shihao94 / xgx

Exploratory Graphics for PKPD data

Overview

This site contains the code used to generate the xGx website for Exploratory Graphics.

This repository displays suggested plots to pursue when exploring different PK/PD datasets, with a focus on exploring the Dose-Exposure-Response relationship. This site is a collection of exploratory plots and code, and could serve as a checklist of graphs someone might create for certain projects.

Many of the codes on the site use functions that we have found to be helpful while exploring PK/PD data. We compiled these helpful functions into the xgxr R-package, which is available on CRAN, and GitHub.

The contents of the xgx repository are as follows:

• The index.html file is the main page that links to all others.
• The majority of files and folders in the root directory are for displaying the website.
• The files most likely to be of interest to you are stored in these 3 subdirectories
  • Data - contains the datasets
  • R - contains R functions
  • Rmarkdown - contains Rmarkdown documents that make up the subpages
• If you update any of the files in the Rmarkdown folder, then to recompile the site, execute "Rmarkdown/000_render_site.R" in R

Most of the Rmarkdown scripts use caching so that recompiling is quick. However, when developing the site, if you change any dependencies (e.g. functions in the R folder or data in the Data folder) you should delete the cache. This means deleting all the folders in Rmarkdown that end in "_cache" DO NOT DELETE SiteResources.

In order to add links to the website, do the following:

• Edit the Rmarkdown/_site.yml. Under the menu of interest, add a text and href entry - follow other examples
• Edit the Rmarkdown/SiteResources/nav_icon.html. Under the menu of interest, add the link and name.
• Then recompile with 000_render_site.R