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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: | 1.2.3 |
| Depends: | R (≥ 3.5.0) |
| Imports: | graphics, grDevices, gtools, inline, methods, Rcpp (≥ 0.12.14), stats, stringr, utils |
| LinkingTo: | Rcpp |
| Suggests: | knitr, rmarkdown, ape, testthat (≥ 3.0.0) |
| Published: | 2023-05-23 |
| 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 |
| Reference manual: | TiPS.pdf |
| Vignettes: |
TiPS |
| Package source: | TiPS_1.2.3.tar.gz |
| Windows binaries: | r-devel: TiPS_1.2.3.zip, r-release: TiPS_1.2.3.zip, r-oldrel: TiPS_1.2.3.zip |
| macOS binaries: | r-release (arm64): TiPS_1.2.3.tgz, r-oldrel (arm64): TiPS_1.2.3.tgz, r-release (x86_64): TiPS_1.2.3.tgz, r-oldrel (x86_64): TiPS_1.2.3.tgz |
| Old sources: | TiPS archive |
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