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biOMICS

Developing with Rstudio

1 - configuring Rstudio with git repo

Tools that will be used in our project

• devtools - An essential suite of tools for turning your code into an R package.
• testthat - testthat provides an easy way to write unit tests for your code projects.
• roxygen2 - A quick way to document your R packages. roxygen2 turns inline code comments into documentation pages and builds a package namespace.
• Test coverage: https://github.com/MangoTheCat/testCoverage
• knitr - creating vignettes
• shiny - UI Tutorial
• lint - Tutorial
• shinydashboard - Tutorial
• XML- Tutorial
• reutils- Tutorial
• downloader - Tutorial
• dataTable - Tutorial

Installing packages necessary for the project

install.packages("devtools")
install.packages("testthat")
devtools::install_github("MangoTheCat/testCoverage")
install.packages("roxygen2")
install.packages("rmarkdown")
install.packages("knitr")
install.packages("RCurl")
install.packages("shiny")
install.packages("rjson")
install.packages("lintr")
install.packages("lint")
install.packages("reutils")
install.packages("downloader")
install.packages("XML")
devtools::install_github("rstudio/shinydashboard")
devtools::install_github("rstudio/DT")

Executing coverage script test

source('~/R/coverage.R') 

Useful commands

devtools::build() # build package
devtools::test() # execute unit test
devtools::use_vignette(name)
lint(file = ".", style = lint.style, recurse = TRUE, text = NULL) # verify style

File structure

• R - main R code
• inst/app - shiny UI code
• tests - Has testthat folder with unit tests and testthat.R calling tests to be executed
• man - manual pages created by rdoxygen2
• R/coverage - all output created by testcoverage
• vignettes - contains package vignette - Detailed document about the package