i have been trying to implement a tikz chunk in bookdown first by myself, then by following this thread.
unfornutately, i keep running into various errors and incompatibilities, such as this one:
Error in tools::texi2dvi(texf, pdf = !to_svg, clean = TRUE) :
unable to run 'pdflatex' on '.\tikzf702b605920.tex'
(even though by itself tinytex::pdflatex('test.tex') works fine)
on his blog and github Yihui Xie mentioned that it's definitely possible, but i wasn't able to find any working example, so i was hoping if perhaps anyone here could share one, please (or point out what am i doing wrong)
#PaulLemmens, i found what was the problem for me. disclaimer here, i use windows and none of my colleagues who use r on linux/macos have this problem.
issue was arising with knitr when engine=tikz is used in one of the chunks. For it to work installation of imagemagick (https://www.imagemagick.org/script/index.php) and GhostScript (https://www.ghostscript.com/) is needed. as well as that, i had to rewrite knitr (https://github.com/darthaline/knitr) slightly. it's a quick and dirty solution, but it worked for me. on line 281 of R/engine.R the path to imagemagick's convert is hardcoded cause otherwise it seems that windows interprets it as 'convert.exe' from System32 directory (ImageMagick PATH not being recognized with engine = "tikz" in knitr)
Related
RStudio has a wonderful set of skeletons for packages and Rmd documents. But, I'd like to know if it's possible to change the defaults to a "skeleton" of your own design. If, like me, you package your research for yourself/clients, you quickly find yourself deleting and copying the same work over and over.
I suppose there are two related questions here:
Can you change the default package skeleton?
Can you change the default Rmd skeleton?
There is no supported way to do this. However, the skeletons are stored as ordinary files in your filesystem, so there's nothing stopping you from modifying them. For instance, if you're on the Mac, this file provides the default Rmd skeleton:
/Applications/RStudio.app/Contents/Resources/resources/templates/r_markdown_v2.Rmd
On Windows, it's here:
C:\Program Files\RStudio\resources\templates\r_markdown_v2.Rmd
I didn't realize it then, but I was actually looking for a custom format. The details of which are documented extensively on the rmarkdown rstudio site.
http://rmarkdown.rstudio.com/developer_custom_formats.html
It is my first experience in writing an R-package. I used roxygen2 by following the instructions given in this link http://kbroman.org/pkg_primer/
Everythig is working fine except few things.. there could be a simpler solution to solve the issues, but I am not finding clues what I am doing wrong. I hope someone here in this blog can give a solution to solve my issues.
First issue is about {\code\link{function-name}} in roxygen2:
In .R script I inlcuded this line:
#' #seealso \code{\link{s2a}}
After documenting (generating .Rd files) there is no hyperlink to s2a ,
in documentation s2a shows like a normal text not like hyperlink..
export(s2a) is listed out in NAMESPACE.
Is there any other place i need to modify ?
Second issue is about data():
I saved the dataset in .Rdata format and placed in the data/ in package directory. I also created the .R script in R/ as like following steps here http://kbroman.org/pkg_primer/pages/data.html
In DESCRIPTION file LazyData: true .
but when I type data(shh) in R console gives a warning message
data(shh)
Warning message:
In data(shh) : data set ‘shh’ not found
Any ideas is of great help:)
It's been a while since you asked this, but I was having the exact same problem with hyperlinks in documentation not appearing correctly, so for anyone who might be having a similar problem: Are you possibly viewing the development documentation? The links don't seem to work there. (You'll know this is the case if you see Using development documentation for your_function_name in your console output when you run ?your_function_name.)
The links should appear in the non-development documentation. To generate this you can try building and reloading your package, for instance by following the steps here: http://r-pkgs.had.co.nz/man.html#man-workflow-2
I am attempting to automate the insertion of JPEG images into Powerpoint. I have a macro done for that already, except using R would be infinitely better for my purposes.
The package R2PPT should do this, I understand. However, I cannot use it. For example, when I try to use PPT.Open, I understand I can do it two different ways by calling method = "rcom" or method = "RDCOMClient". Using the latter, R will always crash, sending an error report to windows. Using the former, it tells me I need to install statconnDCOM , before giving the error:
Error in PPT.Open(x) : attempt to apply non-function.
I cannot install statconnDCOM freely, as I wouldn't call this work non-commercial. So if there isn't a way to get around this issue, are there at least some free alternatives to R2PPT so that I can save several hours of manual work with a simple R code? If there is a way for me to use R2PPT, that would be ideal.
Thanks!
Edit:
I'm using R version 2.15 and downloaded the most recent version of R2PPT. Powerpoint is 2007.
Do you have administrative privileges on this machine?
There is an issue with package RDCOMClient. It needs permissions to write file rdcom.err in the root of drive C:. If you don't have privileges to write to c:, there is a rather cumbersome workaround:
Close R
Create "c:\temp" folder if it doesn't exist.
Locate on your hard drive file rdcomclient.dll. It usually placed in \R\library\RDCOMClient\libs\i386\ and in \R\library\RDCOMClient\libs\x64\ (you need to patch file which corresponds your Windows version - 32 bit or 64 bit). It's recommended to make backup copy of this files before patching.
Open rdcomclient.dll in text editor (Notepad++, for example -http://notepad-plus-plus.org/)
Find in file string c:\rdcom.err - it occurs only once.
Go into overwrite mode (usually by pressing "Ins" key). It is very important that new path will have the same number of characters as original one. Type C:\temp\e.rr instead of c:\rdcom.err
Save the file.
Now all should work fine.
Arguably not an answer, but have you looked at using Sweave/knitr to render your presentations in LaTeX using something like Beamer? (As discussed on slide 17 here.)
Wouldn't help any with getting JPGs into a PowerPoint, but would certainly make putting R-output (numerical or graphical) into a presentation much easier!
Edit: if you want to use knitr (which I recommend), here's another reference.
Has anyone managed to get color syntax-highlighting working in the output of Sweave documents? I've been able to customize the output style by adding boxes, etc. in the Sweave.sty file as follows:
\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontseries=bc,frame=single}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{frame=leftline}
\DefineVerbatimEnvironment{Scode}{Verbatim}{fontseries=bc}
And I can get the minted package to do syntax highlighting of verbatim-code blocks in my document like so:
\begin{minted}{perl}
use Foo::Bar;
...
\end{minted}
but I'm not sure how to combine the two for R input sections. I tried the following:
\DefineVerbatimEnvironment{Sinput}{minted}{r}
\DefineVerbatimEnvironment{Scode}{minted}{r}
Any suggestions?
Yes, look at some of the vignettes for Rcpp as for example (to pick just one) the Rcpp-FAQ pdf.
We use the highlight by Romain which itself can farm out to the hightlight binary by Andre Simon. It makes everything a little more involved---Makefiles for the vignettes etc pp---but we get colourful output from R and C/C++ code. Which makes it worth it.
I have a solution that has worked for me, I have not tried it on any other systems though so things may not work out of the box for you. I've posted some code at https://gist.github.com/797478 that is a set of modified Rweave driver functions that make use of minted blocks instead of verbatim blocks.
To use this driver just specify it when calling the Sweave function with the driver=RweaveLatexMinted() option.
Here's how I've ended up solving it, starting from #daroczig's suggestion.
\usepackage{minted}
\renewenvironment{Sinput}{\minted[frame=single]{r}}{\endminted}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{frame=leftline}
\DefineVerbatimEnvironment{Scode}{Verbatim}{}
While I was at it, I needed to get caching working because I'm using large data sets and one chunk was taking around 3 minutes to complete. So I wrote this zsh shell function to process an .Rnw file with caching:
function sweaveCache() {
Rscript -e "library(cacheSweave); setCacheDir(getwd()); Sweave('$1.Rnw', driver = cacheSweaveDriver)" &&
pdflatex --shell-escape $1.tex &&
open $1.pdf
}
Now I just do sweaveCache myFile and I get the result opened in Preview (on OS X).
This topic on tex.StackExchange might be interesting for you, as it suggest loading the SweaveListingUtils package in R for easy solution.
I've been struggling for a week now trying to figure out how to generate reports in R using either Sweave or Brew. I should say right at the beginning that I have never used Tex before but I understand the logic of it.
I have read this document several times. However, I cannot even get a simple example to parse. Brew successfully converts a simple markup file (just a title and some text) to a .tex file (no error). But it never ever converts tex to a pdf.
> library(tools)
> library(brew)
> brew("population.brew", "population.tex")
> texi2dvi("population.tex", pdf = TRUE)
The last step always fails with:
Error in texi2dvi("population.tex", pdf = TRUE) :
Running 'texi2dvi' on 'population.tex' failed.
What am I doing wrong?
The report I am trying to build is fairly simple. I have 157 different analysis to summarize. Each one has 4 plots, 1 table and a summary. I just want
output plot 1,2,3,4
output table
\pagebreak
...
that's it. Can anyone help me get further? I use osx, don't have Tex installed.
thanks
You cannot run this without texi2dvi or TeX installed.
An alternative may be html output -- the hwriter package is useful for that.
That said, if you want to produce pdf out, Sweave is the way to go. Frank Harrell's site has a lot of useful info but all this requires a bit of familiarity with LaTeX so you may need to install and learn that first.
If you are on OSX, might as well install the full tex live
http://mirror.ctan.org/systems/mac/mactex/MacTeX.mpkg.zip
It is a big download, but it will be nice to never have to install additional packages.
Another solution: the ascii package in conjonction to your favorite markup language (asciidoc, txt2tags, restructuredtext, org or textile).
http://eusebe.github.com/ascii/
It may be worthwhile spending a week or so just using LaTeX without R and going through a bunch of introductory LaTeX tutorials.
Thus, when you start producing Sweave or Brew documents and you get errors, you will be better able to identify whether the error is arising from LaTeX or Sweave / Brew.
A couple of Windows tools that make it easy to get started with LaTeX include MikTeX + TeXnicCenter or MikTeX + WinEdt.
Another solution is to try a solution of connecting R to microsoft.
It is much weaker then Sweave, but for basic reporting might be what you need.
You might want to go through the example sessions given here: Exporting R output to MS-Word with R2wd (an example session)
I've also been hearing a lot of good things about the knitr package. It seems to resemble Sweave a lot, but add some more to it. I would definitely take a look at it.