TiPS: Trajectories and Phylogenies Simulator

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: 1.1.0
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: 2021-11-12
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
SystemRequirements: C++11
Citation: TiPS citation info
CRAN checks: TiPS results

Documentation:

Reference manual: TiPS.pdf
Vignettes: TiPS

Downloads:

Package source: TiPS_1.1.0.tar.gz
Windows binaries: r-devel: TiPS_1.1.0.zip, r-devel-UCRT: TiPS_1.1.0.zip, r-release: TiPS_1.1.0.zip, r-oldrel: TiPS_1.1.0.zip
macOS binaries: r-release (arm64): TiPS_1.1.0.tgz, r-release (x86_64): TiPS_1.1.0.tgz, r-oldrel: TiPS_1.1.0.tgz
Old sources: TiPS archive

Linking:

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