How to include raw data in an R package - r

I'm working on the final assignment of the course Building R Packages.
In this assignment, we need to create an R package based on some example functions provided by the instructors. We need to organize and document the package, then make it available on GitHub. My package is called FARS and is already available in this GitHub repo.
I'm having trouble with making raw data available with the package. After following the instructions provided in the course's readings and also in chapter 14.3 of the book Building R Packages, the files are still not being recognized.
What did I do so far?
Prepared all the package's documentation, including roxygen2 tags, DESCRIPTION, README.Md, and vignette, following these steps in addition to instructions provided in the readings and book mentioned;
Created a subdirectory named inst/extdata in the package's directory;
Copied all three example files (.csv.bz2) with raw data to inst/extdata;
Tested the functions using testthat;
Installed my FARS package.
Now I'm trying to check if one of the files is available after installing the package:
system.file("extdata", "accident_2013.csv.bz2",
package = "FARS",
mustWork = TRUE)
I get an error message:
Error in system.file("extdata", "accident_2013.csv.bz2", package = "FARS", :
no file found
These data files need to be available with the package, so the examples provided in the vignette work properly.

Here's a "real-life" example, using a simple package I wrote recently.
I have a "data" directory in the build directory.
EDIT To clarify the comments found in R-exts, the directory tree packagename/inst/extdata is intended for data that your functions call directly, by specifying that directory path. Since you want to load data into your workspace, use the data directory.
My "data" directory contains one file named preciseNumbersAsChar.r . That file contains assignments such as
charE <- {long number string}
If you read the help page for the command data, it explains that files ending in .r are sourced when called.
library(FunWithNumbers)
data('preciseNumbersAsChar') #works
Which is to say, the defined objects are now in my environment.
It's worth reading the help page for data in detail as different file types are handled slightly differently.

Related

How do I reference a model object in the example section of documentation in an R package

I'm creating an R package. In my package project folder, I have a model object saved as a .rds file. in a folder called data. Additionally, I have a function saved in the R folder.
How do I reference the model object in the example section of documentation of the function in the R folder?
I also have the same questions for dataset files saved as .rds files in the data folder. How do I reference those datasets in the example section when documenting functions.
Everything you need you could find out in the R packages book which is distributed for free. Hadley Wickham and Jenny Bryan
This part of the book is directly connected with your question but please check others too
I recommend usage of usethis package, which togather with roxygen2 does most things you need.

How to use an R package's own data when writing a vignette

I have written most of an R package and now wish to write a vignette that uses my own data, that is already in the package. The data is correctly stored as my_data.Rda in the Data folder, and when the package is loaded I can access it in the Console, for instance by using data(my_data).
My problem comes when, using usethis::use_vignette("my_vignette") , I want to include something like this (much more complex in practice, of course) in the vignette:
The mean of my_data is given by
```{r} data(my_data)
mean(my_data)
```
When I knit the vignette I get the message
"Error in assert_engine(is_numeric, x, .xname = get_name_in_parent(x),
: object 'my_data' not found"
I have looked at this post: How to add external data file into developing R package? but that addresses external data.
What am I doing wrong?
I have created a minimal R package with the relevant Rmd file in the vignettes folder. link to Github
I think you are supposed to use
data(my_dataset, package = "my_package")
to load your package's data into the session where your vignette is built.
Could you confirm that your datasets are stored inside the ./data directory of your package as *.rda files

Edit the default PDF manual generated while building R package

I have succsesfully performed the below steps to create my own R package :
created skeleton of the package and pasted .Rd, NAMESPACE and DESCRIPTION files.
executed R CMD check package_name : no errors, it also generated 2 pdf's
One of which contains the output's from .Rd file examples and second is the PDF manual that comprises the documentation itself.
My question is how to make edits to this manual created, such as to change the font size or add an Introductory page to this manual? I read that roxygen / devtools might help but no resource on that was attained. I also went through the Writing R Extensions link that is available but couldn't help me.
Would there be a way using Rd2pdf? but such that even non .Rd files are also included

How to access/open arbitrary formatted (.pdf etc) documents from R's console?

http://cran.r-project.org/doc/manuals/r-release/R-exts.html#Writing-package-vignettes states:
"...In addition to the help files in Rd format, R packages allow the inclusion of documents in arbitrary other formats. The standard location for these is subdirectory inst/doc of a source package, the contents will be copied to subdirectory doc when the package is installed. Pointers from package help indices to the installed documents are automatically created. Documents in inst/doc can be in arbitrary format, however we strongly recommend providing them in PDF format, so users on almost all platforms can easily read them..."
I used roxygen package. It produced .Rd files for me. I produced .pdf of my package via " R CMD Rd2pdf causfinder/" from Windows command line ( or, via during build/install process via "roxygenize("causfinder"); build("causfinder"); install("causfinder")".)
I wanted to add some supplementary .pdf help files (that I created outside of R; from Word via save as .pdf etc.) to my package other than the one that is produced via above techniques. These supplementary .pdf files include the detailed mathematical theory and lots of samples of the functions of my package which illustrate the usage of the functions via various plots, graphs, etc. I called it TheoryOfcausfinder.pdf.
I wanted to add this supplementary .pdf file to my package. As is directed from R's above manual, I put TheoryOfcausfinder.pdf to inst\doc folder in my R's working directory. Upon build/install process, I obtained causfinder/doc/index.html and causfinder/doc/TheoryOfcausfinder.pdf in my R's library location.
The content of index.html:
"...Vignettes from package 'causfinder': The package contains no vignette meta-information.
Other files in the doc directory: TheoryOfcausfinder.pdf..."
I want the future users of causfinder to easily access/open this supplementary TheoryOfcausfinder.pdf. (I will add that there is such a file in functions' help documents)
Is there a way to open/access TheoryOfcausfinder.pdf in R's library location from (within) R's console?
(Important: By the way, since I am novice of Sweave and knitr, I do not wanna enter that path! I look for a solution outside Sweave and knitr.)
Any help will be greatly appreciated.
I don't know if you have found another solution or not yet, but I am posting some possible ideas below.
source http://www.r-bloggers.com/show-me-the-pdf-already/
# under Unix types
pdf <- getOption("pdfviewer", default='')
f <- system.file("doc", "TheoryOfcausfinder.pdf", package = "causfinder")
system2(pdf, args = f)
source http://www.r-bloggers.com/show-me-the-pdf-already/
# under MS Windows
f <- system.file("doc", "TheoryOfcausfinder.pdf", package = "causfinder")
shell.exec(normalizePath(f))
source Opening PDF within R studio using file.show studio-using-file-show/33791818
# under OS X
f <- system.file("doc", "TheoryOfcausfinder.pdf", package = "causfinder")
system2('open', args = f, wait = FALSE)

Where is the .R script file located on the PC?

I want to find the location of the script .R files which are used for computation in R.
I know that by typing the object function, I will get the code which is running and then I can copy and edit and save it as a new script file and use that.
The reason for asking to find the foo.R file is
Curiosity
Know what is the algorithm used in the numerical computations
More immedietly, the function from stats package I am using, is running results for two of the arguments and not the others and have to figure out how to make it work.
Error shown by R implies that there might be some modification required in the script file.
I am looking for a more general answer, if its possible.
Edit: As per the comments so far, here is the code to compute spectrum of a time series using autoregressive methods. The data input is a univariate series.
x = ts(data)
spec.ar(x, method = "yule-walker") 1
spec.ar(x, method = "burg") 2
command 1 is running ok.
command 2 gives the following error.
Error in ar.burg.default(x, aic = aic, order.max = order.max, na.action = na.action, :
Burg's algorithm only implemented for univariate series
I did try specify all the arguments correctly like na.action=na.fail, order.max = NULL etc but the message is the same.
Kindly suggest possible solutions.
P.S. (This question is posted after searching the library folder where R is installed and zip files which come with packages, manuals, and opening .rdb, .rdx files)
See FAQ 7.40 How do I access the source code for a function?
In most cases, typing the name of the function will print its source
code. However, code is sometimes hidden in a namespace, or compiled.
For a complete overview on how to access source code, see Uwe Ligges
(2006), “Help Desk: Accessing the sources”, R News, 6/4, 43–45
(http://cran.r-project.org/doc/Rnews/Rnews_2006-4.pdf).
When R installs a package, it evaluates all the ".R" source files and re-saves them into a binary format for faster loading. Therefore you typically cannot easily find the source file.
As has been suggested elsewhere, you can simply type the function name and see the source code, or download the source package and find the source there.
library(plyr)
ddply # prints the source for ddply
# See the content of the R directory for plyr,
# but it's only binary files:
dir(file.path(find.package("plyr"), "R"))
# [1] "plyr" "plyr.rdb" "plyr.rdx"
# Get the source for the package:
download.packages("plyr", "~", type="source")
# ...then unpack and inspect the R directory...
.libPaths() should tell you all of your current library locations. It's possible to have more than one installation of a package if there are two libraries but only the one that is in the first library will be used. Unless you offer the code and the exact error message, it's not likely that anyone will be able to offer better advice.
I think you are asking to see what I call the source code for a function in a package. If so, the way I do it is as follows, which has worked successfully for me on the three times I have tried. I keep these instructions handy in a few places and just copied and pasted them here:
To see the source code for a function in Program R download the package containing the function. Specifically, download the file that ends in "tar.gz". This is a compressed file. Expand the compressed file using, for example, "WinZip". Now you need to open the uncompressed file that ends in ".tar". Download the free software "7-Zip". Click on the file "7zFM.exe" and navigate to the directory containing the ".tar" file. You can extract the contents of that ".tar" file into a new folder. The contents consist of R files showing the source code for the functions in the R package.
EDIT:
Today (July 8, 2012) I was able to open the 'tar.gz' file using the latest version of 'WinZIP' and could copy the contents (the source code) from there without having to use '7-Zip'.
EDIT:
Today (January 19, 2013) I viewed the source code for functions in base R by downloading the file
'R-2.15.2.tar.gz'
To download that file go to the http://cran.at.r-project.org/ webpage and click on that file in this line:
"The latest release (2012-10-26, Trick or Treat): R-2.15.2.tar.gz, read what's new in the latest version."
Unzip the file. WinZip will work, or it did for me. Then search your computer for readtable.r or another base R function.
agstudy noted here https://stackoverflow.com/questions/14417214/source-file-for-r-function that source code for read.csv is located in the file readtable.r, so do not expect every base R function to have its own file.

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