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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 (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

Documentation:

Reference manual: TiPS.pdf
Vignettes: TiPS

Downloads:

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

Linking:

Please use the canonical form https://CRAN.R-project.org/package=TiPS to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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