In conjunction with trying to find a solution for myself in regards to this question, I find myself plunged into trying to write valid Rd markup. What I want is to add a section named Raw Function Code and put the code of the function under it. I've achieved limited success in this regard by writing a script to modify the Rd files to include
\section{Raw Function Code}{\code{
# some piece of R script will eventally provide this part of the text
}}
However, even if I manually properly spaced text into the .Rd file (using either spaces or tabs), the initial white space of each line seems to get stripped away leaving an undesirable looking function. I've noticed that if I provide a starting character before the white space the white space is retained. However, I did not want to provide a starting character because I'd like people to be able to copy and paste directly from the produced PDF.
I have reviewed parseRd and I know there are three types of text LaTeX-
like, R-like, and verbatim. I have tried to put my function code in \code and in \verb and neither seemed to yield the desired results. What can I do to hold onto my initial white space?
The \section macro contains LaTeX type of text, but as you want to write code, you could use \synopsis macro, i.e.
\synopsis
# some piece of R script will eventally provide this part of the text
}
There is one problem with this though; you cannot give name to this section, it is automatically named as another usage section. Same thing could be achieved by using \examples macro, but now the name of the section is Examples, which is probably even more dubious (not to mention that you probably already have Examples section).
It isn't possible without modifying the usage or examples sections of your Rd code. See Hemmo's answer for a usable workaround. It produces text in the verbatim mode which is sub-optimal, but far better than nothing.
(This answer is set community Wiki in case this state of affairs changes. This result is current as of R-2.15.1)
If you want a super hacky way to do it, you can use \Sexpr to make zero width characters and add spaces between them:
#' first line \cr
#'\Sexpr{"\u200B"} \Sexpr{"\u200B"} \Sexpr{"\u200B"} \Sexpr{"\u200B"} indented line
A warning however - your package will build fine, but R CMD CHECK will throw a fit.
Related
I know that three backticks ``` are used to indicate a code block in RMarkdown and if you put a language inside of braces R markdown will try to run it but what does it mean if the language is not in braces? I can see that Yihui uses ```yaml, ```r, ```bibtex to cause code blocks to appear with color highlighting in the RMarkdown book. Does anybody know a reference to what that is actually doing and best practices with the notation? I am thinking it means show (but don't execute) this code block (and indicate the language for anybody who bothers to look into the source). If that is right, where is it documented? Does anybody know how to set the color of the words that are rendered inside such a (language named but not braced) code block in a html and/or pdf document?
I am trying to use R Markdown documents for report writing in a way I used Word before for a couple of months. While RStudio/Markdown is generally great, there is one thing that keeps embarrassing me: the need to input two spaces to force a line break. My whole life related to writing on the computer screen is a life when pressing Enter means breaking the line. Moreover, I see in the editor that line is broken and new paragraph starts, but after the compilation of Rmd-file I see a wall of text, without line breaks, and have to go back and check whether all line endings have two spaces on their end. It is awful. I understand that maybe I need to develop a habit to input two spaces (which does not seem intuitive), but it is hard.
Is there a way to enforce Markdown parser in RStudio count end of the line in Rmd document as a line break, so I can avoid entering two spaces to force a line break? Maybe, there are workarounds, like RStudio addins or something else? I have searched these on the Internet but has not found any.
I love knitr & rmarkdown, but I often find myself in situations where I have a lengthy report that takes some nontrivial amount of time to run. After it's generated, I notice my inevitable typos in text. However, re-knitting everything to just fix a couple typos (just in text, not code) takes a long time and seems avoidable. I was about to start taking a hack at developing my own solution to this, but I'm thinking it's the kind of thing that could already have a mature solution which would likely be more robust than the one I'd build.
I'm wondering if there is solution out there within knitr or third party that would allow me to edit just the text of my reports without rerunning code, generating plots and outputs etc. I know, I can simply edit the generated html text, but then those changes must be replicated in the R/Rmd code that generated it, or they get out of sync. I'm envisioning a function like this:
argument 1: the R/Rmd script with text edits (no code changes)... perhaps a warning is generated when code chunks change
argument 2: the html output file from the last time the R script in argument was knitted without the text edits.
return: the html report (argument 2) updated with the comments in the R/Rmd script (argument 1).
I use the cache option sometimes for large datasets. I toggle eval and echo on and off when developing if I'm just working on the text of my report. However, I'm looking for a function that would take care of all this for me, so one doesn't have to mess with the code and chunk options to make small edits to text.
Here's an interim solution that lets you retain the speed of making changes directly to the rendered text, but you have to do a little work after you're done making changes.
Assuming the following files:
input.knitr is the original Knitr file with text and code integrated.
output.html is the resulting HTML code that has been rendered by Knitr.
Consider making direct text edits to output.html and then running something like Meld visual merge tool:
meld output.html input.knitr
Then manually select the edits in output.html that are new and should be fixed in the original source input.knitr. Tools such as Meld do a pretty good job of aligning the texts so that the chunks and knitted output will appear as large "changes" that, in practice, you would ignore. You would focus on the small changes in the non-chunk sections.
more a tip question that can save lots of time in many cases. I have a script.R file which I try to save and get the error:
Not all of the characters in ~/folder/script.R could be encoded using ASCII. To save using a different encoding, choose "File | Save with Encoding..." from the main menu.
I was working on this file for months and today I was editing like crazy my code and got this error for the first time, so obviously I inserted a character that can not be encoded while I was working today.
My question is, can I track and find this specific character and where exactly in the document is?
There are about 1000 lines in my code and it's almost impossible to manually search it.
Use tools::showNonASCIIfile() to spot the non-ascii.
Let me suggest two slight improvements this.
Process:
Save your file using a different encoding (eg UTF-8)
set a variable 'f' to the name of that file. something like this f <- yourpath\\yourfile.R
Then use tools::showNonASCIIfile(f) to display the faulty characters.
Something to check:
I have a Markdown file which I run to output to Word document (not important).
Some of the packages I used to initialise overload previous functions. I have found that the warning messages sometimes have nonASCII characters and this seems to have caused this message for me - some fault put all that output at the end of the file and I had to delete it anyway!
Check where characters are coming back from Warnings!
Cheers
Expanding the accepted answer with this answer to another question, to check for offending characters in the script currently open in RStudio, you can use this:
tools::showNonASCIIfile(rstudioapi::getSourceEditorContext()$path)
Many of the math textbooks and other literature I read is in PDF format, so I frequently find myself annotating these with the Adobe Reader comments tool.
I did find a helpful guide here, but sometimes I'd like the option of inserting math symbols, too. Has anyone found a reliable way to insert math symbols, TeX, or other arbitrary formatting into the annotations?
So far, the best I've come up with is to enter the unicode prefixed by "0x" and hit alt+X after it. Maybe with the Adobe javascript SDK you could write a script to shortcut this.
I don't think any of the current commercial editors make this easy, which is too bad. I am sure the vendors monitor this site, so there is hope.
In the meantime, here is a manual workaround.
Use tikz to create your comment boxes. Here are the two examples I found to be most relevant: Boxes and Positioning. Play around with the options to get both the shape and the placement you want. Generate a pdf file from the latex source that contains your comments.
IMPORTANT: if your comments end before the last page of the original document, insert:
\pagebreak{} % create empty page
\thispagestyle{empty} % get rid of page numbers et al
~ % put a space so the page gets generated
before your \end{document}, to get an empty last page. The following command will reuse the last page of your comments document on all subsequent pages of the original document.
Use a recent version of pdftk with the multistamp command to overlay your equations file with your original file like so:
pdftk original.pdf multistamp comments.pdf output out.pdf
Also see this question.
The free (as speech) PDF tool, Okular, supports this functionality by putting latex formula directly between $$...$$.