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 (2020) <doi:10.1101/2020.11.09.373795>.
| Version: | 1.0 |
| Depends: | R (≥ 3.2.0) |
| Imports: | graphics, grDevices, gtools, inline, methods, Rcpp (≥ 0.12.14), stats, stringr, utils |
| LinkingTo: | Rcpp |
| Suggests: | knitr, rmarkdown, ape |
| Published: | 2021-09-13 |
| Author: | Gonche Danesh [aut, cre, cph], Emma Saulnier [aut, cph], Marc Choisy [aut, cph, ths], Samuel Alizon [aut, cph, ths] |
| Maintainer: | Gonche Danesh <gonche.danesh at gmail.com> |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| NeedsCompilation: | yes |
| SystemRequirements: | C++11 |
| CRAN checks: | TiPS results |
| Reference manual: | TiPS.pdf |
| Vignettes: |
TiPS |
| Package source: | TiPS_1.0.tar.gz |
| Windows binaries: | r-devel: TiPS_1.0.zip, r-devel-UCRT: TiPS_1.0.zip, r-release: TiPS_1.0.zip, r-oldrel: TiPS_1.0.zip |
| macOS binaries: | r-release (arm64): TiPS_1.0.tgz, r-release (x86_64): TiPS_1.0.tgz, r-oldrel: TiPS_1.0.tgz |
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