title: gems: An R Package for Simulating from Disease Progression Models.
abstract: Mathematical models of disease progression predict disease outcomes and are useful epidemiological tools for planners and evaluators of health interventions. The 𝖱 packagegemsis a tool that simulates disease progression in patients and predicts the effect of different interventions on patient outcome. Disease progression is represented by a series of events (e.g., diagnosis, treatment and death), displayed in a directed acyclic graph. The vertices correspond to disease states and the directed edges represent events. The packagegemsallows simulations based on a generalized multistate model that can be described by a directed acyclic graph with continuous transition-specific hazard functions. The user can specify an arbitrary hazard function and its parameters. The model includes parameter uncertainty, does not need to be a Markov model, and may take the history of previous events into account. Applications are not limited to the medical field and extend to other areas where multistate simulation is of interest. We provide a technical explanation of the multistate models used bygems, explain the functions ofgemsand their arguments, and show a sample application.
authors.affiliation: Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
authors.forename: Nello
authors.initials: N
authors.lastname: Blaser
authors.affiliation: Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
authors.forename: Luisa Salazar
authors.initials: LS
authors.lastname: Vizcaya
authors.affiliation: Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
authors.forename: Janne
authors.initials: J
authors.lastname: Estill
authors.affiliation: Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
authors.forename: Cindy
authors.initials: C
authors.lastname: Zahnd
authors.affiliation: Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
authors.forename: Bindu
authors.initials: B
authors.lastname: Kalesan
authors.affiliation: Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland ; Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa.
authors.forename: Matthias
authors.initials: M
authors.lastname: Egger
authors.affiliation: Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
authors.forename: Thomas
authors.initials: T
authors.lastname: Gsponer
authors.affiliation: Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
authors.forename: Olivia
authors.initials: O
authors.lastname: Keiser
keywords: Monte Carlo simulation; compartmental model; multistate model; prediction; survival analysis; 𝖱