README.md

In Certara.VPCResults: Generate Visual Predictive Checks (VPC) Using 'shiny'

Certara.VPCResults

Overview

Certara.VPCResults is an R package and Shiny application used to parameterize and plot a Visual Predictive Check (VPC).

Use the GUI to select from various binning or binless methods and specify options such as censoring, stratification, and prediction-corrected.

Users are not limited by the GUI however, Certara.VPCResults will generate the underlying tidyvpc and ggplot2 code (.R and/or .Rmd) for you inside the Shiny application, which you can then use to recreate your plot and table objects in R, ensuring reproducibility and traceability of VPC's for reporting output.

Installation

install.packages("Certara.VPCResults",
  repos = c("https://certara.jfrog.io/artifactory/certara-cran-release-public/", 
  "https://cloud.r-project.org"), method = "libcurl")

Usage

Certara.VPCResults supports both NLME and NONMEM VPC output files. The data requirements to use Certara.VPCResults are the same as the tidyvpc package:

• DV cannot be missing in observed/simulated data i.e. subset MDV == 0
• Observed data must be ordered by: Subject-ID, IVAR (Time)
• Simulated data must be ordered by: Replicate, Subject-ID, IVAR (Time)

Use the built in data objects from the tidyvpc package to explore functionality inside Certara.VPCResults.

library(Certara.VPCResults)
library(tidyvpc)

vpcResultsUI(observed = obs_data, simulated = sim_data)

Features

• Supports RsNLME, Phoenix NLME, and NONMEM model output files
• Traditional binning and new binless methods using the tidyvpc package
• Support for continuous and categorical DV
• Generate R and R Markdown code for VPC generation from Shiny GUI
• Create and customize diagnostic plots using ggplot2
• Interactive plot visualizations using plotly
• Render model diagnostic output to word, pdf, or html

...and more!

Reporting

With Certara.VPCResults you can create output reports from your tagged model diagnostics inside the Shiny GUI. After tagging various model diagnostic plots or tables, navigate to the REPORT tab and drag one or more tagged diagnostics to the Report Output container.

Custom MS Word style template

Does your organization have their own MS Word style template? Use a custom style template with Certara.VPCResults by overwriting the default report_template.docx in your R package library e.g., C:\Program Files\R\R-4.0.5\library\Certara.VPCResults\extdata\report_template.docx.

Make sure to save your new template with the name report_template.docx.

Learn more about using a style template with Certara.VPCResults here.

System Requirements

In order to render reports to pdf, the rmarkdown package requires a LaTeX distribution available on the system. You can easily install this in R using the command below:

install.packages('tinytex')
tinytex::install_tinytex()

Certara.VPCResults documentation built on Oct. 11, 2024, 1:09 a.m.