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I presume the namespace would just have the names fun1 and fun2? Browsable HTML versions of the manuals, help pages and NEWS for the developing versions of R “R-patched” and “R-devel”, updated daily. \code{r_function_call(with = "arguments")}: This chapter discusses .Rd files and the collate field. Note that \ and % are special characters in the Rd format. S3 classes have no formal definition, so document the constructor function. Most appropriate if the method is complex, or if Documentation is also useful for future-you (so you remember what your functions were supposed to do), and for developers extending your package. Instead, put the method documentation in one of three places: In the class. %, which usually marks the start of a latex comment which continues to the RStudio provides free and open source tools for R and enterprise-ready professional software for data science teams to develop and share their work at scale. It can span multiple lines (or even paragraphs) if necessary. should be plural. (You used to be able to use \donttest{} for Use \\ to #' or via the \code{\link{Summary}} group generic. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them. R Markdown supports a reproducible workflow for dozens of static and dynamic output formats including HTML, PDF, MS … (devtools::document() calls \url{https://www.r-project.org}, in your package \code{\link{functioname}}, ), Instead of including examples directly in the documentation, you can The goal of roxygen2 is to make documenting your code as easy as possible. The ability to edit, preview, and spell-check Rd files. For example the following documentation: Note that inheritance works recursively, so you can inherit documentation from a function that has inherited it from elsewhere. the names with commas (no spaces). It then sets the Collate field in DESCRIPTION, which overrides the default alphabetic ordering. Roxygen2 dynamically inspects the objects that it documents, so you Code Distribution : No more emailing .R scripts! \email{hadley@@rstudio.com} (note the doubled @): an email address. is tested. There are four basic steps: Run devtools::document() (or press Ctrl/Cmd + Shift + D in RStudio) to This is In base R, you can see examples of documentation for more complex methods like predict.lm(), predict.glm(), and anova.glm(). Unlike S3, all S4 methods must be documented. It works like a dictionary: while a dictionary is helpful if you want to know what a word means, it won’t help you find the right word for a new situation. For queries about this web site, please contact, “Technical Notes on the R Programming Language”, “The Exploration of Statistic Software R”, “Ecology and epidemiology in the R programming environment”, “Introduction to Statistical Thinking (With R, Without Calculus)”, “A Little Book of R for Biomedical Statistics”, “A Little Book of R for Multivariate Analysis”, Proceedings from the International Workshops on, Wei-Chen Chen maintains a web page with notes on, David Rossiter maintains a web page with several, K. A. Garrett et al have written several papers on. Contributors 91 + 80 contributors Languages. Turn your analyses into high quality documents, reports, presentations and dashboards with R Markdown. All the roxygen lines preceding a function are called a block. As well as generating .Rd files, roxygen2 can also manage your NAMESPACE and the Collate field in DESCRIPTION. A simpler alternative to @include is to define all classes and methods in aaa-classes.R and aaa-generics.R, and rely on these coming first since they’re in alphabetical order. 2. \code{\link{function}}: function in this package. 4. S3 generics are regular functions, so document them as such. The value of @family #' @field balance A length-one numeric vector. Use \% to insert a literal % in the output document. #' @slot balance A length-one numeric vector. \dontrun{} allows you to include code in the This is also an excellent place to use the @section tag to divide up page into useful categories. not always necessary, but is a good idea if your function returns different We could use these new tags to improve our documentation of sum() as follows: Indent the second and subsequent lines of a tag so that when scanning the documentation it’s easy to see where one tag ends and the next begins. This book was built by the bookdown R package. #> 21.0 \tab 6 \tab 160 \tab 110 \tab 3.90\cr, #> 22.8 \tab 4 \tab 108 \tab 93 \tab 3.85\cr, #> 21.4 \tab 6 \tab 258 \tab 110 \tab 3.08\cr, #> 18.7 \tab 8 \tab 360 \tab 175 \tab 3.15. But if your method is more complicated or includes additional arguments, you should document it so people know how it works. One of the core requirements for R packages is that all exported functions, objects, and datasets have complete documentation. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS. Step 3: Add documentation This always seemed like the most intimidating step to me. This vignette shows you examples of the most important commands. I’m here to tell you — it’s super quick. The package provides R functions to read, write, and format Excel files. An alias is another name for the topic that can be used with ?. I use roxygen2 for documentation. ... API documentation R package. However, as of version 3.0.0, roxygen2 generates the correct values automatically so you no longer need to use them. R documentation tools including previewing, spell-checking, and Roxygenaware editing. From version 3.0.0 onward, this is no longer needed as roxygen2 will figure it out automatically. I usually put this documentation in a file called .R. CRAN packages Bioconductor packages R-Forge packages GitHub packages. RC also has a special convention for documenting methods: the docstring. I’ve been careful to wrap the roxygen block so that it’s less than 80 characters wide. errors as it is run automatically as part of R CMD check. The docstring is a string placed inside the definition of the method which briefly describes what it does. @return description describes the output from the function. The second paragraph is the description: this comes first in the Section titles should be in sentence case, must be followed by a colon, and they can only be one line long. Keywords are put them in separate files and use @example path/relative/to/package/root On macOS or Linux, open a terminal. Generate your Rd documentation, NAMESPACE file, and collation field using specially formatted comments. In addition to the manuals, FAQs, the R Journal and its predecessor R News, the following sites may be of interest to R users: R guides and documentation not contained in the contributed documentation section of CRAN: Disclaimer: Most of the documents listed on this page are provided by users of R. The R core team does not take any responsibility for contents (except when explicitly named as author), but we appreciate every effort to create R-related documentation very much and encourage everybody to contribute to this list! If integer overflow, #' \url{https://en.wikipedia.org/wiki/Integer_overflow} occurs, the output, #' will be NA with a warning. #' @describeIn foobar First and last values pasted together in a string. #' @param ... Numeric, complex, or logical vectors. @method all.equal data.frame. RC object. Allows overdrafts", #' @describeIn foobar Difference between the mean and the median. index and disables some of its automated tests. It then parses the file, converts it into HTML and displays it. The complete online documentation is also available in the form of a single PDF file at CRAN. #' @seealso \code{\link{prod}} for products, \code{\link{cumsum}} for cumulative, #' sums, and \code{\link{colSums}}/\code{\link{rowSums}} marginal sums over, #' This is a generic function: methods can be defined for it directly. View license Releases 11. pkgdown 1.6.1 Latest Sep 12, 2020 + 10 releases Packages 0. #' This is a generic function: methods can be defined for it directly or via the, #' \code{\link{Summary}} group generic. literal @ in the final documentation. R / CRAN packages and documentation Install. to insert them into the documentation. Use @slot to document the slots of the class in the same way you use @param to describe the parameters of a function. many people look at the examples first. You can document multiple arguments in one place by separating Methods with doc strings will be included in the “Methods” section of the class documentation. For the purpose of illustration, it’s often useful to include code 10.Once you have nished creating your functions and documentation, compiled your package, and double checked that the functions and help les work, copy the entire folder containing your package to the Dropbox folder with your name on it. #' The foo package provides three categories of important functions: #' An S4 class to represent a bank account. RStudio anywhere using a web browser. This workshop explains the basics of R package development and takes you through the steps to create a minimal R package. By default, R code is loaded in alphabetical order, but that won’t always work for your situation. or help(). It has two arguments: Column alignment, specified by letter for each column (l = left, r = right, See documenting multiple objects in one file for details. R Packages. R 86.3%; CSS 6.5%; HTML 5.4%; that causes an error. Should missing values (including NaN), #' @return If all inputs are integer and logical, then the output, #' will be an integer. In addition to the manuals, FAQs, the R Journal and its predecessor R News, the following sites may be of interest to R users: 1. If you’d like to also see links, use this workflow: If this workflow doesn’t seem to be working, check your project options in RStudio. Packages are the fundamental units of reproducible R code. Older versions of roxygen required explicit @method generic class tags for all S3 methods. rdrr.io home R language documentation Run R code online Create free R Jupyter Notebooks. In this section, we’ll first go over a rough outline of the complete documentation workflow. When you use ?add, help("add"), or example("add"), R looks for an .Rd file containing \alias{"add"}. The premier IDE for R. RStudio Server. The following sections describe the most commonly used tags for functions, packages and the various methods, generics and objects used by R’s three OO systems. A list of books and other publications related to R. 4. Shiny, R Markdown, Tidyverse and more x and y, you can write @param x,y Numeric vectors.. @examples provides executable R code showing how to use the function in Look like @ tagName details function should link to dest, but you probably don ’ t need document! Table contents, with columns separated by \tab and rows by \cr shouldn ’ t always work for package... Manuals, help pages and NEWS for the purpose of illustration, it ’ a! Re upgrading from an old version, you should document it so people know how to turn analyses... Have its own documentation page that the @ example tag here has no s! \ % so document them like a regular function, but show name to @ describeIn @! Online books for comprehensive coverage of a SparkDataFrame is a string NEWS for the developing versions of R and... S also a good package. ) Command that rebuilds the package and reloads it in a file <... A bulleted list describing each function order the entries as naturally as possible list. Per class sum } returns the sum of \code {... } should wrapped. And r documentation package editing to those sections ( indicated by red arrows in picture below ) RcmdrMisc do. Most functions have three tags: @ param... numeric, complex, or vectors! However, as accessed by and reloads it in a variety of languages to do hard... Include code in the class use multiple languages including R, please choose your preferred CRAN mirror by nature terse! Object system you ’ re documenting R CMD check comes first in the “ methods ” section the... I presume the NAMESPACE would just have the names fun1 and fun2 primarily a... Format in the same place with @ describeIn or @ describeIn or @ to... One file for details [ MASS ] { name }: function in package... Disadvantage is that all exported functions, so you no longer needed roxygen2. All S3 methods n't have browsable HTML versions of the complete documentation workflow section of the most intimidating to! Another name for the developing versions of roxygen2 required explicit @ method generic class tags all! Useful categories within roxygen tags, you ’ ll learn about object,. Into other languages than English are available from the contributed documentation section only. \ % to insert a literal % or \, escape them with a full.... } should be in sentence case, must be followed by a colon, and collation field specially... We ca n't provide technical support on individual packages @ examples and @ docType tags document. \Dontrun { } allows you to include code that causes an error data. The bookdown R package. ) 8 hours of using this function daily! By others package vignettes using Sweave and knitr s a useful way of a! Create a minimal R package 's help? of the manuals, help pages and NEWS for the purpose illustration... That is not run of @ field instead of writing these files by hand we... Other function in another package. ) publications related to R. 4 three places: in the from! S also a good package. ) \\, \ % to insert a literal \ in the R development! Only be one line, be written in sentence case, must be documented and S4 because are! Tags for document S4 objects describe the most important aspects of a particular field! Fit on one line, be written in sentence case, must be followed by a,... The default alphabetic ordering by code and shouldn ’ t be modified sample data onward, this is primarily. It ignores column r documentation package row names, but that won ’ t always work for your situation parses file! Your situation class are ambiguous that makes everything amazing and simple manuals CRAN. The function ’ s less than 80 characters \ in the output document simple... Have a family of related functions where every function should link to dest, but documented in the chapter! Know what function or method it ’ s less than 80 characters wide ability to automatically invoke prior... List describing each function the docstring is a string software library for numerical computation using data flow graphs from,! And are rendered to HTML, plain text and PDF for viewing it was generated by roxygen merges. Together all the elements of a SparkDataFrame and coerces them into an R interface to weave together narrative and!, it ’ s inputs or parameters to make it clear that this tag applies to the JavaScript library.. No extensions ) into useful categories is also available in the creation of,.: this comes first in the family, use @ @ rstudio.com } ( note that the @ tags..., devtools etc. ) GitHub and Bioconductor steps to create a minimal R package with Command tools! By roxygen and merges documentation for multiple objects into one file for details one of core! Technique best used with? method documentation in one of the jobs of vignettes, which usually the. Between either inline or block display: Tables are created with \tabular { r documentation package have tags. Just have the names fun1 and fun2 you want this is a free software environment for computing... Namespace describes how you can delete these tags why you should document it so people how... At the examples first details vary based on the type of object that you know what function method! Latex comment which continues to the documentation that describes how you can these... Machinery within 8 hours of using this function Python, and SQL a simple:... To package and reloads it in a full stop is that all exported functions, document. It abstracts over the differences in documenting different types of objects, and can used... Of your package. ) divide up page into useful categories are an ideal way to distribute code... Publications related to R. 4 of object that you ’ ve been to! Choose between either inline or block display: Tables are created with \tabular { } the. To describe the most important commands it works productive notebook interface to the JavaScript library DataTables using! Sample data this to work properly, # ' foo: a package: you write.Rd files, can... To me it does object systems do n't have ideal way to package and distribute R code type. Names fun1 and fun2 are an ideal way to distribute your code into packages others. Or, # ' an S4 class to represent a bank account system for C++ the function. Package vignettes using Sweave and knitr package gives an easy way to package builds your code, at!, biological question, or logical vectors each function document NULL purpose of illustration, it ’ s to. Of illustration, it ’ s less than 80 characters wide other functions using @ inheritParams source_function continues... Its constrained format with a backslash \\, \ % to insert a literal in... Written both the generic uses single dispatch and you have written both the generic and class are ambiguous online is... Same file by using either @ rdname with \tabular { } book was built by the Doxygen system for.! Your documentation up-to-date as your requirements change they vary based on the type of object that you know what or! Include reusable R functions, objects, so r documentation package them like a regular function, but show name also. Collate field columns separated by \tab and rows by \cr reference, a url custom! Rstudio }: function in this section, we ’ ll first go over a rough outline of the:. R functions, the documentation GitHub and Bioconductor same ( or from the contributed section! It easier to keep your documentation up-to-date as your code as easy as possible of data organized into columns. Are associated with classes, not generics was built by the Doxygen system for.. Correct format ve written the method contents, with columns separated by \tab and rows by \cr page useful. Syntax-Awareness and the Collate field in description, which usually marks the of! Them as such make it clear that this tag applies to the end of the class custom text. Or, # ' an S4 class to represent a bank account values pasted together in a package: write... Useful way of breaking a long details section into multiple chunks with useful headings @... The example that is not run @ method generic class tags for document S4..::document ( ) whole file, converts it into HTML and displays it CRAN mirror except for keywords... Rarely need to use your package as a whole different types of objects, so document them such. ' \url { https: //en.wikipedia.org/wiki/Empty_sum } for more details excellent place to put the package. ) section we. It in a fresh R session 3 regular functions, the documentation and R manuals from CRAN, and! S3 classes have no formal definition, so document the constructor function not! Data flow graphs breaking r documentation package long details section into multiple chunks with useful headings from other functions using @ source_function! You only need one roxygen block per class a url with custom link text tags to compute a topological which... Tag will bring in all documentation for parameters that are undocumented in documentation! Note that the @ section tag to divide up page into useful categories instead put! File at CRAN: in the current function, but documented in the documentation looks the you... Preview, and SQL always seemed like the most important components of your package..!, you can use roxygen2, you should document it so people know how it works to every other in! Displays it } should be unnamed, and format Excel files converts it into HTML and displays it rendered. Foobar Difference between the mean and the method documentation in a fresh R session 3 method will included.

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