@article{Cannoodt2021,
  doi = {10.1038/s41467-021-24152-2},
  url = {https://doi.org/10.1038/s41467-021-24152-2},
  year = {2021},
  month = jun,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {12},
  number = {1},
  author = {Robrecht Cannoodt and Wouter Saelens and Louise Deconinck and Yvan Saeys},
  title = {Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells},
  journal = {Nature Communications}
}
@article{Gillespie2001,
  doi = {10.1063/1.1378322},
  url = {https://doi.org/10.1063/1.1378322},
  year = {2001},
  month = jul,
  publisher = {{AIP} Publishing},
  volume = {115},
  number = {4},
  pages = {1716--1733},
  author = {Daniel T. Gillespie},
  title = {Approximate accelerated stochastic simulation of chemically reacting systems},
  journal = {The Journal of Chemical Physics}
}
@article{PinedaKrch2008,
  doi = {10.18637/jss.v025.i12},
  url = {https://doi.org/10.18637/jss.v025.i12},
  year = {2008},
  publisher = {Foundation for Open Access Statistic},
  volume = {25},
  number = {12},
  author = {Mario Pineda-Krch},
  title = {{GillespieSSA}: Implementing the Stochastic Simulation Algorithm in R},
  journal = {Journal of Statistical Software}
}
@article{Cao2004,
  doi = {10.1063/1.1778376},
  url = {https://doi.org/10.1063/1.1778376},
  year = {2004},
  month = sep,
  publisher = {{AIP} Publishing},
  volume = {121},
  number = {9},
  pages = {4059--4067},
  author = {Yang Cao and Hong Li and Linda Petzold},
  title = {Efficient formulation of the stochastic simulation algorithm for chemically reacting systems},
  journal = {The Journal of Chemical Physics}
}
@book{Kot2001,
  doi = {10.1017/cbo9780511608520},
  url = {https://doi.org/10.1017/cbo9780511608520},
  year = {2001},
  month = jul,
  publisher = {Cambridge University Press},
  author = {Mark Kot},
  title = {Elements of Mathematical Ecology}
}
@article{Gillespie1977,
  doi = {10.1021/j100540a008},
  url = {https://doi.org/10.1021/j100540a008},
  year = {1977},
  month = dec,
  publisher = {American Chemical Society ({ACS})},
  volume = {81},
  number = {25},
  pages = {2340--2361},
  author = {Daniel T. Gillespie},
  title = {Exact stochastic simulation of coupled chemical reactions},
  journal = {The Journal of Physical Chemistry}
}
@article{PinedaKrch2007,
  author = {Pineda-Krch, Mario and J. Blok, Hendrik and Dieckmann, Ulf and Doebeli, Michael},
  title = {A tale of two cycles – distinguishing quasi-cycles and limit cycles in finite predator–prey populations},
  journal = {Oikos},
  volume = {116},
  number = {1},
  pages = {53-64},
  doi = {https://doi.org/10.1111/j.2006.0030-1299.14940.x},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.2006.0030-1299.14940.x},
  eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.2006.0030-1299.14940.x},
  abstract = {Periodic predator–prey dynamics in constant environments are usually taken as indicative of deterministic limit cycles. It is known, however, that demographic stochasticity in finite populations can also give rise to regular population cycles, even when the corresponding deterministic models predict a stable equilibrium. Specifically, such quasi-cycles are expected in stochastic versions of deterministic models exhibiting equilibrium dynamics with weakly damped oscillations. The existence of quasi-cycles substantially expands the scope for natural patterns of periodic population oscillations caused by ecological interactions, thereby complicating the conclusive interpretation of such patterns. Here we show how to distinguish between quasi-cycles and noisy limit cycles based on observing changing population sizes in predator–prey populations. We start by confirming that both types of cycle can occur in the individual-based version of a widely used class of deterministic predator–prey model. We then show that it is feasible and straightforward to accurately distinguish between the two types of cycle through the combined analysis of autocorrelations and marginal distributions of population sizes. Finally, by confronting these results with real ecological time series, we demonstrate that by using our methods even short and imperfect time series allow quasi-cycles and limit cycles to be distinguished reliably.},
  year = {2007}
}
@book{Brown1993,
  title={Models in biology: mathematics, statistics and computing.},
  author={Brown, David and Rothery, Peter and others},
  year={1993},
  publisher={John Wiley \& Sons Ltd.}
}
@article{Eddelbuettel2011,
  doi = {10.18637/jss.v040.i08},
  url = {https://doi.org/10.18637/jss.v040.i08},
  year = {2011},
  publisher = {Foundation for Open Access Statistic},
  volume = {40},
  number = {8},
  author = {Dirk Eddelbuettel and Romain Fran{\c{c}}ois},
  title = {$\less$b$\greater$Rcpp$\less$/b$\greater$: Seamless$\less$i$\greater$R$\less$/i$\greater$and$\less$i$\greater$C$\mathplus$$\mathplus$$\less$/i$\greater$Integration},
  journal = {Journal of Statistical Software}
}
