In sbfnk/fitR: Tool box for fitting dynamic infectious disease models to time series

fitR: Functions for model fitting and inference

The functions contained in this package have been developed in support of a course on Model fitting and inference for infectious disease dynamics run annually at the London School of Hygiene & Tropical Medicine.

The main purpose of this package is to be a teaching tool, and the implementation of inference algorithms in this package is not particularly efficient of stable. For vastly superior alternative options for fitting models to data in R we recommend to consider, amongst others

• rstan, an interface to Stan.
• pomp, for partially observed Markov processes.
• rbi, an interface to LibBi.

Installation

The easiest way to install fitR is to use the remotes package:

# install.packages("remotes")
library(remotes)
install_github("sbfnk/fitR", dependencies = TRUE)

Included data sets

The package includes a number of data sets that are used for the course. They havae been generated using the scripts in the scripts/generate-data directory of the corresponding github repo.

sbfnk/fitR documentation built on July 18, 2023, 3:28 p.m.