Roxygen also plays a prominent roll in the devtools package, a package developed by hadley wickham of rstudio that makes it easier to build and document r packages. Add documentation this always seemed like the most intimidating step to me. The r programming language r core team 20 has become one of the most dominant programming languages for data analysis and visualization in recent years. Return a vector of names of packages loaded by devtools. R create reference manual with r cmd check stack overflow. A variety of diagnostic checks on directory structure, index and control files are performed.
A comprehensive index of r packages and documentation from cran, bioconductor, github and r forge. Before we start creating r packages we have to clarify some terms which sometimes get confused. A read is counted each time someone views a publication summary such as the title, abstract, and list of authors, clicks on a figure, or views or downloads the fulltext. Take the first num rows of a sparkdataframe and return the results as a r ame. Dec 17, 2019 using roxygen for package documentation is generally much easier than composing rd files directly and is highly recommended for new package documentation. Create start a new plot frame graphicsdefunct defunct functions in package graphics graphics package the r graphics package grid add grid to a plot hist histograms hist. If youre releasing the package to a more specific audience, interested either in the data e. This tutorial is meant as a starting point on how to create an r package, see r development core team 2008b for the full reference manual. Here is my understanding of how to do it, i create an empty rpackage project on rstudio and then have a source file named getsomething. To add documentation to an r package, you need to create a subdirectory man containing a set of files, one per function, in a special r documentation format. You can find more information on the markdown syntax for citations in the bibliographies and citations article in the online documentation. R provides a standard way of documenting the objects in a package. You dont actually need to write a r package to get your c code into there, but once youve already fought 710ths of the battle, you might as well complete the whole.
Documentation document collections, journals and proceedings. I find package vignettes useful because they can be access directly from r via vignette, and thus also be linked in other documentation. Consider different audiences when writing package documentation. Anyway, my question is how do i create a pdf documentation of my package and its functions. The whole package creating process worked without any errors and warnings. Apr 24, 2020 if you are using github, the easiest way to make this your package website is to check into git, then go to settings for your repo and make sure that the github pages source is set to master branch docs folder. An extension of the r base system with code, data and documentation in standardized format. You can create a new rd file for an existing function, dataset. As you prepare a package for sharing with others, you may want to create a pdf manual, which provides a more userfriendly format for proofreading all the package help files. Posixt histogram of a date or datetime object identify identify points in a scatter plot image display a color image layout specifying complex plot arrangements legend add. And r is a free software environment for statistical computing and graphics, used by people like me. I can get a pdf manual using r cmd but i am really curious as to whether this can be done using devtools.
The package uses the latex document class apa6 and a. Instead of writing these files by hand, were going to use roxygen2 which turns specially formatted comments into. Less documentation generally results in higher burdens, so its best add extensive documentation as early as possible. I am making an r package using devtools and roxygen2. This is a minimum, and will be increased with a warning if necessary. Translations of manuals into other languages than english are available from the contributed documentation section only a few translations are available the latex or texinfo sources of the latest version of these documents are contained in every r source distribution in the subdirectory docmanual of the extracted archive. Then on the following screen specify the project type as r package. Browsable html versions of the manuals, help pages and news for the developing versions of r rpatched and rdevel, updated daily. I use the following directoryfile structure in my package. Without it, users wont know how to use your package. Check r packages from package sources, which can be directories or package tar archives with extension.
Rd or r documentation files when you created your package. Documentation is also useful for futureyou so you remember what your functions were supposed to do, and for developers extending your package. Instructions for creating your own r package in song kimy phil martinz nina mcmurryx andy haltermanmarch 18, 2018 1 introduction the following is a stepbystep guide to creating your own r package. You can use it for descriptive statistics, generalized linear models, kmeans clustering, logistic regression, classification. They include reusable r functions, the documentation that describes how to use them, and sample data. Now, any package can provide a vignette engine, a standard interface for. The package roxygen2 provides a tool for creating documentation from annotated. For more details see the documentation on r markdown metadata. These will be the source for the documentation for each function. The package roxygen2 that makes everything amazing and simple. Be sure to update the url on your github repository homepage so others can easily navigate to your new site. Even beyond this course, you may nd this useful for storing functions you create for your own research or for editing existing r packages to suit.
Many aspects of the latex template used to create pdf documents can be customized using metadata. This was challenging because sweave only worked with latex, and latex is both hard to learn and slow to compile. To create a new package use the create project command available on the projects menu and on the global toolbar and select the new directory option. The revoscaler library is a collection of portable, scalable, and distributable r functions for importing, transforming, and analyzing data at scale. To add documentation to an r package, you need to create a subdirectory man. Here is my understanding of how to do it, i create an empty r package project on rstudio and then have a source file named getsomething. Rd files are saved in the man directory of an r package.
The whole packagecreating process worked without any errors and warnings. These files use a custom syntax, loosely based on latex, and are rendered to html, plain text and pdf for viewing. Now, any package can provide a vignette engine, a standard interface for turning input files into html or pdf vignettes. I am able to create the packag successfully and on load able to use the functions too. In this directory you could find the file packagemanual. Asking for help, clarification, or responding to other answers. The goal of this book is to teach you how to develop packages so that you can write your own, not just use other peoples.
I am trying to add documentation via roxygen2 in a package. Note that if you have existing r scripts that youd like to use as the basis for the new package you can specify them here and. They include reusable r functions, the documentation that. R processes them to create plain text, pdf, and html versions. The quality of documentation for an r package can determine success or failure. Moreover, papaja supplies rfunctions that facilitate reporting results of your analyses in accordance with apa guidelines. Packages are the fundamental units of reproducible r code. The package roxygen2 provides a tool for creating documentation from annotated source code much like doxygen, javadoc and docstringspydoc do. You can create one with the r cmd rd2pdf shell command. Using roxygen for package documentation is generally much easier than composing rd files directly and is highly recommended for new package documentation.
Create start a new plot frame graphicsdefunct defunct functions in package graphics graphicspackage the r graphics package grid add grid to a plot hist histograms hist. I managed to create a package using rstudio and roxygen2. If you are using github, the easiest way to make this your package website is to check into git, then go to settings for your repo and make sure that the github pages source is set to master branch docs folder. A package in r is simply a reusable r functions with standard and selfexplanatory documentation on how to use it. Making an r package pdf manual using devtools stack overflow. The r graphics model does not distinguish graphics objects at the level of the driver interface. R package, show how to document the code properly and nally discuss the tools for package validation and distribution. Create a sparkdataframe from a sparksql table or view. Nov 21, 2012 creating the package choose create new project, file new project.
You can read more about the rd format in the r extensions manual. Documentation is one of the most important aspects of a good package. In addition to the manuals, faqs, the r journal and its predecessor r news, the following sites may be of interest to r users. A comprehensive index of r packages and documentation from cran, bioconductor, github and rforge. The package is installed into the log directory and production of the package pdf manual is tested. Writing an r package from scratch not so standard deviations.
To use this, open a shell and navigate to the parent directory of your r package directory an easy way to do this. If you arent already familiar with the basics of r package development, the following links provide additional documentation and tutorials. Choose y when asked about using a personal library, and y again if asked to create one. See the documentation on pandoc online documentation for details on creating custom templates. In case you want to save larger maps produced with mapview i. Thanks for contributing an answer to stack overflow.
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