Sorry if I'm asking a stupid question, but I'm kinda new to R/Sweave.
I have noticed that if I run my file, RStudio automatically generates a pdf-file for each figure plotted (as well as a pdf-file containing all generated figures from the Sweave-file). For example, suppose I have the following chunk of code in RStudio (simplified version):
\begin{figure}[htbp]
\centering
<<fig1, fig=TRUE, echo=FALSE>>=
plot(pts.X,1:length(pts.X),
main = "Type I error for X-var IT")
#
\caption{}
\label{X-var}
\end{figure}
Then, RStudio saves a pdf-file called R/SweaveFileName-fig1.pdf as well as a pdf-file Rplots.pdf which will also contain any other figure included in the Sweave-file. Since my R/Sweave files contain a lot of figures, I was wondering whether it is possible to change this option in R/Sweave. And, if not, is it possible to redirect these pdf-files into a separate folder?
You can't avoid generating the figures. RStudio isn't really doing much of the work here; it's just directing other software to do it.
R generates the figure, and the LaTeX source code to import it.
LaTeX imports the figure and produces the final .pdf for the whole document.
You can tell R to put the files in a particular place using \SweaveOptions{prefix.string = figs/}. Put this into your document somewhere
pretty early, and all figures will be put into a directory called "figs" (which must exist for this to work).
For more details about the options in Sweave, see the vignette in the utils package.
Related
I have read previously asked similar questions here, here, and here (among many more).
Unfortunately, none of the solutions offered to those questions seem to solve my issue.
I tried the function written by #bryanshalloway here but that did not have the desired result.
For more context, I am producing scientific manuscripts using an R Markdown workflow. I perform EDA in one notebook and later come back to write the manuscript in a different notebook. I import the data, wrangle it, create tables, and do some basic visualizations in the EDA notebook and include narrative text (mostly for myself).
I then create a separate notebook to write the manuscript. To keep it reproducible, I want to include all of the steps from the EDA with respect to data import, tidying, and wrangling, however I do not need the commentary that went along with it. Additionally, I may want some (but definitely not all) of the tables and basic visualizations I created during the EDA, but I would need to build them up substantially to get them publication ready.
My current workflow is just copying and pasting the relevant code chunks and then adding to those where necessary for tables and figures (i.e., adding labels and captions to a ggplot).
Is there a way to "source" these individual code chunks from one R Markdown file/R Notebook into another? Perhaps using knit_child (but not bring the entire R Markdown file into the current parent file)?
I would like to avoid copying the desired code chunks into separate R scripts.
Thanks!
It is very possible with knitr purl and spin:
Ok lets say this is your initial Rmarkdown report:
call the file report1.Rmd
---
title: Use `purl()` to extract R code
---
The function `knitr::purl()` extracts R code chunks from
a **knitr** document and save the code to an R script.
Below is a simple chunk:
```{r, simple, echo=TRUE}
1 + 1
```
Inline R expressions like `r 2 * pi` are ignored by default.
If you do not want certain code chunks to be extracted,
you can set the chunk option `purl = FALSE`, e.g.,
```{r, ignored, purl=FALSE}
x = rnorm(1000)
```
Then you go to the console and purl the file:
> knitr::purl("report1.Rmd")
this creates an R file called report1.R in the same directory you are in,
with only the chunks that are not purl=false.
Its an simple R script looking like this:
## ---- simple, echo=TRUE----------------------------------------------------------------------------
1 + 1
Lets rename the file for safety purposes:
> file.rename("report1.R", "report_new.R")
Finally lets spin it back to report_new.Rmd :
> knitr::spin("report_new.R", format = "Rmd", knit=F)
This gives you a new Rmd file called report_new.Rmd containing only the relevant chunks and nothing else
```{r simple, echo=TRUE}
1 + 1
```
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 am working on a LaTeX report template that automatically generates a beamer document, pulling in figures from specified directories and placing them one per slide.
Here is an example of the code that I am using for this, as a code chunk in my .Rnw document:
<<results='asis',echo=FALSE>>=
suppressPackageStartupMessages(library("Hmisc"))
# get the plots from the common directory
Barplots_dir<-"/home/figure/barplots"
Barplots_files<-dir(Barplots_dir)
# create a beamer slide for each plot
# use R to output LaTeX markup into the document
for(i in 1:length(Barplots_files)){
GroupingName<-gsub("_alignment_barplot.pdf", "", Barplots_files[i]) # strip this from the filename
file <- paste0(Barplots_dir,"/",Barplots_files[i]) # path to the figure
cat("\\subsubsection{", latexTranslate(GroupingName), "}\n", sep="") # don't forget you need double '\\' because one gets eaten by R !!
cat("\\begin{frame}{", latexTranslate(GroupingName), " Alignment Stats}\n", sep="")
cat("\\includegraphics[width=0.9\\linewidth,height=0.9\\textheight,keepaspectratio]{", file, "}\n", sep="")
cat("\\end{frame}\n\n")
}
#
However I recently came across this article by Yihui Xie which includes a remark about cat("\\includegraphics{}") being a bad idea. Is there a reason for this, and is there a better option?
To be clear, these figures are generated by other programs as part of a larger pipeline; generating them within the document is not an option, but I need the document to be able to dynamically find and insert them into the report. I know that there are some capabilities to do this directly from within LaTeX itself but cat'ing out the LaTeX markup I need seemed like an easier and more flexible task.
cat("\\includegraphics{}") is likely to be a bad idea if you are from the old Sweave world (where one might need to open a graphics device, draw a plot, close the device, and cat("\\includegraphics{}")). No kittens will be killed as long as you understand what you are doing. Your use case seems to be very reasonable to me, and I don't have a better approach.
I have a file for my thesis, which include the chapters.
A few weeks ago, I worked with R-Statistic and *.rnw files to produce a *.tex paper.
Now, I want to include these *.tex paper in my thesis. However, every time I get several errors.
Structure
/home/UserName/R-files/Dokumentation5.rnw
/home/UserName/tex-Files/Dokumentation5.tex // from Dokumentation5.rnw files
In the following folder, I put the TeX and the figures (*.pdf).
/home/UserName/Documentation/chapter/
Edit the Dokumentation5.tex, remove the beginning and "end document"
In thesis file, I added the following commands:
\usepackage{Sweave} \include /home/UserName/Documentation/chapter/
run latex
If I run LaTeX, I got several errors like:
File `Dokumentation5-004' not found.
\begin{document} ended by \end{Schunk}.
Too many }'s
File `Dokumentation5-033' not found.
Create a file master.Rnw that contains nothing but the LaTeX setup (packages to be used, geometry, title, begin/end document, bibliography style and file......)
If you need to use R functions in various places in your paper, create a file func.Rnw where you create these functions. Make this file the first to \SweaveInput{func.Rnw} in your master.Rnw - see here for details
Now create one file for each "unit" of your paper (chapter, section, whatever you like). Make them all chapX.Rnw files, whether they contain R code or not.
\SweaveInput{chapX.Rnw} them in the desired order in your master.Rnw file.
At any time during the process, run Sweave("master.Rnw") in R and then pdflatex master.tex from the console to see what you have produced.
my question(s) might be less general than the title suggests. I am running R on Mac OS X with a MySQL database to store the data. I have been working with the Komodo / Sciviews-R for some time. Recently I had the need for auto-generated reports and looked into Sweave. I guess StatET / Eclipse appears to be the "standard" solution for Sweavers.
1) Is it reasonable to switch from Komodo to StatET Eclipse? I tried StatET before but chose Komodo over StatET because I liked the calltip / autosuggest and the more convenient config from Komodo so much.
2) What´s a reasonable workflow to generate Sweave files? Usually I develop my R code first and then care about the report later. I just learned today that there is one file in Sweave that contains R code and Latex code at once and that from this file the .tex document is created. While the example files look handily and can't really imagine how to enter my 250 + lines of R code to a file and mixed it up with Latex.
Is it possible to just enter the qplot() and ggplot() statements to a such a document and source the functionality like database connection and intermediate results somehow?
Or is it just a matter of being used to the mix of Latex and R code?
Thx for any suggestions, hints, links and back-to-the-roots-shout-outs…
You've asked several questions, so here's several answers;
Is StatEt/Eclipse the right way to do Sweave ?
Not nessarily (note: I'm an avid StatEt/Eclipse user, and use it for both pure R and Sweave/R and love it, I haven't used Komodo / sciviews-R). You should be able to run the sweave command from any R command line which will generate a .tex file. You can then turn the .tex file into something readable (like pdf) from any tex environment.
What's a good Sweave workflow ?
When I have wanted to turn an r script into a sweave report I generaly start with an empty sweave template and copy/paste my entire R script into a sweave R block just after the title, i.e;
<<label=myEntireRScript, echo=false, include=false>>
#Insert code here
myTable<-dataframe(...)
myPlot<-qplot(....)
#
Then I go through and find the parts I want to report. For instance, if i want to put a table into the report, I'll cut the R block and put an xtable block in, and the same for variables and plots.
<<label=myEntireRScript, echo=false, include=false>>=
#Insert code here
#
Put any text I want before my table here, maybe with a \Sexpr{print(variable)} named variable
<<label=myTable, result=Tex>>=
myTable<-dataframe(...)
print(xtable(mytable,...),...)
#
Any text I want before my figure
<label=myplot, result=figure>>=
myPlot<-qplot(....)
print(qplot)
#
You may want to look at these related SO posts. The rest of my post relates to your question 2.
When creating reports with Sweave, I usually keep most of the R code and the report text separate. If the R code is fast to run, then I prefer I will include something like the following at the start of the .Rnw file:
<<>>
source('/path/to/script.r')
#
On the other hand, if the R code takes a long time, I will often include something like the following at the end of the R script:
Sweave('/path/to/report.Rnw'); system('pdflatex report.tex')
That way, I can re-generate the report quickly, without needing to run all the R code again. Then, the only work R has to do in the Sweave file is print tables, make graphs and maybe extract a few figures.
Like nullglob, I prefer to keep the R and Sweave files separate, but I prefer to save the workspace with save.image() rather than to source() the file. This avoids running the R calculations with each .Rnw file compiling (and I always end up tinkering with the typesetting more than I'd like).
My general work flow is to do each paper/project in it's own folder with it's own R file(s). When the calculation side is "done", I save.image() to store all the workspace variables as-is.
Then, in the .Rnw file in the same directory I set the working directory with setwd() and load all variables with load(".Rdata"). Of course, you can change the name you use for your workspace, but I do one workspace per folder and keep the default name. Oh, and if you tinker with the R file, be sure save the workspace image and watch out for variables that linger in the workspace and .Rnw file, but are no longer part of the R file... this is where the save.image() approach can cause some headaches.
I am on a Mac and I suggest TextMate if you're mildly geeky and emacs/ess if you're really geeky. I use vim and command line R, but emacs/ess works best for most. If you're in this for the long haul, I doubt you'll regret learning emacs/ess for R, Sweave, and LaTeX.