I'm using a RMD file to create a package vignette. My. rmd file is stored in
.../path_to_package/vignettes/vignette.rmd
When creating a PDF the last line in the R Markdown console window is "Output created: /tmp/....".
How is it possible to create the PDF directly in the vignettes folder and not in a /tmp/.. folder?
I'm using Ubuntu 14.04 LTS and R 3.3.0, rmarkdown 0.9.6 and knitr 1.13.
Regards,
Johannes
rmarkdown::render does indeed output to the same directory as the input folder by default, but you can override that by supplying an output_dir argument to it (and an output_file one if you'd like to specify a different filename to the input file too).
I'm not sure why the Knit button in RStudio is doing something different for you—in my case it also outputs to the same folder as the source (even when I haven't specified a working folder and my home directory is the default), and RStudio doesn't show the function it's calling when you click the button, so it's a little hard to be sure. I'd stick to using rmarkdown::render() with the specified arguments for now.
Instead use
devtools::build_vignettes()
It will automatically put the files where they're supposed to go. Also check out Hadley Wickham's guide. It rocks!
Related
I wish to use libraries across multiple .Rmd files in an r notebook without having to reload the library each time.
An example: I have loaded the library kableExtra in the index.Rmd file but when I call it in another .Rmd file such as ExSum.Rmd I would get this error:
Error in Kable....: could not find funciton "kable" Calls:...
If I load the kableExtra library again this problem goes away. Is there a workaround?
R Markdown files are intended to be standalone, so you shouldn't do this. There are two workarounds that come close:
If you process your .Rmd files within the R console by running code like rmarkdown::render("file.Rmd") then any packages attached in the session will be available to the code in the .Rmd file.
You can put all the setup code (e.g. library(kableExtra)) into a file (called setup.R, for example), and source it into each document in the first code chunk using source('setup.R'). Every file will run the same setup, but you only need to type it once.
The second is the better approach.
I am trying to run the tutorial for written exams in the exams package (http://www.r-exams.org/tutorials/exams2nops/). Everything works fine until I am about to process the scanned documents using the nops_scan function, which normally should create a zip file.
In the console it says "Creating ZIP file", but nothing happens after that. Last output:
> nops_scan(dir = "nops_scan")
Loading required namespace: png
Reading PNG files:nops_scan1.png: Trimming PNG, rotating PNG,
extracting information, done.nops_scan2.png: Trimming PNG, rotating
PNG, extracting information, done.
Creating ZIP file:
... and then nothing happens.
I have tried to run dir("nops_scan") and it confirms that no zip file has been generated and placed in this folder.
The files in the tutorial are png-files, so what the tutorials says about running pdftk and ImageMagick, should not apply. From the tutorial: "Note that if there were PDF files that need to be scanned, then the PDF toolkit pdftk and the function convert from ImageMagick need to be available outside of R on the command line."
Could the problem still be related to the above comment about pdftk or ImageMagick? (Which program is used to create the zip files?) I do not know how to make these programs "available outside of R", so instruction on this would be appreciated!
The base zip() function from the tools package is used, see ?zip. If you are on Windows maybe you need to install the Rtools? These are available from CRAN at https://CRAN.R-project.org/bin/windows/Rtools/.
PDFTk and ImageMagick are not involved in this case, they are only needed to convert PDF files to PNG which can then be processed in R. (And just in case anybody else is looking for this information: http://www.R-exams.org/tutorials/installation/ provides links to installation files for these applications.)
I'm using an R Notebook and I'd like my plots to automatically save to disk when the code is run, as well as display inline.
knitr: include figures in report *and* output figures to separate files addresses this for R Markdown but the solution given doesn't work for an R Notebook. Is there a similar option for R Notebooks?
Try setting the knitr fig.path option:
knitr::opts_chunk$set(fig.path = "path/to/figures/")
Where path/to/figures/ is the path to a subdirectory where your figures will be saved. The trailing slash is necessary. This should be a relative path, either relative to the RNotebook file or to the project directory. See here::here() for a handy way to locate the project directory.
This will put each figure into that directory; figure names will be based on the chunk name (so name your chunks!)
This is what eventually worked for me (see #TCZhang 's answer to my question here):
In addition to setting the knitr chunk fig.path="figures/" option suggested by #DonJ, try setting output: html_document, or just press the dropdown next to the Preview [Notebook] button at the top and press Knit to HTML. I think the reason this isn't working is that your output is set to output: html_notebook.
I don't know why this doesn't work specifically when the doc is in R Notebook format. I would also prefer if this worked for output: html_notebook, so it might be an issue we need to open with RStudio or knitr.
In Ubuntu, suppose in /home/folder1 I have test.Rnw. To generate a pdf I will go (assuming this directory is my getwd) within my R console:
Sweave(test.Rnw)
texi2pdf(test.tex)
However, my objective is to have the pdf save in another existing folder called /home/folder2. How do I compile the .Rnw (which is to remain in /home/folder1) and the resulting .tex (don't care which folder this gets into) such that the pdf ends up in /home/folder2?
It seems that I want to interfere with either the arguments in Sweave(...) or texi2pdf(...) but haven't found a parameter I can toggle to set export directory.
It is simpler to use knitr package:
knit2pdf(input=/home/folder1/test.Rnw,
output =/home/folder2/test.pdf)
Another option is to use pandoc :
pandoc -f latex /home/folder1/test.tex -s -o /home/folder2/test.pdf
What commands are run when pressing "Knit HTML" on an R Markdown file in Rstudio 0.96?
My motivation is that I might want to run the same command when I'm in another text editing environment or I might want to combine the command in a larger makefile.
Basic Script
So now that the R markdown package has been released, here is some code to replicate the features of Knit to Html.
require(knitr) # required for knitting from rmd to md
require(markdown) # required for md to html
knit('test.rmd', 'test.md') # creates md file
markdownToHTML('test.md', 'test.html') # creates html file
browseURL(paste('file://', file.path(getwd(),'test.html'), sep='')) # open file in browser
where test.rmd is the name of your R markdown file.
Note that I'm not 100% confident about the browseURL line (hence my question here about opening files in a web browser).
markdownToHTML Options
The good thing about markdownToHTML is that there are heaps of options in how the HTML is created (see ?markdownHTMLOptions). So for example, if you want just a code fragment without all the header information, you could write:
markdownToHTML('test.md', 'test.html', options='fragment_only')
or if you don't like hard wrapping (i.e., inserting line breaks when there are single manual line breaks in the markdown source), you can omit the 'hard_wrap' option.
# The default options are 'hard_wrap', 'use_xhtml',
# 'smartypants', and 'base64_images'.
markdownToHTML('test.md', 'test.html',
options=c('use_xhtml', 'base64_images'))
Makefile
This could also all be added to a makefile perhaps using Rscript -e (e.g., something like this). Here's a basic example makefile I put together, where test indicates that the rmd file is called test.rmd.
RMDFILE=test
html :
Rscript -e "require(knitr); require(markdown); knit('$(RMDFILE).rmd', '$(RMDFILE).md'); markdownToHTML('$(RMDFILE).md', '$(RMDFILE).html', options=c('use_xhtml', 'base64_images')); browseURL(paste('file://', file.path(getwd(),'$(RMDFILE).html'), sep=''))"
The makefile uses my preferred markdown options: i.e., options=c('use_xhtml', 'base64_images')
Put Sys.sleep(30) in a chunk and you will see clearly what commands are called by RStudio. Basically they are
library(knitr); knit() to get the markdown file;
RStudio has internal functions to convert markdown to HTML;
The second step will be more transparent in the next version of the markdown package. Currently you can use knitr::knit2html('your_file.Rmd') to get a similar HTML file as RStudio gives you.
Update on 2019/09/17: The above answer applies to RStudio v0.96 (in the year 2012). Now R Markdown is compiled through rmarkdown::render(), which uses Pandoc instead of the retired R package markdown. See the post Relationship between R Markdown, Knitr, Pandoc, and Bookdown for more details.
Very easy command line method from knitr in a knutshell:
R -e "rmarkdown::render('knitr_example.Rmd')"
This requires rmarkdown to be installed with install.packages(rmarkdown) and that pandoc is installed (apparently it comes with Rstudio, see knitr in a knutshell for more details).
So far when I've used this it nicely puts all the plots in the HTML file rather than as images in a figure directory and cleans up any intermediate files, if any; just like compilation in RStudio does.
It seems you should call rmarkdown::render() instead of knitr::knit2html() because a.rmd appears to be an R Markdown v2 document.