similar to: RFC: "R::Wrapper" perl module

Hi, In support of reproducible research at my Institute, I seek an approach to re-creating the R environments in which an analysis has been conducted. By which I mean, the exact version of R and the exact version of all packages used in a particular R session. I am seeking comments/criticism of this as a goal, and of the following outline of an approach: === When all the steps to an workflow

There are numerous tools like scons, make, ruffus, ant, rake, etc. that can be used to build complex pipelines based on task dependencies. These tools are written in a variety of languages, but I have not seen such a thing for R. Is anyone aware of a package available? The goal is to be able to develop robust bioinformatic pipelines driven by scripts written in R. Thanks, Sean

I've posted a message twice to this list, and never seen it appear yet ... perhaps this one will go through ... ? -- Aaron J. Mackey, Ph.D. Dept. of Biology, Goddard 212 University of Pennsylvania email: amackey at pcbi.upenn.edu 415 S. University Avenue office: 215-898-1205 Philadelphia, PA 19104-6017 fax: 215-746-6697

Hello, I'm trying to write a function using tcltk to interactively modify a plot and gather locator() data. I've read Peter's articles in Rnews, the help pages in tcltk, http://bioinf.wehi.edu.au/~wettenhall/RTclTkExamples/, plus a post in R-help sometime ago, but haven't found a solution. The idea goes something like this: require(tcltk) testplot <- function() { getcoords

I have a 47k x 47k adjacency matrix that is very sparse (at most 30 entries per row); my textual representation therefore is simply an adjacency list of connections between nodes for each row, e.g. node connections A B C D E B A C D C A E D A E A F F E G H I'd like to import this into a dataframe of node/connection (character/vector-of-characters) pairs. I've experimented with

Dear R-users, I am developing a plotting function, which receives expressions and character/numerical vectors as part of the many input arguments and which tries to concatenate them before displaying the result to the plot. I currently cannot find a way to make this concatenation works. I have read several posts in the list that solved this problem by pasting the different elements together

Dear R-users, I am preparing graphs for an upcoming article using the different functions of the ggplot2 package and I've been having problems with the legend background. It doesn't seem to scale when the text size is increased. Here's the mandatory reproducible example: library(ggplot2) repFrame <- data.frame(A= 1:10, B= rnorm(1:10), groupNum = rep(c("First group",

I am trying to use computer modern fonts in postscript files for a latex document. Ultimately I want to automate this through sweave. I've read the documentation ans have tried the following code to use lattice to produce a graph using computer modern: library(lattice) library(grid) testPlot=( xyplot(seq(1:10) ~ seq(1:10), main="one to ten",

I am looking for a way to save a plot (graphics contents) to a file after the plot has been calculated but before it has been rendered. More specifically, assume that I made a plot that took a very long time to produce, I would like to save this plot to a generic file that I can later, on a different machine, render to either PDF, PNG, SVG using the usual R graphics devices, without recalculating

I am looking for a way to save a plot (graphics contents) to a file after the plot has been calculated but before it has been rendered. More specifically, assume that I made a plot that took a very long time to produce, I would like to save this plot to a generic file that I can later, on a different machine, render to either PDF, PNG, SVG using the usual R graphics devices, without recalculating

Hello, I am an absolutely beginner with regards to R, so forgive me for my potentially very stupid questions. I have been attempting to create recurrence plots using R. The data I am using is based on a mutually exclusive and exhaustive coding scheme with over 40 individual codes which can be assigned to 6 higher order categories. When I carry out the usual rqa command, my plot is pretty much

Is there anyway I can write a script which feed input datasource from stdin and let R process it (maybe frequency report) then output the report to stdout? I can't seem to find much info on documentation or FAQ on this topic. Thanks! Soichi Hayashi ********************************************************************** The information contained in this communication is confidential,

Happy New Year to all R users! I have two short questions concerning a xyplot with a color key: 1) How do I properly place (align) the color key beside the xyplot? As you can see from the code listed below, the placement of the color key is not correct. I would like the upper and lower end point of the color key to be perfectly aligned with the upper and lower line of the xyplot. Adjusting

Hello: I have problems generating big JPG plots in functions. the following code runs fine in the script: #### runs fine in script, generate 40k "test1.jpg" in the given directory plotPlatesAlong <- c(1:5) plotDirPath <- paste(dataPath, "OutputPlots\\", sep="") filename <- paste(plotDirPath,"test1.jpg", sep="") jpeg(file=filename)

I'm haveing trouble connecting an Ericsson Webswitch 100 to asterisk. Has anyone gotten a Webswitch running? When I try to connect asterisk thinks everything works fine, while the webswitch just rings. I belive chan_h323 is picking the wrong port to talk at the webswitch on, however I'm not sure, nor am I sure how to fix it. Any clues/hints? A tcpdump is attached to show the session.

For teaching purposes, I prepared a little R program. I want to give this to students who can run it and dump out many formats and then compare their use in LaTeX documents. I do not have too much trouble with xfig or postscript format, but I've really run into a roadblock where png files are concerned. My original problem was that the png device does not accept a family option. How can I

Dear list. I am preparing a R package, and the last step is to write a package vignette using Sweave. However, I am experiencing some trouble when trying to include plots in my Sweave document. That is, in my package I have made some plotting functions in which I start by calling 'new.dev()' to start a graphics device of a certain width and height, and then proceed with plot(). These

Ian No differences with Adobe X with the following windows(6,6) #pdf(file = "TestPlot.pdf", 6, 6) #{ plot(b, l, type = "l", ylim = c(y.min, y.max), lwd = 2, xlab = expression(beta), ylab = "", col = "green", yaxt = "n", xaxt = "n") points(b, p, type = "l", lty = "dotted", lwd = 2, col = "red") points(b,

I just thought that I would put this out there and see if anyone else sees this problem with Samba 1.9.18p4 (under Solaris 2.6). It appears that after some reboots of Solaris, Samba printing is partly dead. What I see in the logs are below, and what happens is that the file to be printed is spooled to /var/spool/samba, like always, but when the lpr command is issued it croaks. I've been

Hi, Iwrote 'pdfc' in analogy to 'lpr': pdfc <- function (file = "Rplot.pdf") { current.device <- dev.cur() dev.off(dev.copy(device = pdf, file = file, ...)) dev.set(current.device) print(paste(file, "generated.")) } lpr <- function (object, file = "Rplotlpr.ps", ...) { if (missing(object)) { current.device <-