TiPS: Rapidly simulating trajectories and phylogenies from compartmental models

Stochastic population dynamics simulations are essential for many ecological and epidemiological studies to generate time series and genealogies that capture the relatedness between individuals. Many software packages allow one to simulate phylogenetic trees but these tend to suffer from one or two major limitations. First, the underlying population dynamics model is often simplistic (e.g. constant population size or exponential growth). Second, the software packages are not appropriate to simulate a large number of trees. We introduce TiPS, an R package to generate trajectories and phylogenetic trees associated with a compartmental model. 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). TiPS is based on the Rcpp package, allowing to combine the flexibility of R for model definition and the speed of C++ for simulations execution. The model is defined in R with a set of reactions, which allow capturing heterogeneity in life cycles or any sort of population structure. TiPS converts the model into C++ code and compiles it into a simulator that is interfaced in R via a function. TiPS is flexible, easy-to-use and available on the CRAN at . Plus, benchmarking analyses show that TiPS is faster than existing packages. This package is particularly well suited for population genetics and phylodynamics studies that need to generate a large number of phylogenies used for population dynamics studies.

Automated summary

Stochastic population dynamics simulations play a crucial role in ecological and epidemiological studies as they can generate time series and genealogies that capture the relatedness between individuals. However, current software packages for simulating phylogenetic trees often have simplified population dynamics models and are not suitable for simulating a large number of trees. To address these limitations, this study introduces TiPS, an R package that can generate trajectories and phylogenetic trees associated with a compartmental model. TiPS uses different simulation algorithms and a backwards-in-time approach to simulate trajectories and trees, respectively. It combines the flexibility of R for model definition and the speed of C++ for simulations execution. Benchmarking analyses show that TiPS is faster than existing packages and it is particularly useful for population genetics and phylodynamics studies that require a large number of phylogenies for population dynamics analysis.