of my models the below error message apears. I`m trying to change startvalues but without success. The manual for sem package did not help me. Does anyone knows how to change startvalues for iteration in sem package? Or it can be another problem with the model? Error in startvalues(S, ram, debug = debug, tol = start.tol)

Hi all, I need to run a program (asreml) thousands of times and each time I have to provide a slightly different dataset. Because I have to run asreml under Windows (DOS or scripts) environment, I have trouble to pass a command variable (or pointer variable or %counter in the following example) to R program so at each counter R can generate a different data set for asreml to run. Any

Using R v. 1.7.0 on Windows 2000 I would like to plot the fitted values of a model as a function of a continuous covariate, augmented with data (e.g., augPred) grouping by combinations of fixed effects. I have not been able to use augPred effectively, and am wondering if it does not handle unbalanced data (3 out of 192 missing). I include below the model and an xyplot that almost does the

Suppose I have a small dataframe > aa Target Eaten ID 50 TPP 0 1 51 TPP 1 2 52 TPP 3 3 53 TPP 1 4 54 TPP 2 5 50.1 GPA 9 1 51.1 GPA 11 2 52.1 GPA 8 3 53.1 GPA 8 4 54.1 GPA 10 5 And I want to reshape it into ID TPP GPA 1 1 0 9 2 2 1 11 3 3 3 8 4 4 1 8 5 5 2 10 I realise that

I can use the gutenberg_download() function in the gutenbergr package on a computer that doeson't use a firewall, but on an almost identical installation that is behind a firewall, nothing happens, not even a time-out. Has anyone succeeded in using gutenberg_download() successfully with a firewall? I tried raising an issue at https://github.com/ropenscilabs/gutenbergr/issues/17 with no

Or, to avoid accusing you of lying. what you think is "vanilla" probably isn't. What exactly did you do? On Unix-likes, I would do something like this echo 'options(repos=list(CRAN="cran.r-project.org"));install.packages("Rcpp")' | R --vanilla (or maybe https://cloud.r-project.org is better...) -pd > On 2 Feb 2018, at 08:15 , Jeff Newmiller

I'm still having trouble installing the lme4 package on RHEL 3. I've asked this list and it seems my problem is not universal. Brian Ripley indicated that the problem was with recognising the Matrix package, even though I've taken care to get the most recent versions of Matrix and lme4. It seems to me that the problem arises because the computer has a site installation of R-2.3.1

I'm still having trouble installing the lme4 package on RHEL 3. I've asked this list and it seems my problem is not universal. Brian Ripley indicated that the problem was with recognising the Matrix package, even though I've taken care to get the most recent versions of Matrix and lme4. It seems to me that the problem arises because the computer has a site installation of R-2.3.1

When i tried to install the hunspell package, I got this error message: Error: package ?Rcpp? 0.12.3 was found, but >= 0.12.12 is required by ?hunspell? So I set about installing a new version of Rcpp but I get this message: Error in unloadNamespace(pkg_name) : namespace ?Rcpp? is imported by ?dplyr? so cannot be unloaded How does one get around that? I tried installing Rcpp in a