My pdf looks like:
How do I make it show the actual pdf?
I loaded pdf-view from https://atom.io/packages/pdf-view and now when I open a pdf file i get it shown onscreen as a it's meant to be displayed. There is also a package named pdf-view-Plus which claims to be better than pdf-view. Just load the package and you should be ready to go.
Atom on his own cant read the PDF document as it is a binary file, in order to view the formatted document you must use a Atom package like https://atom.io/packages/pdf-view
You would need to install some other extension as Atom can't read PDFs on it's own. You could use something such as https://atom.io/packages/pdf-view.
Related
I am using R Studio and I want to save my script (i.e., the upper left panel). However, the only ways that I can find to do it are by either clicking the blue floppy disk icon to save or using the drop down menu File > Save > name.R
Is there any way besides using these shortcuts to save the script to a .R file or is the shortcut the only way?
Thanks.
You can use rstudioapi::documentSave() to save the currently open script file to disk.
From the source documentation, one can see that it can be used in conjunction with the id returned with getActiveDocumentContext()$id to make sure the document saved is the one running the script.
For your intended use, try:
rstudioapi::documentSave(rstudioapi::getActiveDocumentContext()$id)
For future reference, here is the reference manual of rstudioapi:
https://cran.rstudio.com/web/packages/rstudioapi/rstudioapi.pdf
I'm not yet allowed to comment, but this refers to the comment above that this does not work with .rmd files:
rstudioapi::documentSave(rstudioapi::getActiveDocumentContext()$id)
I tried and in Rstudio Version 1.2.5042 it does seem to work.
Every new tab in R(created by ctrl+shift+n) can be independently saved by using ctrl+s in the respective tab. If you intend to rename the file though, you may do it as you would rename any file in windows(goto the file location and single click on the filename). Hope my answer was of some help!
I'm using a RMD file to create a package vignette. My. rmd file is stored in
.../path_to_package/vignettes/vignette.rmd
When creating a PDF the last line in the R Markdown console window is "Output created: /tmp/....".
How is it possible to create the PDF directly in the vignettes folder and not in a /tmp/.. folder?
I'm using Ubuntu 14.04 LTS and R 3.3.0, rmarkdown 0.9.6 and knitr 1.13.
Regards,
Johannes
rmarkdown::render does indeed output to the same directory as the input folder by default, but you can override that by supplying an output_dir argument to it (and an output_file one if you'd like to specify a different filename to the input file too).
I'm not sure why the Knit button in RStudio is doing something different for you—in my case it also outputs to the same folder as the source (even when I haven't specified a working folder and my home directory is the default), and RStudio doesn't show the function it's calling when you click the button, so it's a little hard to be sure. I'd stick to using rmarkdown::render() with the specified arguments for now.
Instead use
devtools::build_vignettes()
It will automatically put the files where they're supposed to go. Also check out Hadley Wickham's guide. It rocks!
Is there a simple way to create R documentation file for simple R functions?
I know I can edit a .Rd file in R-studio and preview it in HTML file. But how to put it into latex to edit and preview? Is there some latex package producing R documentation format?
There is the Rd2latex function in the tools package that will convert from the .Rd format to LaTeX format. This will let you preview the documentation in LaTeX. However this does not allow converting edits to the LaTeX document back to the .Rd document.
Look at Sweave, maybe it helpful for you.
Sweave is a tool that allows to embed the R code for complete data analyses in latex documents.
The purpose is to create dynamic reports, which can be updated automatically if data or analysis change. Instead of inserting a prefabricated graph or table into the report, the master document contains the R code necessary to obtain it. When run through R, all data analysis output (tables, graphs, etc.) is created on the fly and inserted into a final latex document.
The report can be automatically updated if data or analysis change, which allows for truly reproducible research.
Check out printr http://yihui.name/printr/ . It should do what you need if you are using knitr.
The problem with Rd2latex is that i haven't figured out which style file I need to use, otherwise it works fine.
When you generate the latex code with the Rd2latex function, make sure that you copy the Rd.sty file from the R directory, paste it and somewhere that latex can see it and use \usepackage{Rd}.
Try the knitr package, an easy way to generate flexible and fast dynamic reports with R for LaTex.
Plain and simple: is there a way to read (not run) .sas files on osx in order to rewrite old SAS programs in another language, e.g. R? Note I do not refer to reading sas data files – I know there are several ways, I am just interested in reading old SAS code.
.sas files containing SAS code should just be a text file. You can use any text editor that you like to open and modify these files. Since the system probably doesn't have .sas files associated with any particular program you can either use the "Open with" option when "right-clicking" on the file or you could open the editor first and then open the file from within the editor.
TextEdit will work. Another editor that I like is Komodo Edit.
If I load data(mtcars) it comes with a very neat codebook that I can call using ?mtcars.
I'm interested to document my data in the same way and, furthermore, save that neat codebook as a pdf.
Is it possible to save the 'content' of ?mtcars and how is it created?
Thanks, Eric
P.S. I did read this thread.
update 2012-05-14 00:39:59 PDT
I am looking for a solution using only R; unfortunately I cannot rely on other software (e.g. Tex)
update 2012-05-14 09:49:05 PDT
Thank you very much everyone for the many answers.
Reading these answers I realized that I should have made my priorities much clearer. Therefore, here is a list of my priorities in regard to this question.
R, I am looking for a solution that is based exclusively on R.
Reproducibility, that the codebook can be part of a automated script.
Readability, the text should be easy to read.
Searchability, a file that can be open with any standard software and searched (this is why I thought pdf would be a good solution, but this is overruled by 1 through 3).
I am currently labeling my variables using label() from the Hmisc package and might end up writing a .txt codebook using Label() from the same package.
(I'm not completely sure what you're after, but):
Like other package documentation, the file for mtcars is an .Rd file. You can convert it into other formats (ASCII) than pdf, but the usual way of producing a pdf does use pdflatex.
However, most information in such an .Rd file is written more or less by hand (unless you use yet another R package like roxygen/roxygen2 help you to generate parts of it automatically.
For user-data, usually Noweb is much more convenient.
.Rnw -Sweave-> -> .tex -pdflatex-> pdf is certainly the most usual way with such files.
However, you can use it e.g. with Openoffice (if that is installed) or use it with plain ASCII files instead of TeX.
Have a look at package knitr which may be easier with pure-ASCII files. (I'm not an expert, just switching over from Sweave)
If html is an option, both Sweave and knitr can work with that.
I don't know how to get the pdf of individual data sets but you can build the pdf of the entire datasets package from the LaTeX version using:
path <- find.package('datasets')
system(paste(shQuote(file.path(R.home("bin"), "R")),"CMD",
"Rd2pdf",shQuote(path)))
I'm not sure on this but it only makes sense you'd have to have some sort of LaTeX program like MikTex. Also I'm not sure how this will work on different OS as mine is windows and this works for me.
PS this is only a partial answer to your question as you want to do this for your data, but if nothing else it may get the ball rolling.
The help page that is displayed when entering ?mtcars is generated from an .Rd file, which is a LaTeX-like file that is used for all of R's help pages. Although .Rd files are LaTeX-like, you don't actually need to know LaTeX to read or write them. The actual mtcars.Rd file is available here: http://commondatastorage.googleapis.com/jthetzel-public/mtcars.Rd , which can be viewed with any text editor.
.Rd files included in the ./man directory of a package are converted to .html files when installing the package. They are converted by functions in the "tools" package.. If you would like functionality like ?mtcars for your datasets, you would need to create a package for them. That might sound complicated if you have never created a package before, but it is easy enough to learn and will make you a better R programmer. There are a number of examples of dataset-only packages on CRAN, for example msProstate: http://cran.r-project.org/web/packages/msProstate/index.html . Consider downloading the package source to see how it is organized.
For more information on creating your own packages, writing .Rd files, and building packages:
http://cran.r-project.org/doc/manuals/R-exts.html, especially "1.1.5 Data in packages".
Edit
And if you want to convert the .Rd file in your package to a .pdf, you can do so when building your package, but you will need a LaTeX compiler. If you are on Windows, see here: http://cran.r-project.org/bin/windows/Rtools/ .
You can't create a PDF with just R; you need to use other software that creates PDFs.
You could use a combination of utils::promptData, tools::Rd2HTML, and a simple custom function to open the created HTML file in the users' browser.
It would probably be easier to just make a package containing your data sets. Look at the "datasets" package for an example.
It looks like that if you want to generate a pdf, an external tool like LaTeX is always needed. I would recommend using a simple ASCII text format to generate such a file. In principle the .Rd files are also ASCII text, but I do not find them particularly readable.
Instead, I would recommend using a plain text ASCII format such as Markdown (which is e.g. used on StackOverflow) to write the text file. Such a file is already much more readable than an .Rd formatted file, and as a bonus it can quite easily be processed into a PDF should you choose to do so later on. The knitr package I think is capable of generating PDF files from Markdown sources. In addition, knitr allows you to mix in R code in the Markdown text. This code can be evaluated and the results (even figures) added to the resulting PDF.
In practice you can use sprintf to generate character vectors that you can pipe to a file in order to dynamically generate the markdown text. Just write the template one time, and mark the places for the text you want to add later like this:
base_text = "
First header
============
This document was generated on %s, by %s.
"
text_forfile = sprintf(text, some_date, some_name)
Just dump the text in text_forfile to a .md file and your done, no external tools needed. See this post on SO for how dump text to a file.