I really need help this time:
Rstudio auto-install some babel-stuff after I've indicate the language of an academic paper in YAML (lang: "fr-FR"). After that point, when I'm knit to pdf, tables and figures doesn't render anymore in the pdf: computation printed in the text are correct, but the pdf produced is now without figure, without table, and cross-references are not working anymore (e.g., the pdf now contain some "Figure #ref(tab:repartition-transport)" where before the language-change there is a number printed like "Figure 1").
I try to set language back to "en-EN" but cross-references, tables and figures doesn't render in the pdf.
The error message said that, when knitting is over:
Package babel Warning: No hyphenation patterns were preloaded for the language 'French' into the format.
Avis : (babel) Please, configure your TeX system to add them and rebuild the format.
Now I will use the patterns preloaded for \language=nohyphenation instead on input line 87.
I don't understand.
Since I don't know how to remove babel (which is not in the packages list), I try to run tinytex::check_installed("babel"), which answer: TRUE. Any help is very appreciated, since I don't know what is the problem.
Thanks
Related
rmarkdown, following {xe|lua}latex, allows to specify fonts for main text, sans-serif text, monspaced text (most notably code chunks !) and math fonts in the YAML header. At least for PDF rendering via xetex, this works.
However, I found no (documented) way to pass options to the underlying setxxxfont \LaTeX command. For example, the YAML fragment :
```
monofont: Inconsolata
```
generates the following \LaTeX fragment :
\setmonofont[Mapping=tex-ansi]{Inconsolata}
I have two questions with this:
why is the Mapping=tex-ansi added ? And how to control it ? (I'm working in UTF8...).
How could I set additional arguments for the font options i.e. \setmonofont[Scale=0.91]{TeX Gyre Cursor}?
The R Markdown book and the Pandoc's User's Guide did not reveal anything pertinent.
Background:
When R Markdown converts the knitted code to the output format (PDF), a pandoc template is used. The template is stored within the package, and any variables which get replaced by the YAML variables are contained in the $$ Notation
1. Encoding
The Mapping=tex-ansi is added to the code as a workaround an issue as reported on GitHub. Therefore I would be cautious of deleting this for potential side effects.
If you do indeed wish to change this code, you will have to make a copy of the LaTeX template file used to convert the document. You can find the default template here. See here for some more information on providing custom templates.
2. Additional Font Options
You can use the monofontoptions YAML argument to add additional arguments to the font options.
Documentation of the variables which can be parsed by the LaTeX output are available in the pandoc documentation
I’m using knitr::rmarkdown (but knitr::knitr does the same) as my VignetteEngine. I then build my package vignette using devtools::build_vignettes().
This works, but only creates HTML and R output files in inst/doc. What I want is a Markdown output file, since only that can be displayed directly within the Github project pages (for HTML files, Github shows the source and for Rmd files it shows a rendered output but — obviously — without executing the R blocks).
I’ve tried finding out how to specify the output for custom VignetteEngines and I think that it should be possible (after all, other packages use this to build PDF vignettes, at a minimum) but I cannot find a way of doing this via devtools::build_vignettes. Is there no way around building the vignette manually (i.e. via knitr::knit or similar mechanisms that ignore the VignetteBuilder directives)?
I can’t find relevant information in the documentation/source either.
The only output formats for vignettes are HTML and PDF (and LaTeX, but it is converted to PDF, not displayed). Markdown isn't supported.
You can have arbitrary documentation files in your package (by convention you put them in inst/doc), but they aren't considered to be vignettes, so they won't be automatically built, functions like browseVignettes() will ignore them, etc.
To convert an Rmd file to md, just run knitr::knit on it.
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 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 want to write an R function which processes some data and then automatically outputs an html report. This report should contain some fixed text, some text changing according to the underlying data and some figures.
What is the best way to go?
R2HTML or knitr?
What are the advantages of one over the other?
As far as I understood R2HTML allows me to build the html file sequentially while knitr already operates on an predefined .Rhtml file.
So, either use R2HTML or stitch and spin from knitr for on the fly report generation.
I would appreciate any suggestions or hints.
I grab this nice opportunity to promote pander a bit :)
This package was written for similar reasons like #Yihui's great knitr, although I wanted to let users really concentrate on the text and R code without dealing with chunk options etc. So letting users generate pretty HTML, pdf or even docx or odt output automatically with some predefined options.
These options affects e.g. the cache engine (handling dependencies without any chunk options) or the default plot options (let it be a "base" R graphics, lattice or ggplot2), so that you do no thave to set the color palette or the minor grid in each of your plots, just once - or live with the package defaults :)
The package captures the results (besides errors/warnings and other messages and the output) of all run R expression and can convert to Pandoc's markdown automatically. There are some helper functions that let you convert the resulting document written in a brew-like syntax automatically to e.g. HTML if you have pandoc installed, or export R objects to markdown/HTML/any other supported format in a live R session with a reference class.
Short demo:
brew file
Pandoc.brew('file_name.brew', output = 'foo.html', convert = 'html')
HTML output
knitr, every time. Handles graphics, lets you write your report with markdown instead of having to write html everywhere (if you want), caches things, makes coffee for you etc.
You can also build an HTML file sequentially as long as you have a decent text editor like Emacs/ESS or RStudio, etc. R2HTML is excellent in terms of its wide support to many R objects (see methods(HTML)), but I'll probably frown on RweaveHTML() due to its root Sweave().
That said, I think it may be a good idea to combine R2HTML and knitr, e.g.
# A LOESS Example
```{r loess-demo, results='asis'}
cars.lo <- loess(dist ~ speed, cars)
library(R2HTML)
HTML(cars.lo, file = '')
```
I was using the R Markdown syntax in the above example. The key is results='asis' which means to writing raw HTML code into the output.
I believe that you can also use Sweave to create HTML files, though I have heard that knitr is easier to use.