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 |