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.
Related
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 fairly new to doing report with R Sweave and know the very basic applications of Latex. And I have been asked to produce some statistical reports. The R markdown is great and simple, and by default it has really nice syntax frame and grey background and syntax highlights, however, it is quite limited in terms of other type setting, not really optimal when you want to produce lengthy reports. Then I am switching to use R Sweave in R studio.
I basically want the same after-effect similar to R markdown in the Sweave. What are the easiest ways to do it? I have previously read the following post discussing:
Sweave syntax highlighting in output. And I have tried reading those package pdf, but have no clues what they are talking about, as they seem to assume readers have prior knowledges about the rendering process.
i have checked them out, but I seem to get stuck in making it to work. Can anyone tell me step by step on how to set it up (such as what to include in preamble), if possible can you kindly upload a simple Rnw file with a demonstration?
Thank!
If you use knitr rather than Sweave, you'll get syntax highlighting. It's probably possible to do it in Sweave, but knitr makes it easier.
Go to your Tools | Global Options | Sweave menu (or the similar one in Project Options) in RStudio, and choose to Weave Rnw files using knitr.
The two systems are very similar, but knitr is generally preferable these days.
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.
I'm looking for some LaTeX template for creating quality output. On R-bloggers I've bumped on Frank Harrel's Rreport package. Due to my quite modest LaTeX abilities, only a user-friendly (and noob-friendly) interface should suffice. Here's a link to an official website. I'm following the instructions, but I cannot manage to install an app. I use Ubuntu 9.10, R version is 2.10.1 (updated regularly from UCLA's CRAN server), and of course, cvs is installed on my system.
Now, I'd like to know if there is some user-friendly LaTeX template package (Sweave is still to advanced/spartan for me). I'm aware that my question is quite confounding, but a brief glance on examples on Rreport page should give you a hint. I'm aware that LaTeX skills are a must, but just for now I need something that will suit my needs (as a psychological researcher).
Is there any package similar with Rreport?
lyx? http://www.lyx.org/
On Ubuntu:
sudo apt-get install lyx
From the lyx page:
LyX combines the power and flexibility
of TeX/LaTeX with the ease of use of a
graphical interface. This results in
world-class support for creation of
mathematical content (via a fully
integrated equation editor) and
structured documents like academic
articles, theses, and books.
If you want to produce Latex with a simpler markup you could use the ASCII package that has a Sweave driver that can be used with reSTructured text, which can then be converted to Latex. Although I would only use it if you want to be able to convert the same doc also to html or odf. In any case it is a good idea to learn the basic Latex.
The online text processor zoho allows export to latex. Maybe this can be helpful to learn latex, but I do not know how to integrate Sweave/R in this. (I did not work with zoho, by the way).
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.