When writing .rmd or .Rnw reports in RStudio, the outline view shows both code chunks and regular sections. While code chunks appear italic, regular sections do not. However, writing large reports with many similar named chunks will lead to a really bulky outline view with many similar labels.
Is there currently a way to turn one of them off? Either regular sections or the code chunks.
As per my comment: global options -> Rmarkdown -> show in document outline change to show sections only
Related
I have been writing a document in bookdown where within the *.Rmd file I call a figure by using the following syntax
\#ref(fig:MyFigureName)
This differs slightly from the notation that you would use in a normal RMarkdown file exporting to latex which would be
\ref{fig:MyFigureName}
The issue I am running into is that when I write something in bookdown the function calling the Figure is not being highlighted properly (see image below).
I have imported my own rsTheme (which is from my understanding, basically a .css file) but I don't see an option to add keywords to highlight.
But I would like for the entire function to be colored differently from the inline text (Photoshop version of desired output shown below)
Does anyone know how I would edit my *rsTheme file in order to accomplish this?
Thanks!
I'm using Rmarkdown/Bookdown to write a paper/PDF document, which is an amazing tool #Yihui, thanks! Now I'm trying to include a table I have already put in LaTeX into the document by reading in this external .tex file. However, when knitting in RStudio with a \include{some-file.tex} or input{some-file.tex} in the body of the .Rmd outside of a chunk a LaTeX Error: Can be used only in preamble. is produced and the process stopped. I haven't found a way how to directly input through knit or otherwise into a chunk as well.
I found this question here: Rmarkdown v2, embed Latex document, although while the question is similar, there is no answer which would reflect how to input/include .tex-files into an .Rmd.
Why would I want this? Sometimes LaTeX tables offer more layout options than building directly in R, like for tables only with text rather than R-computed numbers. Also, when running models on a cluster, exporting results directly into .tex ready for compilation saves a lot of computation compared to have to open all these heavy .RData files just for getting the results into a PDF. Similarly, having sometimes multiple types of reports with different audiences, having the full R code in one main .Rmd file and integrating only the necessary results in other files reduces complexity by not having to redo all steps in each file newly. This way, I can keep one report with the full picture and do not have to check if I included every little change in various documents simultaneously.
So finally the question is how to get prepared .tex-Files into a .Rmd-document?
Thanks for your answers!
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.
I have a .Rnw document in which I include childs. The childs produce tables via the 'latex' command of the Hmisc library in R.
When I make changes in the child documents, these changes do not anymore change the pdf document. My first guess was to use the chunk option 'eval=TRUE', but this does not change anything. Then, I saw, that the tables are actually saved to a .tex file with same name as the .Rnw document. I deleted this file and after compilation with knitr I got an error:
Error: Latexmk: Could not find file documentname.tex.
I assume, this is not the way to do it. Now I am out of ideas what to do. I appreciate some help on my problem.
Best
Simon
Allright, when trying to construct a simple example, I actually found out, that neither the packages I included nor the nesting of child documents interfere with the compilation via knitr. The reason was a simple error in the low-level .Rnw document, where a Hmisc latex table had a label, that missed a closing speech mark.
This causes then the output pdf not to change - I assume, that in this case the already constructed .tex file is included instead of letting knitr recompile the .Rnw documents and this hasn't changed since the last compilation?
What I wonder about is the different format of the landscape ctable in the document. Using a simple knitr document just with \documentclass{article} produces well placed tables. In my document using a template for the JFE, I get a table that extends over the whole page and even in footnotesize it is far away from the great appearance in the simple document. There is only a margin of less than half a cm on the right and the left. Page size is the same: both US letter... Can I probably control that via knitr or only via resizebox?
I'm currently looking into lyx because I'm starting to get fed up with writing LaTeX by hand. The problem is, LyX seems to be a bit opiniated about how sections should be written - I'm used to writing
\subsection{}
\subsubsection{}
...
\subsubsection{}
etc., because in the documents I'm writing I don't want titles for my sections. I just want them to be numbered. LyX doesn't seem to like that though, and ends up deleting my sections (and subsections, and subsubsections) when I don't have any text in their titles.
I can just insert a hard space, but this feels kind of weird. I don't understand why lyx wouldn't just let me hit enter and be done with it.
Try to us a 'hard space' as title of the sections, through <Ctrl>+<space>, that should do the trick (it's the keyboard shortcut for LaTeX's "~").
You can insert Evil Red Text (raw LaTeX commands) in LyX. Look for Insert -> TeX Code menu. I just tried it and inserted \subsection{} inside the ERT, and it compiled successfully and showed the section numbers.