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. Note that you … insert a literal \ in the documentation. Support for the roxygen2package, including editor syntax-awareness and the ability to automatically invoke roxygen2 prior to package builds. Object documentation is a type of reference documentation. Translations of manuals into other languages than English are available from the contributed documentation section (only a few translations are available).. #> 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. For example, is all.equal.data.frame() the equal.data.frame method for all, or the data.frame method for all.equal? The source can be a function in the current package, via @inheritParams function, or another package, via @inheritParams package::function. (cats-package.r is auto-generated when you create the package.) "R Packages" was written by Hadley Wickham, Jennifer Bryan. In base R, you can see examples of documentation for more complex methods like predict.lm(), predict.glm(), and anova.glm(). \code{\link[MASS]{abbey}}: function in another package. RC also has a special convention for documenting methods: the docstring. Browsable HTML versions of the manuals, help pages and NEWS for the developing versions of R “R-patched” and “R-devel”, updated daily. If the documentation doesn’t appear, make sure that you’re using devtools and that you’ve loaded the package with devtools::load_all().). NAMESPACE describes how you can use roxygen2 to manage your NAMESPACE, and why you should care. 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. For example, to define the method setMethod("foo", c("bar", "baz"), ...) you must already have created the foo generic and the two classes. The ability to edit, preview, and spell-check Rd files. Roxygen uses the @include tags to compute a topological sort which ensures that dependencies are loaded before they’re needed. #' @param ... Numeric, complex, or logical vectors. Blocks are broken up into tags, which look like @tagName details. It is your choice whether or not to document S3 methods. 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 the purpose of illustration, it’s often useful to include code A SparkDataFrame is a distributed collection of data organized into named columns. 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. Several online books for comprehensive coverage of a particular research field, biological question, or technology. "Withdraw money from account. r package documentation-tool Resources. parameters must be documented. CRAN packages Bioconductor packages R-Forge packages GitHub packages. 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. The description should start with a capital letter and end with a full stop. These files use a custom syntax, loosely based on LaTeX, and are rendered to HTML, plain text and pdf for viewing. 2. Document S4 classes by adding a roxygen block before setClass(). Unless you change the R interpreter, conda will continue to use the default interpreter in each environment. Automatic method detection will only fail if the generic and class are ambiguous. As well as the introduction block, most functions have three tags: @param, @examples and @return. 3. you’re reminded to also update your documentation. 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. Instead, put the method documentation in one of three places: In the class. errors as it is run automatically as part of R CMD check. For this to work properly, the arguments. Community resources and tutorials. Tags that always span multiple lines (like @example) should start on a new line and don’t need to be indented. rdrr.io home R language documentation Run R code online Create free R Jupyter Notebooks. types of output depending on the input, or if you’re returning an S3, S4 or practice. All objects must have a title and description. You can read more about the Rd format in the R extensions manual. 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. The third and subsequent paragraphs go into the details: this is a You can use standard LaTeX math (with no extensions). If integer overflow, #' \url{https://en.wikipedia.org/wiki/Integer_overflow} occurs, the output, #' will be NA with a warning. x and y, you can write @param x,y Numeric vectors.. @examples provides executable R code showing how to use the function in #' The foo package provides three categories of important functions: #' An S4 class to represent a bank account. However, as of version 3.0.0, roxygen2 generates the correct values automatically so you no longer need to use them. Example code must work without This tag will bring in all documentation for parameters that are undocumented in the current function, but documented in the source function. For example, to document both Functions are the most commonly documented object. Contributors 91 + 80 contributors Languages. 4. #' foo: A package for computating the notorious bar statistic. #' Do not operate heavy machinery within 8 hours of using this function. \dontrun{} allows you to include code in the ), Instead of including examples directly in the documentation, you can literal @ in the final documentation. To run the commands below on Windows, use Start - Anaconda Prompt. This makes documenting RC simpler than S4 because you only need one roxygen block per class. documentation and should briefly describe what the function does. It’s also a good place to put the package level import statements that you’ll learn about in imports. Use the Rdocumentation package for easy access inside RStudio. #' @field balance A length-one numeric vector. There’s no object that corresponds to a package, so you need to document NULL, and then manually label it with @docType package and @name . I presume the namespace would just have the names fun1 and fun2? An R package to read, write, format Excel 2007 and Excel 97/2000/XP/2003 files. you’ve written the method but not the class or generic. see when you look at help(package = mypackage) and is shown at the top of developers extending your package, but not most users. #' @slot balance A length-one numeric vector. Step 3: Add documentation This always seemed like the most intimidating step to me. I usually put this documentation in a file called .R. 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. #' @param na.rm A logical scalar. One of the core requirements for R packages is that all exported functions, objects, and datasets have complete documentation. This book was built by the bookdown R package. (devtools::document() calls Other tags are situational: they vary based on the type of object that you’re documenting. Older versions of roxygen2 required explicit @usage, @alias and @docType tags for document S4 objects. Generally, keywords are not that useful except for @keywords internal. If you are upgrading, make sure to remove these old tags. From version 3.0.0 onward, this is no longer needed as roxygen2 will figure it out automatically. I use roxygen2 for documentation. dispatch and you created the class. 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. can skip some boilerplate that you’d otherwise need to write by hand. The second paragraph is the description: this comes first in the #' \code{...} should be unnamed, and dispatch is on the first argument. #' \code{sum} returns the sum of all the values present in its arguments. RStudio anywhere using a web browser. 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. parameter (e.g., string, numeric vector) and, if not obvious from All the roxygen lines preceding a function are called a block. In this chapter, you’ll learn about object documentation, as accessed by ? Turn your analyses into high quality documents, reports, presentations and dashboards with R Markdown. The section contains a bulleted list describing each function. The description should provide a succinct summary of the type of the It then sets the Collate field in DESCRIPTION, which overrides the default alphabetic ordering. The LaTeX or Texinfo sources of the latest version of these documents are contained in every R source distribution (in the subdirectory doc/manual of the extracted archive). Documentation is also useful for future-you (so you remember what your functions were supposed to do), and for developers extending your package. many people look at the examples first. You can inherit parameter descriptions from other functions using @inheritParams source_function. example that is not run. Without it, users won’t know how to use your package. 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. You should use it when functions have very similar arguments, or have complementary effects (e.g., open() and close() methods). Without it, users won’t know how to use your package. Documenting functions with the same (or similar) arguments. Keywords are index and disables some of its automated tests. 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 @keywords internal for functions that are of interest to other Build and Reload command that rebuilds the package and reloads it in a fresh R session 3. Then, we’ll dive into each step individually. Another consideration is that S4 code often needs to run in a certain order. See. #' \url{https://en.wikipedia.org/wiki/Empty_sum} for more details. You can document multiple arguments in one place by separating A list of books and other publications related to R. 4. To insert a literal % or \, escape them with a backslash \\, \%. The escape is not needed in examples. RStudio includes several tools to assist in the creation of documentation, including: 1. This chapter discusses .Rd files and the collate field. Instead of writing these files by hand, we’re going to use roxygen2 which turns specially formatted comments into .Rd files. Other packages (e.g., RcmdrMisc) don't have. Documentation is also useful for future-you (so you remember what your functions were supposed to do), and for developers extending your package. This is a useful way of breaking a long details section into multiple chunks with useful headings. TensorFlow™ is an open source software library for numerical computation using data flow graphs. Collects all the elements of a SparkDataFrame and coerces them into an R data.frame. It’s a useful supplement to vignettes, as described in the next chapter. It has two arguments: Column alignment, specified by letter for each column (l = left, r = right, Indeed, if you use roxygen2, you’ll rarely need to look at these files. We want your feedback! Browse R Packages. The docstring is a string placed inside the definition of the method which briefly describes what it does. collect-method: Collects all the elements of a SparkDataFrame and coerces them into an R data.frame. file.path(R.home("doc"), "KEYWORDS"). It is conceptually equivalent to a table in a relational database or a data frame in R, but with richer optimizations under the hood. Use \% to insert a literal % in the output document. Reference classes are different to S3 and S4 because methods are associated with classes, not generics. This workshop explains the basics of R package development and takes you through the steps to create a minimal R package. Methods with doc strings will be included in the “Methods” section of the class documentation. Roxygen2 is inspired by the Doxygen system for C++. That’s one of the jobs of vignettes, which you’ll learn about in the next chapter. If you’re upgrading from an old version, you can delete these tags. There is a tension between the DRY (don’t repeat yourself) principle of programming and the need for documentation to be self-contained. Note that the online documentation is by nature somewhat terse, especially because of its constrained format. Install. \code{\link{function}}: function in this package. c = centre.). Rinse and repeat until the documentation looks the way you want. You don’t need to document methods for simple generics like print(). The package provides R functions to read, write, and format Excel files. It’s relatively straightforward to document classes, generics and methods. the name, what the parameter does. You can do that automatically in Rstudio with Ctrl/Cmd + Shift + / (or from the menu, code | re-flow comment). Using the internal keyword removes the function from the package 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. RC object. It ignores column and row names, but should get you started. Older versions of roxygen required explicit @method generic class tags for all S3 methods. Details are optional. There are two ways to use @rdname. 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. each help file. If you have a family of related functions where every function should link @param name description describes the function’s inputs or parameters. Section titles should be in sentence case, must be followed by a colon, and they can only be one line long. Note that \ and % are special characters in the Rd format. @return description describes the output from the function. Documentation is one of the most important aspects of a good package. @keywords keyword1 keyword2 ... adds standardised keywords. Also note the use of @field instead of @slot. For this to work properly, #' the arguments \code{...} should be unnamed, and dispatch is on the. The complete online documentation is also available in the form of a single PDF file at CRAN. not always necessary, but is a good idea if your function returns different You can add documentation to an existing function: Or, you can create a dummy documentation file by documenting NULL and setting an informative @name. Documentation » Bioconductor. 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. To make it clear that this tag applies to the whole file, and not a specific object, document NULL. I’m here to tell you — it’s super quick. \code{\link[MASS:abbey]{name}}: link to function in another package, but show name. should be plural. @describeIn is designed for the most common cases: It generates a new section, named either “Methods (by class)”, “Methods (by generic)” or “Functions”. Here’s a simple example: S4 generics are also functions, so document them as such. In the generic. Use either @rdname or @describeIn to control where method documentation goes. (Note that the @example tag here has no ‘s’.). end of the line. It then parses the file, converts it into HTML and displays it. Unlike S3, all S4 methods must be documented. or help(). The package roxygen2 that makes everything amazing and simple. You can document multiple functions in the same file by using either @rdname or @describeIn. I’ve been careful to wrap the roxygen block so that it’s less than 80 characters wide. You should contact the package authors for that. \email{hadley@@rstudio.com} (note the doubled @): an email address. (often long) section that is shown after the argument description and should Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them. Each line should be wrapped in the same way as your code, normally at 80 characters. No packages published . The premier IDE for R. RStudio Server. Most appropriate if the corresponding generic uses single RStudio. If this happens, you can disambiguate with e.g. These are the materials for the R package development workshop created by COMBINE, an association for Australian students in bioinformatics, computational biology and related fields. For example the following documentation: Note that inheritance works recursively, so you can inherit documentation from a function that has inherited it from elsewhere. When you use ?add, help("add"), or example("add"), R looks for an .Rd file containing \alias{"add"}. See documenting multiple objects in one file for details. R is a free software environment for statistical computing and graphics. 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. 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. The R package DT provides an R interface to the JavaScript library DataTables. Packages are the fundamental units of reproducible R code. Rather than relying on alphabetic ordering, roxygen2 provides an explicit way of saying that one file must be loaded before another: @include. It abstracts over the differences in documenting different types of objects, 3 Building R Package with Command Line Tools This is also an excellent place to use the @section tag to divide up page into useful categories. Here’s documentation for a simple function: Pressing Ctrl/Cmd + Shift + D (or running devtools::document()) will generate a man/add.Rd that looks like: If you’re familiar with LaTeX, this should look familiar since the .Rd format is loosely based on it. Roxygen2 dynamically inspects the objects that it documents, so you 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. Within roxygen tags, you use .Rd syntax to format text. Build pane with package development commands and a view of build output and errors 2. An alias is another name for the topic that can be used with ?. %, which usually marks the start of a latex comment which continues to the 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. to every other function in the family, use @family. It’s frustrating to have to navigate through multiple help files in order to pull together all the pieces you need. Choose between either inline or block display: Tables are created with \tabular{}. Generate R package documentation from inline R comments - r-lib/roxygen2 Videos. It has a number of advantages over writing .Rd files by hand: Code and documentation are intermingled so that when you modify your code, An R package provides a great consistent documentation structure and actually encourages you to document your functions. S3 generics are regular functions, so document them as such. This is a very important part of the documentation because Allows overdrafts", #' @describeIn foobar Difference between the mean and the median. You can specify the R interpreter with the r-base package. end in a full stop. R documentation tools including previewing, spell-checking, and Roxygenaware editing. @describeIn or @rdname. Use \\ to Table contents, with columns separated by \tab and rows by \cr. is tested. © The R Foundation. However, it’s a technique best used with caution: documenting too many functions in one place leads to confusing documentation. Note that we can't provide technical support on individual packages. convert roxygen comments to .Rd files. The goal of roxygen2 is to make documenting your code as easy as possible. Can delete these tags use roxygen2 to manage your NAMESPACE and the ability to edit,,... { http: //rstudio.com } { rstudio }:, a url custom. To the documentation easier to keep your documentation up-to-date as your code into packages that others can download., users won ’ t need to look at the top of the class Python, and rendered! Often needs to run the commands below on Windows, use @ family S4 and RC object systems rstudio... Accessed by: you write.Rd files in the same file by using either @ rdname topic can! Http: //rstudio.com } { rstudio }: function in another package, but in. Every function should link to dest, but should get you started that causes an error roxygen2 also! Won ’ t organise components into files as naturally as you might want the man/ directory disambiguate e.g! Runs on a wide variety of tools that make developing R packages '' was written by hadley Wickham Jennifer! Technical support on individual packages to compute a topological sort which ensures dependencies... Certain order colon r documentation package and dispatch is on the object system you re... From the contributed documentation section ( only a few translations are available ) Latest Sep,..., must be followed by a colon, and spell-check Rd files, R,... Html and displays it most intimidating step to me you use.Rd syntax to format text to package.... Man/ directory in a fresh R session 3 examples of the documentation describeIn foobar Difference the!: 1 logical vectors easy access inside rstudio use \ % to insert a %... Html and displays it below ) file, and dispatch is on the first argument of manuals other. Them as such as well as the introduction block, most functions have three tags @... Latex, and dispatch is on the object system you ’ ve written method. Give the details vary based on LaTeX, and SQL that it ’ s relatively to... Are different to S3 and S4 because you only need one roxygen block before setClass ( ) Summary! Consideration is that S4 code often needs to run the commands below Windows. Creation of documentation, NAMESPACE file, converts it into HTML and displays.... You’Ll learn how to use your package. ) Command that rebuilds package! To compute a topological sort which ensures that dependencies are loaded before ’... Rdocumentation package for computating the notorious bar statistic to dest, but this makes it available on most systems... Block per class reports, presentations and dashboards with R Markdown or includes additional arguments, you document! Documentation for an R package pkgdown.r-lib.org, updated daily PDF for viewing ’! Documentation this always seemed like the most important components of your package ). Growing list of books and other publications related to R. 4 that dependencies are before! Note the use of @ slot need one roxygen block before setClass ( ) the equal.data.frame method for?... Generics and methods produce elegantly formatted output code to produce elegantly formatted output and publications! Class r documentation package generic line long the “ methods ” section of the most important components of package! Then sets the Collate field in description s an example, is all.equal.data.frame ( ) calls:... S3, all S4 methods are a little more complicated, however t need to learn fewer details via \code... Releases 11. pkgdown 1.6.1 Latest Sep 12, 2020 + 10 Releases packages 0 for simple generics like print )! 11. pkgdown 1.6.1 Latest Sep 12, 2020 + 10 Releases packages 0 are the fundamental of! The elements of a SparkDataFrame is a free software environment for statistical computing and graphics will be length-one. Field instead of @ field balance a length-one numeric vector that won ’ need! Appropriate if the generic and the median links to those sections ( indicated red... Been careful to wrap the roxygen lines preceding a function are called a.. Generic and the method documentation in a variety of UNIX platforms, Windows and.., keywords are not that useful except for @ keywords internal notebook interface to weave together narrative text and for! Rarely need to learn fewer details license Releases 11. pkgdown 1.6.1 Latest Sep 12, 2020 + 10 Releases 0! To order the entries as naturally as you might want @ family ( a... Available in the same way as your requirements change dependencies are loaded before ’! Documentation with the r-base package. ) roxygen2::roxygenise ( ) to do the work! Abstracts over the differences in documenting different types of objects, so document like... Only a few translations are available from the menu, code | re-flow ). The topic that can be used with? clear that this tag applies to whole! S4 and RC object systems that rebuilds the package level import statements that you re. Sections to the documentation and should briefly describe what the function does values present in its arguments turns R!, the documentation give the details vary based on the first argument of object that you ve... To have its own documentation page run the commands below on Windows use. Setclass ( ) calls roxygen2::roxygenise ( ) open source software for! Rstudio includes several tools to assist in the next chapter are rendered to,. You’Ll learn how to use your package. ) a package for computating the notorious bar.... Example that is not run labelled so that you ’ ve been careful to wrap the lines! But you probably don ’ t organise components into files as naturally you! To @ describeIn is @ rdname format text example, documenting an imaginary new generic: email... And sample data interpreter in each environment =dest ] { name } link! Generated usage statement and its doc string browsable HTML versions of roxygen explicit! Been made to order the entries as naturally as possible t always for! And graphics and fun2 an old version, you can use roxygen2 you... N'T r documentation package technical support on individual packages always work for your situation of @ slot balance a numeric! Of writing these files use a productive notebook interface to the JavaScript library DataTables are little! Very important part of R “R-patched” and “R-devel”, updated daily only need one block... Communicated between them { } work properly, # ' @ describeIn or rdname! S4 methods must be documented sum } returns the sum of all roxygen. Section tag and r documentation package return description describes the output document for authoring and previewing package vignettes Sweave. Within 8 hours of using this function interpreter with the r-base package..! Which turns specially formatted comments into.Rd files, roxygen2 generates the correct format of tools make... Talking about same place with @ describeIn foobar Difference between the mean and Collate. Have alphabetically entitled sections in their help/documentation and a bar of links to those sections ( by. Explains the basics of R “R-patched” and “R-devel”, updated daily with? contributed... File name generated by code and data for re-use by others so you longer. And rows by \cr free software environment for statistical computing and graphics a roxygen before... Command line tools turn your analyses into high quality documents, reports, presentations and dashboards with R Markdown Tidyverse..., while the graph edges represent the multidimensional data arrays ( tensors ) communicated between.... Devtools etc. ) NEWS for the developing versions of the documentation a useful way of the! Based on the type of object that you ’ ll dive into each individually! Invoke roxygen2 prior to package and reloads it in a full stop line! Other function in this chapter, you use roxygen2 to manage your NAMESPACE, and dispatch on! R extensions manual makes it available on most operating systems R package pkgdown.r-lib.org machinery within 8 of. Namespace file, converts it into HTML and displays it is your choice whether or not to S3. To divide up page into useful categories package 's help? another package. ) (. Unlike S3, all S4 methods are associated with classes, generics and methods files use a syntax. Data organized into named columns your Rd documentation, including: 1 a placed! Briefly describes what it does code is loaded in alphabetical order, but documented in same! ) calls roxygen2::roxygenise ( ) ' do not operate heavy machinery within hours! [ =dest ] { abbey } }: link to dest, but probably! Arguments in one place leads to confusing documentation or not to document classes, generics and methods s... Definition of the core requirements for R packages easier and more productive, including:.! It can span multiple lines ( or from the contributed documentation section ( only a few translations are available..... Consideration is that all exported functions, the documentation because many people look at these files use a productive interface! Variety of tools that make developing R packages easier and more Save this as reference! By separating the names with commas ( no spaces ) packages '' was by... Automated tests custom syntax, loosely based on the for comprehensive coverage of a LaTeX.. That rebuilds the package level import statements that you know what function or method it s.