R Packages

An package is the fundamental unit of shareable code R. Packages bundle together code, data, documentation, and tests in a redefined template. When build a package is easy to share with others.

Writing R extensions is the official manual and reference for package development, but can be a challenging read. A more accessible description is given in R Packages book. The dynatop development broadly follows the philosophy of expressed in the book that “anything that can be automated, should be automated” though not always using the tools used in the book (particularly RStudio projects).

A high degree of automation in the package building is achieved though the use of further R packages, particularly devtools which can be install with

install.packages(c("devtools", "roxygen2", "testthat", "knitr", "rmarkdown", "bookdown"))

Package Contents

The following screen shot shows the contents of the cloned dynatop directory

Contents of the dynatop directory

Briefly the directories contain:

• R - the R source code
• src - C++ source code
• test - scripts for automatic tests used during the package build
• man - manual pages, these are automatically generated during the package build
• vignettes - contains script executed during the build to create longer form examples and the web page
• build_script - contains scripts and tools for use in building the package. This does not form part of the build package

Key files within the folder include:

• DESCRIPTION - a description of the package
• NAMESPACE - this controls the the attachment of the package to an R workspace. Automatically generated as part of the build process so DO NOT edit by hand
• README.md - A general introduction as seen on the project Github site
• NEWS.md - A change-log of the differences between versions
• .Rbuildignore - controls what files in the dynatop folder are not included in the build package

Automatic documentation

Open up the xts_utilities.R file in the R folder. The contents will looks similar to

Partial contents of xts_utilities.R

The initial lines beginning #' contains material processed by the roxygen2 package to produce the function documentation.

The files in the vignettes folder are written in Rmarkdown which can be build in different ways to produce responsive documents or websites such as the dynatop website - or this training course.