I am doing report generation in R with knitr.
So basically I have a dataset, do some preprocessing and then call knitr to output an html report.
This means the entire workflow consists of several R code files and some .Rhtml templates which are needed later on for report generation.
I would like to wrap all of this into a R package.
Having just .r files I would just run package.skeleton() and have a start..
But, how do I deal with the .Rhtml files. What is the proper way to deal with these when building a R package?
Thanks,
Ben Bolkers answer:
put them in a directory within an inst directory and use system.file() to retrieve them.
Related
In order to include statistical tables when using R-exams, I know that one can just use the option pages inside the function exams2nops(). But when using exams2moodle() how should one proceed?
In Moodle one can upload a file within a question and add a link to the embedded file. Is it possible to do it through R exams?
You can easily include various kinds of supplementary files in R/exams and then export them to Moodle or other learning management systems. Two steps need to be taken:
While processing the .Rmd or .Rnw exercise the supplementary file(s) need to be created in the current working directory (which is a temporary directory by default). This can either be done be creating the file via some R code or by copying an existing file. The convenience function include_supplement() simplifies this.
The supplementary file then needs to be included as a link in the question text. In .Rmd this would be something like [myfile.pdf](myfile.pdf) and in .Rnw exercises \url{myfile.pdf}.
An example for such an inclusion is the lm exercise template shipped along with the package, see: http://www.R-exams.org/templates/lm/. This exercise creates a .csv file on the fly within R and then includes it.
An example for the include_supplement() function is available in the Rlogo exercise template that copies the R logo image from the R system and then includes it in the exercise. See: http://www.R-exams.org/templates/Rlogo/.
Final comment: For a distribution table it would also be possible to include this directly as an HTML table in Moodle. For example, you could generate suitable Markdown or LaTeX code within the R code of the exercise.
I wish to use libraries across multiple .Rmd files in an r notebook without having to reload the library each time.
An example: I have loaded the library kableExtra in the index.Rmd file but when I call it in another .Rmd file such as ExSum.Rmd I would get this error:
Error in Kable....: could not find funciton "kable" Calls:...
If I load the kableExtra library again this problem goes away. Is there a workaround?
R Markdown files are intended to be standalone, so you shouldn't do this. There are two workarounds that come close:
If you process your .Rmd files within the R console by running code like rmarkdown::render("file.Rmd") then any packages attached in the session will be available to the code in the .Rmd file.
You can put all the setup code (e.g. library(kableExtra)) into a file (called setup.R, for example), and source it into each document in the first code chunk using source('setup.R'). Every file will run the same setup, but you only need to type it once.
The second is the better approach.
I am writing a package and the sole purpose of this package is to create reports. I am using knit to generate the reports from a .Rnw file. This all happens within a function in the package. e.g.
create_report <- function(data) {
knit2pdf(from = "myreport.Rnw", to = "myreport.tex")
# The Rnw in the knit2pdf function uses the data passed to this function
}
My question is simple. Where within my package folders do I store the .Rnw file? Currently my package has the following folders:
.Rproj.user
data
man
R
I am just not sure where my Rnw scripts should go? Do I need another folder called LaTeX for example? This is like having a separate folder for C++ scripts, for example.
Note, I am not looking to create a vignette. I know how to do this. This package is used to do some data manipulation and then generate a report on the data.
I have tried to lay everything out as clearly as I can as some questions I have asked on here before have been misinterpreted. Please ask if anything is unclear.
To answer this question:
Include the .Rnw files in ./pkgname/inst/latex then when you build the package, the ./latex folder will go to the root level of the package. You can then extract the .Rnw files using system.file("latex", "mytemplate.Rnw", package = "pkgname").
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.
I wonder whether I can use knitr markdown to just create a report on the fly with objects stemming from my current workspace. Reproducibility is not the issue here. I also read this very fine thread here.
But still I get an error message complaining that the particular object could not be found.
1) Suppose I open a fresh markdown document and save it.
2) write a chunk that refers to some lm object in my workspace. call summary(mylmobject)
3) knitr it.
Unfortunately the report is generated but the regression output cannot be shown because the object could not be found. Note, it works in general if i just save the object to .Rdata and then load it directly from the markdown file.
Is there a way to use objects in R markdown that are in the current workspace?
This would be really nice to show non R people some output while still working.
RStudio opens a new R session to knit() your R Markdown file, so the objects in your current working space will not be available to that session (they are two separate sessions). Two solutions:
file a feature request to RStudio, asking them to support knitting in the current R session instead of forcibly starting a new session;
knit manually by yourself: library(knitr); knit('your_file.Rmd') (or knit2html() if you want HTML output in one step, or rmarkdown::render() if you are using R Markdown v2)
Might be easier to save you data from your other session using:
save.image("C:/Users/Desktop/example_candelete.RData")
and then load it into your MD file:
load("C:/Users/Desktop/example_candelete.RData")
The Markdownreports package is exactly designed for parsing a markdown document on the fly.
As Julien Colomb commented, I've found the best thing to do in this situation is to save the large objects and then load them explicitly while I'm tailoring the markdown. This is a must if your data is coming through an ODBC and you don't want to run the entire queries repeatedly as you tinker with fonts and themes.