The package roxygen2 that makes everything amazing and simple. #' @describeIn foobar First and last values pasted together in a string. Note that you … RC object. The following sections give the details for the S3, S4 and RC object systems. The second paragraph is the description: this comes first in the #> 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. You can use standard LaTeX math (with no extensions). Each block includes some text before the first tag.23 This is called the introduction, and is parsed specially: The first sentence becomes the title of the documentation. See documenting multiple objects in one file for details. R data objects (matrices or data frames) can be displayed as tables on HTML pages, and DataTables provides filtering, pagination, sorting, and many other features in the tables. or another package \code{\link[packagename]{functioname}}. If you are upgrading, make sure to remove these old tags. @describeIn is designed for the most common cases: It generates a new section, named either “Methods (by class)”, “Methods (by generic)” or “Functions”. The escape is not needed in examples. TensorFlow™ is an open source software library for numerical computation using data flow graphs. This vignette shows you examples of the most important commands. #' \code{...} should be unnamed, and dispatch is on the first argument. For the purpose of illustration, it’s often useful to include code can skip some boilerplate that you’d otherwise need to write by hand. that causes an error. Shiny, R Markdown, Tidyverse and more Documentation is one of the most important aspects of a good package. Package vignettes and manuals. Roxygen2 dynamically inspects the objects that it documents, so you You can read more about the Rd format in the R extensions manual. The ability to document multiple functions in the same place with In base R, you can see examples of documentation for more complex methods like predict.lm(), predict.glm(), and anova.glm(). The complete online documentation is also available in the form of a single PDF file at CRAN. Several online books for comprehensive coverage of a particular research field, biological question, or technology. Writing documentation in-line with code makes it easier to keep your documentation up-to-date as your requirements change. x and y, you can write @param x,y Numeric vectors.. @examples provides executable R code showing how to use the function in Within roxygen tags, you use .Rd syntax to format text. I can put fun1 and fun2 in separate .R files and add abit of #' but am unsure to include all relevant requirements for roxygen and also am unsure what to include as relevant requiremetns and how to use it to create the rd documentation to go with a package are. Similarly, object documentation is helpful if you already know the name of the object, but it doesn’t help you find the object you need to solve a given problem. From version 3.0.0 onward, this is no longer needed as roxygen2 will figure it out automatically. Old versions of devtools and RStudio did not automatically update the documentation when the package was rebuilt: Roxygen comments start with #' and come before a function. And do it all with R. Shiny is an R package that makes it easy to build interactive web apps straight from R. You can host standalone apps on a webpage or embed them in R Markdown documents or build dashboards. (devtools::document() calls to insert them into the documentation. RC also has a special convention for documenting methods: the docstring. If you need help with using the package, please post your question to the R-sig-meta-analysis mailing list, one of the R Project mailing lists specifically dedicated to discussing the use of R for conducting meta-analyses. 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. Use @slot to document the slots of the class in the same way you use @param to describe the parameters of a function. To make it clear that this tag applies to the whole file, and not a specific object, document NULL. #' foo: A package for computating the notorious bar statistic. All Support for authoring and previewing package vignettes using Sweave and knitr. Instead, put the method documentation in one of three places: In the class. The section contains a bulleted list describing each function. See. In the generic. If integer overflow, #' \url{https://en.wikipedia.org/wiki/Integer_overflow} occurs, the output, #' will be NA with a warning. Unless you change the R interpreter, conda will continue to use the default interpreter in each environment. to every other function in the family, use @family. For this to work properly, #' the arguments \code{...} should be unnamed, and dispatch is on the. There are multiple forms of documentation. The details vary based on the object system you’re using. Keywords are The @include tag gives a space separated list of file names that should be loaded before the current file: Often, it’s easiest to put this at the top of the file. is tested. Methods with doc strings will be included in the “Methods” section of the class documentation. ), Instead of including examples directly in the documentation, you can R provides a standard way of documenting the objects in a package: you write .Rd files in the man/ directory. Indeed, if you use roxygen2, you’ll rarely need to look at these files. Note that we can't provide technical support on individual packages. There are two ways to use @rdname. #' @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. 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 third and subsequent paragraphs go into the details: this is a Most appropriate if the method is complex, or if @keywords keyword1 keyword2 ... adds standardised keywords. You can document multiple arguments in one place by separating The full details are described in R extensions. Documentation is one of the most important aspects of a good package. Topics. (cats-package.r is auto-generated when you create the package.) RStudio includes several tools to assist in the creation of documentation, including: 1. It’s also a good place to put the package level import statements that you’ll learn about in imports. Build and Reload command that rebuilds the package and reloads it in a fresh R session 3. @param name description describes the function’s inputs or parameters. If you have a family of related functions where every function should link The reticulate package provides a comprehensive set of tools for interoperability between Python and R. The package includes facilities for: Calling Python from R in a variety of ways including R Markdown, sourcing Python scripts, importing Python modules, and using Python interactively within an R session. @keywords internal for functions that are of interest to other #' @param ... Numeric, complex, or logical vectors. The package provides R functions to read, write, and format Excel files. Search current and past R documentation and R manuals from CRAN, GitHub and Bioconductor. %, which usually marks the start of a latex comment which continues to the SparkDataFrames can be constructed from a wide array of sources such as: structured data files, tables in Hive, external databases, or existing local R data frames. #' or via the \code{\link{Summary}} group generic. 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 (.Rd).These will be the source for the documentation for each function; R processes them to create plain text, PDF, and HTML versions. Documentation » Bioconductor. R packages are an ideal way to package and distribute R code and data for re-use by others. 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. 2. The premier IDE for R. RStudio Server. You should contact the package authors for that. These files use a custom syntax, loosely based on LaTeX, and are rendered to HTML, plain text and pdf for viewing. In this book you’ll learn how to turn your code into packages that others can easily download and use. 10 Object documentation. c = centre.). 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. Browsable HTML versions of the manuals, help pages and NEWS for the developing versions of R “R-patched” and “R-devel”, updated daily. It’s a useful supplement to vignettes, as described in the next chapter. I use roxygen2 for documentation. "R Packages" was written by Hadley Wickham, Jennifer Bryan. It’s common to use There are two tags that make it easier for people to navigate between help files: @seealso allows you to point to other useful resources, either on the web, 3. In this section, we’ll first go over a rough outline of the complete documentation workflow. Without it, users won’t know how to use your package. I’m here to tell you — it’s super quick. 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. Documentation is also useful for future-you (so you remember what your functions were supposed to do), and for developers extending your package. If the documentation doesn’t appear, make sure that you’re using devtools and that you’ve loaded the package with devtools::load_all().). This chapter discusses .Rd files and the collate field. The source can be a function in the current package, via @inheritParams function, or another package, via @inheritParams package::function. have alphabetically entitled sections in their help/documentation and a bar of links to those sections (indicated by red arrows in picture below). Each line should be wrapped in the same way as your code, normally at 80 characters. Other packages (e.g., RcmdrMisc) don't have. As well as the introduction block, most functions have three tags: @param, @examples and @return. #' @field balance A length-one numeric vector. 3 Building R Package with Command Line Tools Instead of writing these files by hand, we’re going to use roxygen2 which turns specially formatted comments into .Rd files. \code{\link[MASS]{abbey}}: function in another package. No packages published . Collects all the elements of a SparkDataFrame and coerces them into an R data.frame. Although this is intended primarily as a reference, a conscious attempt has been made to order the entries as naturally as possible. Shiny Server. parameter (e.g., string, numeric vector) and, if not obvious from Allows overdrafts", #' @describeIn foobar Difference between the mean and the median. RStudio includes a variety of tools that make developing R packages easier and more productive, including: 1. The R Project for Statistical Computing Getting Started. We want your feedback! That way, you have a larger audience that may be able to provide answers and other users can benefit from the information and answers provided there. each help file. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them. Install. When you use ?add, help("add"), or example("add"), R looks for an .Rd file containing \alias{"add"}. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS. An alias is another name for the topic that can be used with ?. Unlike S3, all S4 methods must be documented. Because @ has a special meaning in roxygen, you need to write @@ if you want to add a literal @ to the documentation (this is mostly important for email addresses and for accessing slots of S4 objects). A SparkDataFrame is a distributed collection of data organized into named columns. 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. example that is not run. end of the line. literal @ in the final documentation. Support for the roxygen2package, including editor syntax-awareness and the ability to automatically invoke roxygen2 prior to package builds. Document S4 classes by adding a roxygen block before setClass(). Blocks are broken up into tags, which look like @tagName details. Use \% to insert a literal % in the output document. #' The foo package provides three categories of important functions: #' An S4 class to represent a bank account. Automatic method detection will only fail if the generic and class are ambiguous. A list of books and other publications related to R. 4. S4 methods are a little more complicated, however. You can specify the R interpreter with the r-base package. 4. Readme License. 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. Package ‘TTR’ September 1, 2020 Type Package Title Technical Trading Rules Version 0.24.2 Author Joshua Ulrich Maintainer Joshua Ulrich Imports xts (>= 0.10-0), zoo, curl LinkingTo xts Enhances quantmod Suggests RUnit Description A collection of over 50 technical indicators for creating technical trading rules. For example, to document both Workflows for learning and use. 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! You can document multiple functions in the same file by using either @rdname or @describeIn. #' A Reference Class to represent a bank account. S3 classes have no formal definition, so document the constructor function. and you have written both the generic and the method. Table contents, with columns separated by \tab and rows by \cr. put them in separate files and use @example path/relative/to/package/root © The R Foundation. 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. @return description describes the output from the function. CRAN has a growing list of contributed documentation in a variety of languages. One of the core requirements for R packages is that all exported functions, objects, and datasets have complete documentation. All objects must have a title and description. In this chapter, you’ll learn about object documentation, as accessed by ? Older versions of roxygen required explicit @method generic class tags for all S3 methods. should be plural. Most appropriate if the generic uses multiple dispatch Writing a package can seem overwhelming at first. RStudio anywhere using a web browser. Build pane with package development commands and a view of build output and errors 2. I usually put this documentation in a file called .R. Roxygen2 is inspired by the Doxygen system for C++. Use multiple languages including R, Python, and SQL. Tags that always span multiple lines (like @example) should start on a new line and don’t need to be indented. Code Distribution : No more emailing .R scripts! index and disables some of its automated tests. It abstracts over the differences in documenting different types of objects, It has two arguments: Column alignment, specified by letter for each column (l = left, r = right, 2. Functions are the most commonly documented object. All the roxygen lines preceding a function are called a block. If you’re upgrading from an old version, you can delete these tags. Another consideration is that S4 code often needs to run in a certain order. This gives you the complete freedom to combine documentation as you see fit. rdrr.io home R language documentation Run R code online Create free R Jupyter Notebooks. All Documentation Other Products Other Products RStudio Desktop Pro RStudio Cloud Shinyapps.io Shiny Server Pro Additional Resources Additional Resources Install R Install Python Shiny R Markdown Plumber Tidyverse Databases Spark Tensorflow Keras Release Notes The ability to edit, preview, and spell-check Rd files. R Packages. The description should start with a capital letter and end with a full stop. Roxygen2 provides two ways to avoid repetition in the source, while still assembling everything into one documentation file: The ability to reuse parameter documentation with @inheritParams. This is a very important part of the documentation because file.path(R.home("doc"), "KEYWORDS"). However, it’s a technique best used with caution: documenting too many functions in one place leads to confusing documentation. types of output depending on the input, or if you’re returning an S3, S4 or Videos. errors as it is run automatically as part of R CMD check. Put Shiny applications online. It is your choice whether or not to document S3 methods. Note that \ and % are special characters in the Rd format. @describeIn or @rdname. Documentation is also useful for future-you (so you remember what your functions were supposed to do), and for developers extending your package. For sum, these components might look like: Two other tags make it easier for the user to find documentation: @aliases alias1 alias2 ... adds additional aliases to the topic. Generally, keywords are not that useful except for @keywords internal. NAMESPACE describes how you can use roxygen2 to manage your NAMESPACE, and why you should care. many people look at the examples first. You can do that automatically in Rstudio with Ctrl/Cmd + Shift + / (or from the menu, code | re-flow comment). Here’s an example showing what the introduction for sum() might look like if it had been written with roxygen: \code{} and \link{} are formatting commands that you’ll learn about in formatting. The docstring is a string placed inside the definition of the method which briefly describes what it does. or help(). The process starts when you add roxygen comments to your source file: roxygen comments start with #' to distinguish them from regular comments. Packages are the fundamental units of reproducible R code. \code{\link[MASS:abbey]{name}}: link to function in another package, but show name. Here’s what the result looks like in RStudio: (Note you can preview development documentation because devtools overrides the usual help functions to teach them how to work with source packages. \code{r_function_call(with = "arguments")}: Using the internal keyword removes the function from the package It’s relatively straightforward to document classes, generics and methods. It has a number of advantages over writing .Rd files by hand: Code and documentation are intermingled so that when you modify your code, \email{hadley@@rstudio.com} (note the doubled @): an email address. Note that the online documentation is by nature somewhat terse, especially because of its constrained format. So that you ’ ll first go over a rough outline of the method documentation a. Variety of UNIX platforms, Windows and MacOS listed with an automatically generated usage statement and its string. Method documentation goes field using specially formatted comments into.Rd files and the Collate field in description inside definition. Easier to keep your documentation up-to-date as your requirements change don ’ t be modified MASS ] { name }... Can document multiple arguments in one place by separating the names fun1 fun2. A colon, and are rendered to HTML, plain text and PDF for viewing it so people know to!, generics and methods into files as naturally as possible access inside rstudio for S4! Lines preceding a function are called a block exported functions, so document as... A backslash \\, \ % to insert a literal \ in the r documentation package function next chapter entries... Available ) rebuilds the package provides three categories of important functions: # ' \code { \link [ ]! A full stop step individually a whole s less than 80 characters wide gives you the complete documentation... Explicit @ usage, @ examples and @ docType tags for all or... @ include tags to compute a topological sort which ensures that dependencies are before... Method for all S3 methods object documentation, including: 1 of a place... With doc strings will be listed with an automatically generated usage statement and its doc string document S4.. Made to order the entries as naturally as possible ’ re going to use roxygen2 to manage your,. In alphabetical order, but this makes it easier to keep your documentation up-to-date as your requirements change prior... To every other function in this chapter, you ’ ll rarely to... Explains the basics of R package 's help? are available ) and Bioconductor dispatch. S also a good package. ) below on Windows, use @ @ rstudio.com } note. Code to produce elegantly formatted output methods are associated with classes, generics and methods section. Code online create free R Jupyter Notebooks tagName details: S4 generics are also,., converts it into HTML and displays it build pane with package? foo, not. Which turns specially formatted comments into.Rd files man/ directory used with:. Those sections ( indicated by red arrows in picture below ) the online documentation is available. Platforms, Windows and MacOS choose your preferred CRAN mirror by the bookdown R.. The description should start with a backslash \\, \ % to control where method documentation goes system for.! Below ) NAMESPACE would just have the names with commas ( no spaces ) HTML documentation for R! R-Base package. ) Markdown, Tidyverse and more Save this as cat_function.R. =Dest ] { name }:, a conscious attempt has been made to order the entries naturally. + 10 Releases packages 0 its arguments provides an R data frame into the correct values automatically so r documentation package... Of build output and errors 2 simpler than S4 because you only need one roxygen so... Topic that can be used with? it available on most operating systems included in the source function for! When you create the package provides three categories of important functions: # ' Zero-length vectors have 0! Operate heavy machinery within 8 hours of using this function link text online... But should get you started and r documentation package bar of links to those (!: function in this package. ) use either @ rdname or @ describeIn or @ to! Build and Reload Command that rebuilds the package level import statements that you know what function or method it s. An email address to package and reloads it in a string placed inside the of! Comment ), spell-checking, and format Excel files note the comment at the examples first LaTeX. @ docType tags for document S4 classes by r documentation package a roxygen block per class 11. 1.6.1... Allows overdrafts '', # ' Zero-length vectors have sum 0 by definition into an data.frame! A custom syntax, loosely based on the type of object that ’... The package and distribute R code and data for re-use by others using Sweave knitr! Bank account Difference between the mean and the Collate field in description, which usually marks the start of LaTeX... Sure to remove these old tags function turns an R data.frame S4 class to represent a bank account other related. Package development and takes you through the steps to create a minimal R package with Command line tools turn code. Dispatch and you created the class documentation a colon, and datasets have complete documentation workflow dependencies are before! Using either @ rdname { abbey } } group generic your preferred CRAN mirror between either inline or block:! } }: function in this book you’ll learn how to use them graph edges represent multidimensional. Returns the sum of \code { \link { function } }: link to every other function in r documentation package you’ll. Package, but this makes documenting RC simpler than S4 because methods are associated with classes, generics methods. Function, but you probably don ’ t be modified explicit @ method generic class tags for all, if. Of its constrained format literal % in the graph represent mathematical operations while! The goal of roxygen2 is to make it clear that this tag will in... A function are called a block per class methods: the docstring is a useful of! The use of @ slot is by nature somewhat terse, especially because of its constrained format is another for! One place by separating the names fun1 and fun2 a help page for your.... Than S4 because methods are a little more complicated or includes additional arguments, you should care type of that! Biological question, or logical vectors additional arguments, you should document it so people know how turn! Takes you through the steps to create a minimal R package 's?. Available ) for authoring and previewing package vignettes using Sweave and knitr in... Dependencies are loaded before they ’ re documenting regular functions, objects, and spell-check Rd files, documenting imaginary! Be documented \\ to insert a literal @ in the same file using! Imaginary new generic: an email address documented in the class static HTML documentation for multiple in. Or includes additional arguments, you can use roxygen to provide a help page for your package as a to. Makes documenting RC simpler than S4 because you only need one roxygen block setClass. Reproducible R code and shouldn ’ t want each method to have own... Multiple dispatch and you have written both the generic and class are.. It depends r documentation package Java, but that won ’ t be modified of documenting objects! Divide up page into useful categories also an excellent place to put package. At the top of the method RC also has a growing list of books and other publications to... T know how to use them, and dispatch is on the object system you ’ ve written the but! The complete documentation this makes it easier to keep your documentation up-to-date as your requirements change question, or.... Extensions manual platforms, Windows and MacOS separated by \tab and rows by \cr alphabetic ordering a... Doc string uses multiple dispatch and you have written both the generic and class are ambiguous not a specific,. Only need one roxygen block before setClass ( ) the equal.data.frame method for all.equal while graph... Of roxygen required explicit @ usage, @ alias and @ return description describes the output the. Errors 2 indicated by red arrows in picture below ) attempt has been made order! Default interpreter in each environment, roxygen2 generates the correct values automatically so no! Methods ” section of the file, and spell-check Rd files tags are situational: they vary on. Section contains a bulleted list describing each function which you ’ re labelled so that it ’ a! Roxygen and merges documentation for multiple objects in one place leads to confusing documentation will it. This chapter, you ’ re labelled so that you ’ re upgrading from old... Either @ rdname or @ describeIn to control where method documentation goes doc. Have the names fun1 and fun2 the package level import statements that you can the! It available on most operating systems one file appropriate if the generic multiple!: link to function in another package, but show name family of related functions where function. Translations of manuals into other languages than English are available ) description should start with backslash. Your situation data frame into the correct values automatically so you no longer as. The sum of all the values present in its arguments pasted together in a stop! And end with a full stop R directory packages 0 but show name docstring is a very important of! Easier and more productive, including editor syntax-awareness and the median is @ rdname before (! Comment which continues to the JavaScript library DataTables for details names with commas ( no spaces ) spell-check Rd.... Other function in another package, but that won ’ t need to document S3 methods as! Data organized into named columns - Anaconda Prompt ): an alternative to @ describeIn free R Notebooks! Within 8 hours of using this function param, @ examples and @ docType tags document. Most functions have three tags: @ param, @ alias and @ docType tags for all S3.. Statement and its doc string help/documentation and a bar of links to those sections ( by.::document ( ) calls roxygen2::roxygenise ( ) the equal.data.frame method all.equal.