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").
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 am writing a basic R package that reads in data from a user specified database and spits out a markdown report with predefined graphs and tables etc. I have placed the .Rmd file in the R folder, and have a user level function that reads in the data and knits it.
# create_doc.R
create_doc <- function(directory = NULL,
database_name_name) {
if (is.null(directory)) directory <- tclvalue(tkchooseDirectory(
title = "Choose Folder for Input and Output"))
rmarkdown::render("R/doc_generator.Rmd", output_dir = directory)
}
This works fine on my computer, but when I build the package, the .Rmd file has been deleted. This means I can't give it to other users for use on other computers. I realise that the R folder may not be the correct place for this file (I guess it deletes any files not ending in .R), but I'm not sure where else to put it. It is not package documentation, it creates the end result when using the package.
Googling has not helped so far. Is it possible to knit a document using a function in an R package? If yes, what am I doing wrong. If no, are there any other suggestions on how to achieve this?
I'm putting together an R package. I would like to show example code in the vignette, where example data files (included in the package) are used to generate an (example) output file.
I read about using example data in Hadley Wickham's post (http://r-pkgs.had.co.nz/data.html), and believe I should keep my example data as raw data, as it must be parsed to generate the output.
So, I created a directory in my package structure
/Users/userName/myPackage/inst/extdata/
with subdirectories InputFiles and OutputFiles.
And I put the example file (exampleData.csv) inside of the InputFiles subdirectory (/Users/userName/myPackage/inst/extdata/InputFiles).
My vignette is located in:
/Users/userName/myPackage/vignettes/myPackage.Rnw
It contains the following syntax:
<<eval=FALSE>>=
fileString = "/Users/userName/myPackage/inst/extdata/InputFiles/exampleData.csv"
doFunction1(fileString)
doFunction2(fileString)
doFunction3(fileString, output ="Users/userName/myPackage/inst/extdata/OutputFiles")
#
I am having two problems with developing this vignette and its example datasets:
1) I am unsure if my use of the extdata file is appropriate. This seemed to be the best directory name and location to place my example files, according to the aforementioned Hadley Wickham reference.
2) I am unsure how to make the pathways relative, instead of absolute, as I have them currently. This example code does not run automatically, as you can see. Instead, I have it under an R chunk of eval=FALSE so that it is simply listed there for the users to test themselves. After running the example code, the users can also check that the output file was indeed created in (/Users/userName/myPackage/inst/extdata/OutputFiles). What is the best way for me to allow the user to not have to use an absolute path when following the example? Is it possible to just follow a relative path from within the package directory myPackage?
My data files consist of .csv, .htm, and .text files. In the past, when constructing a package, I have saved a data frame as .rda file, and then the user could simply use:
data(example.rda)
to read that file. They would not have to write the entire pathway. Is there a similar function that can be used to read .csv, .html, and .text files, and then output them to an example output location - without having to use the full pathway? Would it be possible to have help functions that also read in the input files and write to the output files? Would this cause a conflict in CRAN if various example help functions in the /man folder physically save the example output file to the example output folder?
The standard way to refer to a file in a package is:
# gives root package directory
system.file(package="myPackage")
# specific file
system.file("extdata/InputFiles/exampleData.csv", package="myPackage")
# best is to use cross-platform way to write a file path:
system.file("extdata", "InputFiles", "exampleData.csv", package="myPackage")
When developing with devtools, the inst subdirectory is ignored, so you never need to worry about absolute paths. This should work in a vignette. Note that a vignette, I think, only ever uses the installed version of a package, not the one you may have loaded in your development environment (specifically, devtools::load_all() does not change the code which is used to build the vignette, you must install() it first).
Finally, using data() is a bit old fashioned. Hadley and others recommend using lazy data, so the data appears in the namespace automatically. Try the following in your DESCRIPTION.
LazyData: true
LazyDataCompression: xz
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.
I am making my first attempts to write a R package. I am loading one csv file from hard drive and I am hoping to bundle up my R codes and my csv files into one package later.
My question is how can I load my csv file when my pakage is generated, I mean right now my file address is something like c:\R\mydirectory....\myfile.csv but after I sent it to someone else how can I have a relative address to that file?
Feel free to correct this question if it is not clear to others!
You can put your csv files in the data directory or in inst/extdata.
See the Writing R Extensions manual - Section 1.1.5 Data in packages.
To import the data you can use, e.g.,
R> data("achieve", package="flexclust")
or
R> read.table(system.file("data/achieve.txt", package = "flexclust"))
Look at the R help for package.skeleton: this function
automates some of the setup for a new source package. It creates directories, saves functions, data, and R code files to appropriate places, and creates skeleton help files and a ‘Read-and-delete-me’ file describing further steps in packaging.
The directory structure created by package.skeleton includes a data directory. If you put your data here it will be distributed with the package.