Advanced R Programming Tutorial 2022: Make your health economic model Shiny!

This repository stores the code, presentations, and material used in the R-HTA in LMICs Advanced 2022 tutorial (held in January 2023). The following sections provide a breakdown of the primary documents and guidance on how to use them for your own personal training. The tutorial is based on several open-source frameworks for modelling Cost-Effectiveness Analysis models and Shiny apps in R for HTA (see the citations section), developed by DARTH group and Dark Peak Analytics.

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The R folder includes a standalone R script code that replicates an original model presented in chapter two of 'Decision Modelling for Health Economic Evaluation by Briggs A., et al.

The Excel folder includes the original model's solution template, developed in Excel, provided by Oxford's Health Economics Research Centre (HERC).

The shiny folder includes the code used to develop and run the Shiny application version of the cost-effectiveness model.

Preliminaries

• Install the RStudio IDE.

• Install the dampack and shiny R packages from CRAN.

# Install release version from CRAN
install.packages(c("dampack", "shiny"))

# For dampack specifically, you can also install the development version of the
# package from GitHub
# devtools::install_github("DARTH-git/dampack")

• Install devtools to install darthtools R package from DARTH's GitHub

# Install release version from CRAN
install.packages("devtools")

# Or install development version from GitHub
# devtools::install_github("r-lib/devtools")

• Install darthtools using devtools

# Install development version from GitHub
devtools::install_github("DARTH-git/darthtools")

For syntax consistency, we follow the coding syntax framework developed by the DARTH group:

• Alarid-Escudero F, Krijkamp EM, Pechlivanoglou P, Jalal HJ, Kao SYZ, Yang A, Enns EA. A Need for Change! A Coding Framework for Improving Transparency in Decision Modeling. PharmacoEconomics, 2190;37(11):1329--1339. https://doi.org/10.1007/s40273-019-00837-x

Lastly, we strongly recommended familiarising yourself with Shiny before undertaking the tutorial:

• Getting started with Shiny
• A Gentle Introduction to creating R Shiny Web Apps

Citations

This tutorial is based on several open-source R coding frameworks for HTA:

Alarid-Escudero F, Krijkamp EM, Enns EA, Yang A, Hunink MGM, Pechlivanoglou P, Jalal H. A Tutorial on Time-Dependent Cohort State-Transition Models in R using a Cost-Effectiveness Analysis Example (https://arxiv.org/abs/2108.13552). arXiv:2108.13552v2. 2022:1-37.

Alarid-Escudero F, Krijkamp EM, Enns EA, Yang A, Hunink MGM, Pechlivanoglou P, Jalal H (2022). R Code for A Tutorial on Time-Dependent Cohort State-Transition Models in R using a Cost-Effectiveness Analysis Example (Version v0.2.0). Zenodo. 10.5281/zenodo.6620902. Last accessed 7 June 2022.

Smith R and Schneider P. Making health economic models Shiny: A tutorial. Wellcome Open Res 2020, 5:69.

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