Inst and Extdata Folders in R Packaging
In the Documentation, R Suggests That Raw Data Files (Not Rdata nor Rda) Should Be Placed in Inst/Extdata/ from the First Paragraph in: the Data Subdirectory...
In the documentation, R suggests that raw data files (not Rdata nor Rda) should be placed in inst/extdata/
From the first paragraph in:
The data subdirectory is for data files, either to be made available via lazy-loading or for loading using data(). (The choice is made by the ‘LazyData’ field in the DESCRIPTION file: the default is not to do so.) It should not be used for other data files needed by the package, and the convention has grown up to use directory inst/extdata for such files.
So, I have moved all of my raw data into this folder, but when I build and reload the package and then try to access the data in a function with (for example):
read.csv(file=paste(path.package("my_package"),"/inst/extdata/my_raw_data.csv",sep=""))
# .path.package is now path.package in R 3.0+
I get the "cannot open file" error.
However, it does look like there is a folder called /extdata in the package directory with the files in it (post-build and install). What's happening to the /inst folder?
Does everything in the /inst folder get pushed into the / of the package?
2 Answers
More useful than using file.path would be to use system.file. Once your package is installed, you can grab your file like so:
fpath <- system.file("extdata", "my_raw_data.csv", package="my_package")
fpath will now have the absolute path on your HD to the file.
You were both very close and essentially had this. A formal reference from 'Writing R Extensions' is:
1.1.3 Package subdirectories
[...]
The contents of the
instsubdirectory will be copied recursively to the installation directory. Subdirectories ofinstshould not interfere with those used by R (currently,R,data,demo,exec,libs,man,help,htmlandMeta, and earlier versions usedlatex,R-ex). The copying of theinsthappens aftersrcis built so itsMakefilecan create files to be installed. Prior to R 2.12.2, the files were installed on POSIX platforms with the permissions in the package sources, so care should be taken to ensure these are not too restrictive:R CMD buildwill make suitable adjustments. To exclude files from being installed, one can specify a list of exclude patterns in file.Rinstignorein the top-level source directory. These patterns should be Perl-like regular expressions (see the help forregexpin R for the precise details), one per line, to be matched(10) against the file and directory paths, e.g.doc/.*[.]png$will exclude all PNG files ininst/docbased on the (lower-case) extension.
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