similar to: Sweave, cacheSweave, and data frame

It's been a while since this thread appeared, but I had the same problem and don't want to keep the solution for myself. A small, reproducible example: <<cache=true>>= a=1 @ <<>>= a+1 @ Compiling with cacheSweave gives an error: > library(cacheSweave) Lade n?tiges Paket: filehash filehash: Simple key-value database (2.0-1 2008-12-19) Lade n?tiges Paket:

Hello all, I would like to ask several questions regarding cacheSweave: 1) Is there a way to set "cache=true" globally? (I tried it using \SweaveOpts but it didn't seem to work) 2) Is there a way to "flush" specific cache once it is created? (other then erasing the entire cache directory)? Changing the code in the code chunk seems to do it, but I am not sure to what

Dear all, When I use the cacheSweave package together with the Sweave option keep.source = TRUE, all the LaTeX code before the Sweave code chunk is included in the TeX file to be compiled. For example, with the following Sweave file \documentclass[12pt]{article} \usepackage[nogin]{Sweave} % Sweave options \SweaveOpts{keep.source=TRUE, strip.white=TRUE, eps=FALSE, pdf=TRUE} \begin{document}

Hi all, I use the excellent packages rjags and cacheSweave, and unfortunately seem to have found an incompatibility between them. Below are a minimal .Rnw file and corresponding JAGS model file which illustrate the problem: *** JAGS model file; name=j.bug *** model { mu ~ dnorm(0,1.0E-5) sigma ~ dunif(0,100) for(i in 1:length(y)) { y[i] ~ dnorm(mu,sigma) } } *** *** .Rnw

Hi there I have a problem with using Sweave in combination with the option driver = cacheSweave. Whichever code I try to run - when it comes to converting the tex file into pdf it comes up with the same errors (\csname \endcsname errors). Does anybody have an idea what it going wrong? > Sweave("pgfSweave-example.Rnw",driver = cacheSweaveDriver) Writing to file

Dear list, I wish to use a specific driver to process an sweave document in the inst/doc directory of a package. Specifically, I would like to use either cacheSweave or pgfSweave to speed up the creation of the vignette which requires lengthy computations. The same request would also apply to the highlight driver, to provide syntax highlighting of R chunks. In "writing R extensions" I

Dear list, I wish to use a specific driver to process an sweave document in the inst/doc directory of a package. Specifically, I would like to use either cacheSweave or pgfSweave to speed up the creation of the vignette which requires lengthy computations. The same request would also apply to the highlight driver, to provide syntax highlighting of R chunks. In "writing R extensions" I

Hi, I'm aware of the definition of a "valid filename" in .SweaveValidFilenameRegexp, but I think it might be better to quote the filename when it contains spaces instead of just giving a warning. This should bring us safer LaTeX code (although I never use spaces in paths). Here is the simple patch: Index: src/library/utils/R/SweaveDrivers.R

This could well be a package-specific issue, and so perhaps not for R-devel. The author of the relevant package is CC'd in any event. I'm seeing some odd behavior from Sweave with keep.source=TRUE when using driver=cacheSweaveDriver from the cacheSweave package. It would seem that code chunks with keep.source=TRUE aren't being parsed correctly; the corresponding Schunk starts at

Dear all I've just tried the brand new 'grdevice' option in Sweave but couldn't make it work. When I declare \SweaveOpts{grdevice=pdf} or \SweaveOpts{grdevice=cairo_pdf} trying to plot something simple <<fig=T, echo=T>>= plot(1:10,1:10,main='Some title') @ would result in an Sweave error: 18:16:47.299: 1 : term verbatim 18:16:47.308: 2 : echo term verbatim

Dear All, I am trying to recode a variable using the functions provided by "memisc" package. Actually I am following the examples on page 9-10 of the vignette: -------------------------------------------------------------------------- d.fig <- within(d.fig,{ sev <- recode(sev, 1 -> 0.9, 2 -> 1.0, 3 -> 1.1, 4 ->

Dear R devel, being constrained to a windows environment at work and having colleagues being accustomed to the Microsoft Office Suite, I was looking for a way to have the RweaveLatex driver for Sweave automatically generating 'win.metafile's in addition to the pdf graphics. Without this functionalilty, the generation of emf-graphics is quite laborious, I think: <<>>= plotit

Dear Sweave users, Could you help me to find a way to place Sweave output files in a subdirectory of the currentfolder without giving them a subname? If the option "prefix.string=foo/" is used, all files are placed in this folder, but begin with an hyphen-minus, which makes it difficult to work with them. If the option "prefix=FALSE" is used, then files won't be placed in

Hi all, I'm struggling a bit to get pgfSweave to lazyload objects when compiling a .Rnw file for a second time. Caching works fine except that for every run all objects get cached again and again. I've used cacheSweave which works fine; all cached objects from code-chunks with option cache = TRUE are lazy loaded. I've tried it on two machines ... I'm pretty sure I'm

Dear All, I am trying to graph a simple scatter plot where the x axis is year and the y axis is a percentage (percentage of infant death). Instead of plotting the raw data, I want to plot summary statistics such as mean and median. Here is the problem: the value range of y is between 0 and 1, but since infant death is a rare event, the mean and median is very low (something like 5%), which shows

Dear All, What is the preferred way to get Bayesian analysis results (such as those from MCMCpacki, MCMCglmm, and DPpackage) into LaTeX table automatically? I have been using the "apsrtable" package and similar functions in "memisc" package, but neither seems to handle MCMC output directly. Many thanks. Shige

Dear All, With kind help from several friends on the list, I am getting close. Now here are something interesting I just realized: for random effects, lmer reports standard deviation instead of standard error! Is there a hidden option that tells lmer to report standard error of random effects, like most other multilevel or mixed modeling software, so that we can say something like "randome

Dear All, I am fitting a simple GAM model using the "gam" function in the "mgcv" package. The only independent variable is a continuous variable representing the time of the event (in year and month) coded so that "0" represents January 1960, "1" represents February 1960, etc. Now when I try to plot the results, my x-axis ranges from "-200" to

At long last pgfSweave has finally made its way to CRAN. The pgfSweave package is about speed and style of graphics. For speed, the package provides capabilities for ?caching? graphics generated with Sweave on top of the caching funcitonality of cacheSweave. For style the pgfSweave package facilitates the integration of R graphics with LaTeX reports through the tikzDevice package and eps2pgf

R has had the ability to generate pdfs with transparent colors for a couple of years now using pdf(..., version="1.4"). By default, Sweave uses just 'pdf' (without version 1.4), so a hack is needed when using Sweave to create pdfs with transparent colors. See http://tolstoy.newcastle.edu.au/R/help/04/11/6655.html I would find my work process simpler if R defaulted to