AudGenDB Template for R Markdown

Author: E. Bryan Crenshaw III, PhD

Description: R Markdown Template for use on the Audiological and Genetic Database (AudGenDB) Project.

Dependencies

• RStudio
• knitr package, and its dependencies from CRAN resource to generate HTML pages.
• Other Packages Used
  • data.table
  • dplyr
  • ggplot2
  • kableExtra
  • notifier (see template comments for instructions on downloading package, which isn't in CRAN)
  • readr
  • yaml

Contents: This folder contains 3 files in addition to this README.md file:

• The 'Rmarkdown document Template HowTo.txt' file
• The 'audgendb_template' folder.
• The 'LoadAudGenDB_Rmarkdown_Template.Rmd' file, which contains a bash script that can be run in RStudio to load the template.

The txt file will give links to support pages to explain how to make and use templates. The folder is ready to place in the template folder for your computer system.

Implementation: The folder 'audgendb_template' should be copied to the Template directory for R on your computer. Alternatively, use the 'LoadAudGenDB_Rmarkdown_Template.Rmd' file that contains a bash script that will run in R Studio.

The files/subfolder structure must be maintained for the template to work.

The template.yml is written in the YAML markdown language, and provides metadata for the template.

The skeleton.Rmd file contains the R Markdown for the template. It must reside in the skeleton subfolder to work properly

Template folder on Mac OS X using Current R version: /Library/Frameworks/R.framework/Versions/Current/Resources/library/rmarkdown/rmarkdown/templates

Version numbering complies with the Semantic Versioning 2.0.0 requirements.

NOTE: only put the skeleton.Rmd file in the skeleton folder or RStudio will make a new directory for each page

Features

• YAML Header Features (Header delimited above and below with ---)
  • title: uses doc_title variable to capture the page title for use below
  • author: uses the working directory in an ifelse query for the user (in Mac OS X)
  • date: automatically inserts date
  • output: sets up theme, and makes a table of contents based on headers in markdown below
• R Markdown Body
  • setup chunk needed to import R scripts into file. Template designed to reside in an rmarkdown subfolder to better organize projects. See comments in this chunk, if Rmd file is placed in main project directory.
  • LoadLibraries chunk for including packages and R scripts (see link for loading R scripts)
  • LoadData designed to read csv files, and capture file names in one place
  • Several standard chunks set up with headers, which will get incorporated into the table of contents automatically
  • OutputData designed to output data, and to generate a metadata file with information on source and purpose of output file
  • SessionInfo chunk saves technical information about the environment in which the file was run, which is hidden on the output using the html detail tag. Saving this information is good practice, but clutters the output, so it is hidden until detail summary is clicked on.
  • The notifier package is used to send a message to the operating system when the file is done, if the user is not in the RStudio environment (Useful for long runs where folks are working on something else waiting for the script to run).

Further Reading

• "Efficient Input/Output" chapter from Efficient R programming - More info on utility of readr versus data.table package functions.