similar to: R-code in R-file documentation

Dear R-listers, does anybody can suggest some manual where I can learn more about how the hooks in knitr work? I am trying to enclose the output of an R command in the Latex verbatim environment. I defined a hook as follows: knit_hooks$set(fsverb = function(x, options) { paste("\\begin(verbatim)\n", x, "\\end(verbatim)\n", sep = "") } then I set a chunk as

Hi there: I'm preparing a report in RStudio 0.96.330 on a Mac OS. I'm running R 2.15.0 I understand from Ross Ihaka's document (http://www.stat.auckland.ac.nz/~stat782/downloads/Sweave-customisation.pdf) that you can modify the line length of Sweave output by a call to options(wdith=x). This works great for me for numeric output, but not for character vectors that I have to print.

I am trying to transition from Sweave to knitr, but there are a few things about customization of the appearence of R input and output that I did not get yet. Maybe somebody on the list can help me. In my Sweave presentations I used a slanted font for the R input and a normal font for the output, both in a small font. I also indented everything by an extra 2em. All this was achieved by the

Hi, Suppose I have x = parse(text = " {y=50+50+50#'asfasf' } ") now x is an expression with some src attributes. > x expression({y=50+50+50#'asfasf' }) attr(,"srcfile") <text> attr(,"wholeSrcref") {y=50+50+50#'asfasf' } My question is, how can I get my string back (the string passed to parse() as the text argument)? >

Hi, I have a function knit_expand() and its source/Rd are below: https://github.com/yihui/knitr/blob/master/R/template.R#L43-L44 https://github.com/yihui/knitr/blob/master/man/knit_expand.Rd When I run R CMD check on the package I get this warning (with both R 2.15.2 and R-devel): * checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object

Hi, Recently I noticed file.copy() would discard the file mode information. Is this the expected behaviour or a bug for file.copy()? > file.create('testfile') [1] TRUE > file.info('testfile') size isdir mode mtime ctime testfile 0 FALSE 644 2011-03-05 17:06:39 2011-03-05 17:06:39 atime uid gid uname grname

Hi, Recently I noticed file.copy() would discard the file mode information. Is this the expected behaviour or a bug for file.copy()? > file.create('testfile') [1] TRUE > file.info('testfile') size isdir mode mtime ctime testfile 0 FALSE 644 2011-03-05 17:06:39 2011-03-05 17:06:39 atime uid gid uname grname

Hi, The problem arises when I lazyLoad() the .Random.seed from a previously saved database. To simplify the process of reproducing the problem, see the example below: ## this assignment may not really make sense, but illustrates the problem delayedAssign('.Random.seed', 1L) typeof(.Random.seed) # [1] "integer" rnorm(1) # Error in rnorm(1) : # .Random.seed is not an integer

Hi, The problem arises when I lazyLoad() the .Random.seed from a previously saved database. To simplify the process of reproducing the problem, see the example below: ## this assignment may not really make sense, but illustrates the problem delayedAssign('.Random.seed', 1L) typeof(.Random.seed) # [1] "integer" rnorm(1) # Error in rnorm(1) : # .Random.seed is not an integer

Hello all, Sometimes I get to make an R code chunk (in Sweave) which is longer then the margins of the page. Is there a way to force it to "go to the next line" (in Sweave) once that happens? Here are two cases this happens in the resulting .tex file (one is a "hard" case, and the other is simpler) \begin{Schunk} \begin{Sinput} >

CRAN task views are useful, but they seem difficult to write and maintain because the XML format is rather limited (no sectioning) and the <packagelist> must be maintained manually. They are also difficult to read because the generated html and .css used are extremely basic, giving an overly dense page. Are there any markdown-like tools for writing a CTV? Is it possible to apply a

Hello everyone. I am in the process of writing a book in Latex with Texshop, on Mac. This book contains a lot of R code, hence the need to use Sweave. I was able to compile Rnw files, and to sync back and forth from the pdf to the source Rnw. My problem now is that the book is divided in Chapters, and every chapter is in its own Rnw file. I can compile them from the main one (book.Rnw) using the

Hi, A Windows user asked me a question and I believe this is a bug of R 3.0.0 under Windows: > plot(1:10) > savePlot('test.wmf') Error in .External(C_savePlot, device, filename, type, restoreConsole) : Incorrect number of arguments (4), expecting 3 for 'savePlot' > sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1]

Hi all, Since roxygen is a great help to document R packages, I am wondering if there exists an approach to go back from the raw Rd files to roxygen-documentation? E.g. turn "\author{Somebody}" into "@author Somebody". This sounds ridiculous, but I believe it helps in the long term for me to maintain R packages. Thanks! Regards, Yihui -- Yihui Xie <xieyihui at

Hi, I observed a slight problem in deparse(): it will add spaces around most operators except /. I wonder if this is easy to fix. I know this is quite trivial, but I will appreciate if / is not treated as an exception. Examples: > deparse(expression(1/1)) [1] "expression(1/1)" > deparse(expression(1+1)) [1] "expression(1 + 1)" > deparse(expression(1%in%1)) [1]

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

Hi dear all, In my laptop(ubuntu 11.10 64bit), I maintained a released R (2.14) and a developmental R, I can specify qplot(..., alpha = ) in R 2.14 , but when I try to use transparency in developmental R, I got a warning message and the plot is clearly not I want. minimal example: > qplot(data = mtcars, x = mpg, y = cyl, alpha = cyl) Warning message: In grid.Call.graphics(L_points, x$x, x$y,

Hi dear all, In my laptop(ubuntu 11.10 64bit), I maintained a released R (2.14) and a developmental R, I can specify qplot(..., alpha = ) in R 2.14 , but when I try to use transparency in developmental R, I got a warning message and the plot is clearly not I want. minimal example: > qplot(data = mtcars, x = mpg, y = cyl, alpha = cyl) Warning message: In grid.Call.graphics(L_points, x$x, x$y,

Hi, I am trying to convert a colleague from using SPSS to R, but am having trouble generating a result that is similar enough to a bootstrapped cox regression analysis that was run in SPSS. I tried unsuccessfully with bootcens, but have had some success with the bootcov function in the rms package, which at least generates confidence intervals similar to what is observed in SPSS. However, the

I often use Lyx/Sweave and I typically write in english. Today I had to write a document in Italian and, as many of you know, many italian popular words use ?, ?, ?. ?, etc. I discovered that if I type in Italian (that is there is at least one letter with accent) with the Sweave module selected lye is not able to correctly compile the document. I tried to change the input encoding, but it