A guide to some R packages that we know about for health economic analysis as compiled by Dr Nathan Green.
Click here to suggest packages.
The packages are generally in one of two groups. Either they are specifically designed to perform (some part of) a cost-effectiveness analysis or they are more generic and can be applied to this context.
-
Generic packages
Below we list the most useful R packages that we know of for each area.
| Name | Description | Package | CRAN (downloads) |
|---|---|---|---|
| BCEA | Bayesian Cost Effectiveness Analysis | ✅ | |
| DALY | The DALY Calculator - Graphical User Interface for Probabilistic DALY Calculation in R | ✅ | |
| heemod | Models for Health Economic Evaluation | ✅ | |
| hesim | Heath economic simulation modeling and decision analysis | ✅ | |
| iSQoL2 | Integration of Survival with QoL or Cost | ||
| radiant | Business Analytics using R and Shiny | ||
| QoLR | Analysis of Health-Related Quality of Life in Oncology | ✅ | |
| PROscorer | Functions to Score Commonly-Used Patient-Reported Outcome (PRO) Measures and Other Psychometric Instruments | ✅ | |
| ArvoRe | Cost-effectiveness Analysis (CEA) implementation for R oriented to compute problems that involve simple decision tree models and Markov models. It offer a graphic user interface (GUI) developed in Tcl/Tk. | ||
| heRomod2 | Reproducible cost-effectiveness modeling | ✅ | |
| HEdtree | Utilities for decision tree like models in health economics | ✅ | |
| DALYcalculator | DALY Calculator R Package | ||
| ICEinfer | Incremental Cost-Effectiveness Inference using Two Unbiased Samples | ✅ | |
| dampack | An R package for decision-analytic modeling | ✅ | |
| rdecision | Classes and functions for modelling health care interventions using decision trees and semi-Markov models. | ✅ | |
| dcurve | Decision Curve Analysis. | ✅ |
These packages help you build and navigate tree-like objects.
- data.tree - General Purpose Hierarchical Data Structure
- igraph - Network Analysis and Visualization
- jsonlite - A Robust, High Performance JSON Parser and Generator for R
- rjson - JSON for R
- jsonvalidate - Validate 'JSON'
The related area of survival analysis has its own CRAN Task View: Survival Analysis. This also has a multistate models section and a Simulation section with useful packages. These packages help you simulate populations at individual or group levels.
Some package not included:
- ggm - Functions for graphical Markov models
- rakeR - Easy Spatial Microsimulation (Raking) in R
- des - Discrete-Event Simulation in R
- simmer - Discrete-Event Simulation for R
Packages for optimal control, dynamic programming or maximum utility theory would be useful. There is already the specific CRAN Task View: Optimization and Mathematical Programming.
Of note, and not included in the Task View is the package
- MDPtoolbox - Markov Decision Processes Toolbox
- mdp
These packages make it easier to program with the R language.
- diagram - Functions for visualising simple graphs (networks), plotting flow diagrams
- DiagrammeR - Create Graph Diagrams and Flowcharts Using R
These packages contain data sets to use as training data or toy examples.
- rgho - Access WHO Global Health Observatory Data from R
- AER Lots of data sets and some other code from the book Christian Kleiber and Achim Zeileis (2008), Applied Econometrics with R
- demography - Forecasting Mortality, Fertility, Migration and Population Data
- ROCR - Visualizing the Performance of Scoring Classifiers
- pROC - Display and Analyze ROC Curves
You can learn more about packages in R with the CRAN task views.