This wiki constitutes the documentation of TiPS with different tutorials to simulate trajectories and phylogenies under different compartment models.

What is TiPS?

TiPS (Trajectories and Phylogenies Simulator) is an R package for generating simulated trajectories and phylogenetic trees under stochastic model describing population dynamics. Trajectories are simulated using Gillespie's exact or approximate stochastic simulation algorithm, or a newly proposed mixed version of the two. Phylogenetic trees are simulated from a trajectory under a backwards-in-time approach (i.e. coalescent).

Tutorials

Tutorial 1: Simulating stochastic dynamics from an epidemiological SIR model

Tutorial 2: Simulating transmission tree under a SIR model, using sampling dates

Tutorial 3: Simulating trajectories and phylogenies from a multi-type birth-death model

Citing TiPS

If you use TiPS as part of research that leads to a publication, please cite the following article:

Danesh G, Saulnier E, Gascuel O, Choisy M, Alizon S. 2022. TiPS: Rapidly simulating trajectories and phylogenies from compartmental models. Methods in Ecology and Evolution, 10.1111/2041-210X.14038.