Generates stochastic time series and genealogies associated with a population dynamics model. Times series are simulated using the Gillespie exact and approximate algorithms and a new algorithm we introduce that uses both approaches to optimize the time execution of the simulations. Genealogies are simulated from a trajectory using a backwards-in-time based approach. Methods are described in Danesh G et al (2022) <doi:10.1111/2041-210X.14038>.
| Version: |
1.3.0 |
| Depends: |
R (≥ 4.0.0) |
| Imports: |
graphics, grDevices, gtools, inline, methods, Rcpp (≥
0.12.14), stats, stringr, utils |
| LinkingTo: |
Rcpp, BH |
| Suggests: |
knitr, rmarkdown, ape, testthat (≥ 3.0.0) |
| Published: |
2025-05-09 |
| DOI: |
10.32614/CRAN.package.TiPS |
| Author: |
Gonche Danesh [aut, cre, cph],
Emma Saulnier [aut, cph],
Olivier Gascuel [aut, cph],
Marc Choisy [aut, cph, ths],
Samuel Alizon [aut, cph, ths] |
| Maintainer: |
Gonche Danesh <gonche.danesh at gmail.com> |
| BugReports: |
https://gitlab.in2p3.fr/ete/tips/-/issues |
| License: |
GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| URL: |
https://gitlab.in2p3.fr/ete/tips/ |
| NeedsCompilation: |
yes |
| Citation: |
TiPS citation info |
| Materials: |
README |
| CRAN checks: |
TiPS results |