ESTIpop: A computational tool to simulate and estimate parameters for continuous-time Markov branching processes

Abstract

ESTIpop is an R package designed to simulate and estimate parameters for continuous-time Markov branching processes with constant or time-dependent rates, a common model for asexually reproducing cell populations. Analytical approaches to parameter estimation quickly become intractable in complex branching processes. In ESTIpop, parameter estimation is based on a likelihood function with respect to a time series of cell counts, approximated by the Central Limit Theorem for multitype branching processes. Additionally, simulation in ESTIpop via approximation can be performed many times faster than exact simulation methods with similar results. Availability and implementation: ESTIpop is available as an R package on Github (https://github.com/michorlab/ estipop).