Health economic simulation modeling

Overview

hesim is a modular and computationally efficient R package for health economic simulation modeling and decision analysis that provides a general framework for integrating statistical analyses with economic evaluation. The package supports cohort discrete time state transition models (DTSTMs), N-state partitioned survival models (PSMs), and individual-level continuous time state transition models (CTSTMs), encompassing both Markov (time-homogeneous and time-inhomogeneous) and semi-Markov processes. It heavily utilizes Rcpp and data.table, making individual-level simulation, probabilistic sensitivity analysis (PSA), and incorporation of patient heterogeneity fast.

Features of the current version can be summarized as follows:

• Cohort DTSTMs, individual-level CTSTMs, and N-state PSMs that encompass Markov and semi-Markov processes
• Options to build models directly from fitted statistical models or by defining them in terms of expressions
• Parameter estimates from either an R based model or from an external source
• Convenience functions for sampling model parameters from parametric distributions or via bootstrapping
• Parameter uncertainty propagated with PSA
• Modeling patient heterogeneity
• Performing cost-effectiveness analyses and representing decision uncertainty from PSAs
• Simulation code written in C++ to boost performance

Installation

You can install the current release from CRAN or the most up to date development version from GitHub.

# Install from CRAN:
install.packages("hesim")

# Install the development version from GitHub:
# install.packages("devtools")
devtools::install_github("hesim-dev/hesim")

Getting started

There are two good places to start:

1. The Introduction to hesim article provides a quick introduction.

2. Our preprint describes the package (including mathematical details) more thoroughly.

You might also want to explore our example analyses which can be found in the preprint and web articles. They are summarized in the table below, with some drawn from the Decision Modeling for Health Economic Evaluation textbook. Key areas of focus are the (i) statistical models of disease progression (in terms of the baseline risk and relative treatment effects) and (ii) the available data (either individual patient data (IPD) or aggregate-level data).

			Baseline risk		Treatment effect
	Name	Model	Disease model	Disease data	Disease model	Disease data	Application
1	Preprint 4.1	iCTSTM	Multi-state model	IPD	Coefficient (AFT)	IPD	Oncology
2	Preprint 4.2	PSM	Survival models	IPD	Coefficient (AFT)	Aggregate	Oncology
3	Preprint 4.3	cDTSTM	Multi-state model (panel data)	IPD	RR	Aggregate	Oncology
4	Simple Markov cohort	cDTSTM	Multinomial	Aggregate	RR	Aggregate	HIV
5	Time inhomogeneous Markov (cohort)	cDTSTM	Custom	Aggregate	Coefficient (HR)	Aggregate	Hip replacement
6	Multinomial logit	cDTSTM	Multinomial logit	IPD	Coefficient (OR)	IPD	Generic
7	Time inhomogeneous Markov (individual)	iCTSTM	Custom	Aggregate	Coefficient (HR)	Aggregate	Hip replacement
8	Semi-Markov multi-state	iCTSTM	Multi-state model	IPD	Coefficient (AFT)	IPD	Generic
9	4-state PSM	PSM	Survival models	IPD	Coefficient (AFT)	IPD	Oncology
Note: iCTSTM = Individual-level continuous time state transition model; PSM = partitioned survival model; cDTSTM = Cohort discrete time state transition model. AFT = accelerated failure time; RR = relative risk; HR = hazard ratio; OR = odds ratio. IPD = individual patient data.

Citing hesim

If you use hesim, please cite as follows:

  Devin Incerti and Jeroen P Jansen (2021). hesim: Health Economic
  Simulation Modeling and Decision Analysis. arXiv:2102.09437
  [stat.AP], URL https://arxiv.org/abs/2102.09437.

A BibTeX entry for LaTeX users is

  @Misc{incerti2021hesim,
    author = {Devin Incerti and Jeroen P. Jansen},
    title = {hesim: Health Economic Simulation Modeling and Decision Analysis},
    year = {2021},
    eprint = {2102.09437},
    archiveprefix = {arXiv},
    primaryclass = {stat.AP},
    url = {https://arxiv.org/abs/2102.09437},
  }