similar to: Reproducible Research task view

Everyone, I've got code in my package that uses LogitBoost from the caTools package. caTools does not have a namespace. My package also uses loads RWeka, which has a namespace, and also has a function called LogitBoost. After loading both packages, how can I be specific about running the version from caTools (since caTools:::LogitBoost won't work)? Thanks, Max

I was trying to produced bagged importance estimates of attributes in earth using the caret package with the following commands:   fit2 <- bagEarth(loyalty ~ ., data=model1, B = 10)   bagImpGCV <- varImp(fit2,value="gcv") My bootstrap estimates are produced however the second command "varImp" produces the following error:    Error in UseMethod("varImp") : no

I've had a lot of requests for additions to the reproducible research task view that fall into a grey area (to me at least). For example, roxygen2 is a tool that broadly enable reproducibility but I see it more as a tool for better programming. I'm about to check in a new version of the task view that includes packrat and checkpoint, as they seem closer to reproducible research, but also

The CRAN policy page (https://cran.r-project.org/web/packages/policies.html) implies that there is a formal procedure for orphaning a package but none is mentioned in the Extensions manual (https://cran.r-project.org/doc/manuals/r-devel/R-exts.html). This page (https://cran.r-project.org/src/contrib/Orphaned/README) implies that one would simply resubmit the package to CRAN with the text

Dear all, i searched for some classification methods and I have no glue if i took the right once. My problem: I have a matrix with 17000 rows and 33 colums (genes and patients). The patients are grouped into 3 diseases. No I want to classify the patients and for sure i want to know which rows are more helpful for the classification than others. I tried SVM and random forest. Do you think this

Everyone, I'm working with scatter plots with different colored symbols (via lattice). I'm currently using these colors for points and lines: col1 <- c(rgb(1, 0, 0), rgb(0, 0, 1), rgb(0, 1, 0), rgb(0.55482458, 0.40350876, 0.04166666), rgb(0, 0, 0)) plot(seq(along = col1), pch = 16, col = col1, cex = 1.5) I'm also using these with transparency (alpha

Hello All, Have recently started learning Sweave and Knitr. Am now trying to learn odfWeave as well. Things went pretty smoothly with Sweave and Knitr but I'm having some trouble with odfWeave. My understanding was that odfWeave should work in pretty much the same way as Sweave. With odfWeave, you set up an input .odt file in a folder, run that file through the odfWeave function, and then

I've noticed a change in the way grep() behaves between the 1.9.0 release and a recent R-patched. On 1.9.0 I get the following output: > x <- dget(file = url("http://www.biostat.jhsph.edu/~rpeng/names.R")) > length(grep("^l\\w+tmean", x, perl = TRUE, value = TRUE)) [1] 84 And on R-patched (2004-06-11) I get > x <- dget(file =

Hi, I am having problems passing arguments to method="gbm" using the train() function. I would like to train gbm using the laplace distribution or the quantile distribution. here is the code I used and the error: gbm.test <- train(x.enet, y.matrix[,7], method="gbm", distribution=list(name="quantile",alpha=0.5), verbose=FALSE,

cut.Date and cut.POSIXt indicate that the breaks argument can be an integer followed by a space followed by "year", etc. but it seems the integer is ignored. For example, I assume that breaks = "3 months" is supposed to cut it into quarters but, in fact, it cuts it into months as if 3 had not been there. > d <- seq(Sys.Date(), length = 12, by = "month") >

Are the functions 'R_Unserialize' and 'R_InitFileInPStream' allowed to be used in R packages? I guess I'm just not clear on the implications of this comment in 'Rinternals.h': /* The connection interface is not yet available to packages. To allow limited use of connection pointers this defines the opaque pointer type. */ I have a function in the

Dear All, I am far from being a guru about parallel programming. Most of the time, I rely or randomForest for data mining large datasets. I would like to give a try also to the gradient boosted methods in GBM, but I have a need for parallelization. I normally rely on gbm.fit for speed reasons, and I usually call it this way gbm_model <- gbm.fit(trainRF,prices_train, offset = NULL, misc =

Hello, I am looking for a good and detailed documentation about Sweave... but can't find anything more that 15 pages asking Google... Any hint on that point ? Cheers Colin -- View this message in context: http://r.789695.n4.nabble.com/Good-documentation-about-Sweave-tp2714326p2714326.html Sent from the R help mailing list archive at Nabble.com.

Dear All, Having now successfully started using Sweave, I have just noticed an odd side effect with fonts. Using plain LaTeX, I have had no problems using \usepackage{palatino} or \usepackage{times} and the font correctly changes. However, once I convert the tex document into Snw, and run it through R CMD SWEAVE, LaTeX seems to ignore this package directive. The LaTeX log suggests the font

Since compiling R 2.5.0 from source on my Mac (PowerBook) I've noticed some strange behavior when plotting. I'm not sure if it's a problem with my setup/compilation because I feel like a problem as basic as this one would have been reported already. I'm running R with X11 and R was built with gcc 4.0.1. Basically, I run > plot(0, 0) > dev.off() X11 4 Warning message:

I have modified the parameters for a function (for my own use) in the stats package, but I assume I need to update the parameter set in another file as I'm getting the following error when I run R: The compile works fine so I assume there is a configuration file in the base package of R that needs modification. Error in parse(file, n, text, prompt) : syntax error on line 11102 Error:

I have written a function to plot data which will be used for various different chemistries. A simplified version is: plot_data <- function(risk,levels,chem,sd2,measure){ plot(risk, levels,main=paste ("per", sd2, measure, "\n in usual", chem)) } The problem is with the title. This works fine if the variable "chem" is just text, but if it is an expression then

All, Does anyone know if there is an option I can set to turn screen-buffered output on and off with the win32 rgui? (Apart from the point and click method). I am running some simulations where it is useful to watch output but it gets mildly tiresome having to manually switch things on and off via the gui. Thanks Toby. > version _ platform i386-pc-mingw32 arch

Greetings, I have been exploring the use of the caret package to conduct some plsda modeling. Previously, I have come across methods that result in a R2 and Q2 for the model. Using the 'iris' data set, I wanted to see if I could accomplish this with the caret package. I use the following code: library(caret) data(iris) #needed to convert to numeric in order to do regression #I

Hello list, despite I already posted a mail on this topic on R help, I guess this place may be more appropriate. I'll make it shorter this time. Sorry for posting twice. I found that using pixmap pictures in a Sweave document was sometimes almost impossible, due to the huge size of the pdf pictures produced. The first solution I found was to save pictures in png, when too heavy in pdf.