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) .


Reference manual

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1.0 by Gonche Danesh, 14 days ago

Browse source code at

Authors: Gonche Danesh [aut, cre, cph] , Emma Saulnier [aut, cph] , Marc Choisy [aut, cph, ths] , Samuel Alizon [aut, cph, ths]

Documentation:   PDF Manual  

GPL (>= 2) license

Imports graphics, grDevices, gtools, inline, methods, Rcpp, stats, stringr, utils

Suggests knitr, rmarkdown, ape

Linking to Rcpp

System requirements: C++11

See at CRAN