I would like to use knitr to create presentations that embed R objects and code.
For IT reasons I am restricted to vim, so i have found the available Rstudio+knitr examples fairly unhelpful. The vim section of the knitr documents is also very skinny, and therefore unhelpful.
Is someone able to provide some guidance on how to compile a *.Rnw or *.Rmd file using knitr (or alternately point me to a decent online tutorial?) using some combination of vim, R, and the command line?
thanks in advance
Instead of going through Rstudio, you can use the functions in the knitr package directly. There are some options you can tweak, but to get started, all you have to do is call the knit() function on your .Rnw file:
library(knitr)
knit('my_input.Rnw')
If you're missing some of Rstudio's features, it's worth remembering that most of them are just making use of things that are already available in various R packages, so you can usually find a way to use them when you don't have Rstudio available.
Related
I'm trying to improve my workflow when working with R and generating documentation. I've been going between TeXStudio, JupyterLab and RStudio for a while, and I'm trying to improve my workflow. TeXStudio has limited R support, and RStudio limited support for LaTeX.
VS Code has support for multiple languages, including R and LaTeX. The fact that it can run both Jupyter notebooks, R notebooks, and LaTeX, and has plugins for other languages as well, makes it seem desirable. However, I am unable to find documentation on how to configure it to work with R and LaTeX code in the same file. In addition, I am unable to configure R notebooks to allow inline code execution output.
However, I am unable to (a) set up code execution output under the code for .Rmd notebooks, and (b) I can't figure out how to weave .Rnw (R/LaTeX) documents with Sweave/knitr.
I'm trying to find an IDE that would include features like:
Markdown, code and code execution output in the same document
Auto R and LaTeX code completion
Automatic display of R function documentation
Spell check
Simple R console access
Compile .Rnw
Syntax highlighting for both R code and LaTeX code
I am, primarily, requesting ways to configure VS Code, or, secondly, way to configure another IDE that can meet my requirements. A tutorial on this would be much appreciated.
After a bit of digging around, I found that VS Code does nearly all the things I need.
Auto R and LaTeX code completion, Display of R function documentation in a tab in VS Code, Simple R console access, and Syntax highlighting for both R code and LaTeX code:
The R and LaTeX Workshop extensions, will provide highlighting and autocompletion of code in both languages. By installing R, you can easily open a session in a terminal window in VS Code, and from there open documentation inside VS Code.
Spell check
Code Spell Checker offers spell check for multiple languages. Install the extension and any desired dictionaries, and set the langauges you want to be included in the extension settings.
Compile .Rnw files
Turns out LaTeX Workshop can actually do this by default.
Markdown, code and code execution output in the same document
This is the only thing VS Code doesn't do as far as I can tell. It can compile .Rmd files, however, but the output can only be seen in the compiled PDF. I consider this less important, since I can use Jupyter notebooks instead.
I was looking at the source code of knitr in order to better understand how the language engines work, and it seems that evaluating code in a single chunk is a relatively simple matter, but what I have trouble understanding is how it is possible for the Python chunks to call the variables across chunks. I get the impression from earlier packages by Yihui that attempts were made to do this with sockets, but it seems that the current code for both reticulate and knitr does not contain code for sockets, hence my question.
This is done through the reticulate package instead of runr. You may see Section 2.7.1 of the R Markdown Definitive Guide for details.
P.S. runr was a very early experiment and never officially used in knitr.
I am new to the R/exams package and I try to produce a pdf document from one of the templates provided by the developers. (http://www.R-exams.org/templates/confint3/)
I am able to compile a Rnw file into a HTML document using the commands
library("exams")
exams2html("confint3.Rnw")
When calling the function
exams2pdf("confint3.Rnw")
it gives the error message
! LaTeX Error: File `Sweave.sty' not found.
I have Latex installed and there are no problems using it in general. I do not understand:
Do I need to tell exams2pdf() the location of the latex installation?
Do I need to define a template (as plain.tex) first? How should it look like?
What is it that I do not understand?
I looked at the documentation of the exams package, I also tried exams2pdf() after installing and calling library("tinytex").
Any help where to look at or what to do is highly appreciated. Thank you!
Minimal example:
install.packages("exams")
install.packages("tth")
library("exams")
set.seed(1090)
exams2html("confint3.Rnw")
set.seed(1090)
exams2pdf("confint3.Rnw")
It is hard to diagnose what exactly goes wrong with the information provided. In any case, when running pdfLaTeX either through utils::texi2dvi() (the default when the R package tinytex is not installed) or through tinytex::latexmk() (the default when the R package tinytex is installed) does not find the Sweave.sty file provided by the R base system. What is not clear to me which LaTeX engine is running in the background: MikTeX on Windows?
There are several strategies that could resolve this issue:
Tell your LaTeX installation about the texmf directory provided by the R base system so that it is found no matter where on your system you call pdfLaTeX.
Use a different LaTeX installation, e.g., by installing TinyTeX (the LaTeX distribution) through tinytex (the R package): tinytex::install_tinytex(). This might be particularly attractive if you are not actually a LaTeX user and just need it to compile PDF exams.
Avoid using the Sweave.sty file in a custom template file, say myplain.tex. A suggestion for such a file is included at the end of this post.
Further details are discussed in this thread: https://tex.stackexchange.com/questions/153193/latex-error-sweave-sty-not-found
As for your three questions:
As already explained above: exams2pdf() leverages either utils::texi2dvi() or tinytex::latexmk(). So these need to know about the LaTeX installation - but this seems to be the case. They just don't find the texmf provided by base R.
You should not have to do this but it is certainly an option that you can use. As a starting point, run exams_skeleton(markup = "latex", writer = "exams2pdf"). Among other things this creates a templates folder where you could put the myplain.tex template below.
As I said above, it's hard to answer that with the information provided. Hopefully, one of the clues provided here gets you a couple of steps forward.
Content of myplain.tex:
\documentclass[a4paper]{article}
\usepackage[utf8]{inputenc}
\usepackage{a4wide,graphicx,color,verbatim,url,fancyvrb,ae,amsmath,amssymb,booktabs,longtable,eurosym}
\newenvironment{question}{\item \textbf{Problem}\newline}{}
\newenvironment{solution}{\textbf{Solution}\newline}{}
\newenvironment{answerlist}{\renewcommand{\labelenumi}{(\alph{enumi})}\begin{enumerate}}{\end{enumerate}}
\providecommand{\tightlist}{\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
\setkeys{Gin}{keepaspectratio}
\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{}
\DefineVerbatimEnvironment{Scode}{Verbatim}{fontshape=sl}
\newenvironment{Schunk}{}{}
\begin{document}
\begin{enumerate}
%% \exinput{exercises}
\end{enumerate}
\end{document}
I am a newbie to the R world-- a couple of weeks. I have been tasked to automate the generation of a database codebook. The thought was to use R, LaTex, and Sweave as a solution. Because of the repetitive nature of the codebook tables and the use of looping over code chunks, Sweave may not be a viable means. It looks like the brew package could be an alternative. As I have been doing some testing with brew, I'm running into an issue with loading in the RMySQL package (via library(RMySQL)) as I cannot suppress the output--
Looking in C:Files/MySQL, C:/MySQL, D:/MySQL, E:/MySQL, F:/MySQL,
G:/MySQL, C:/xampp/MySQL, D:/xampp/MySQL, E:/xampp/MySQL, F:/xampp/MySQL,
G:/xampp/MySQL, C:/Apps/MySQL, D:/Apps/MySQL, E:/Apps/MySQL, F:/Apps/MySQL,
G:/Apps/MySQL Found C:Files/MySQL
I have tried to set the Library function arguments verbose=TRUE and quietly=TRUE but that did not work. In Sweave, I am able to suppress by setting the code chunk option to results=hide. Is there any alternative to suppress this output information when using brew?
In determining whether or not brew is a good solution for the codebook generation, should I be aware of any limitations of brew as compared to Sweave?
To supress messages during loading of a library:
suppressMessages(library(RMySQL))
Also, definitely take a look at the knitr package. It roughly does what Sweave does, but then better. It supports caching of objects (which kept me from heavily using Sweave), and much more flexibility. Take a look at the website, or on a blogpost of mine showing a simple example of a presentation in Latex made using knitr and beamer.
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.