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A stochastic simulator of birth-death master equations with application to phylodynamics.

Vaughan TG, Drummond AJ - Mol. Biol. Evol. (2013)

Bottom Line: Importantly, phylogenetic trees or networks can be generated alongside the histories they correspond to, enabling investigations into the interplay between genealogies and population dynamics.Summary statistics such as means and variances can be recorded in place of the full ensemble, allowing for a reduction in the amount of memory used--an important consideration for models including large numbers of individual subpopulations or demes.Simulated phylogenetic trees can be recorded using the standard Newick or NEXUS formats, with extensions to these formats used for non-tree-like inheritance relationships.

View Article: PubMed Central - PubMed

Affiliation: Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand. t.g.vaughan@massey.ac.nz

ABSTRACT
In this article, we present a versatile new software tool for the simulation and analysis of stochastic models of population phylodynamics and chemical kinetics. Models are specified via an expressive and human-readable XML format and can be used as the basis for generating either single population histories or large ensembles of such histories. Importantly, phylogenetic trees or networks can be generated alongside the histories they correspond to, enabling investigations into the interplay between genealogies and population dynamics. Summary statistics such as means and variances can be recorded in place of the full ensemble, allowing for a reduction in the amount of memory used--an important consideration for models including large numbers of individual subpopulations or demes. In the case of population size histories, the resulting simulation output is written to disk in the flexible JSON format, which is easily read into numerical analysis environments such as R for visualization or further processing. Simulated phylogenetic trees can be recorded using the standard Newick or NEXUS formats, with extensions to these formats used for non-tree-like inheritance relationships.

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MASTER input file specifying a single fixed time length simulation of a stochastic SIR model.
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mst057-F1: MASTER input file specifying a single fixed time length simulation of a stochastic SIR model.

Mentions: The basic MASTER input file, which can be used to simulate the population size dynamics under this model, is shown in figure 1. Here, we have selected the “Trajectory” simulation type and have used the simulationTime attribute to specify that the simulation should run for 50 time units. The <model> element has been used to specify that the model contains the three compartment populations, and that these populations are subject to the two reactions given earlier. The <initialState> element has been used to initialize the simulation with 1,000 individuals, including 999 susceptible and 1 infected (note that we do not need to explicitly set the R compartment population size to zero, as this is the default). Finally, the <output> element is used to specify a JSON-formatted output file named “SIR_output.json.”Fig. 1.


A stochastic simulator of birth-death master equations with application to phylodynamics.

Vaughan TG, Drummond AJ - Mol. Biol. Evol. (2013)

MASTER input file specifying a single fixed time length simulation of a stochastic SIR model.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3649681&req=5

mst057-F1: MASTER input file specifying a single fixed time length simulation of a stochastic SIR model.
Mentions: The basic MASTER input file, which can be used to simulate the population size dynamics under this model, is shown in figure 1. Here, we have selected the “Trajectory” simulation type and have used the simulationTime attribute to specify that the simulation should run for 50 time units. The <model> element has been used to specify that the model contains the three compartment populations, and that these populations are subject to the two reactions given earlier. The <initialState> element has been used to initialize the simulation with 1,000 individuals, including 999 susceptible and 1 infected (note that we do not need to explicitly set the R compartment population size to zero, as this is the default). Finally, the <output> element is used to specify a JSON-formatted output file named “SIR_output.json.”Fig. 1.

Bottom Line: Importantly, phylogenetic trees or networks can be generated alongside the histories they correspond to, enabling investigations into the interplay between genealogies and population dynamics.Summary statistics such as means and variances can be recorded in place of the full ensemble, allowing for a reduction in the amount of memory used--an important consideration for models including large numbers of individual subpopulations or demes.Simulated phylogenetic trees can be recorded using the standard Newick or NEXUS formats, with extensions to these formats used for non-tree-like inheritance relationships.

View Article: PubMed Central - PubMed

Affiliation: Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand. t.g.vaughan@massey.ac.nz

ABSTRACT
In this article, we present a versatile new software tool for the simulation and analysis of stochastic models of population phylodynamics and chemical kinetics. Models are specified via an expressive and human-readable XML format and can be used as the basis for generating either single population histories or large ensembles of such histories. Importantly, phylogenetic trees or networks can be generated alongside the histories they correspond to, enabling investigations into the interplay between genealogies and population dynamics. Summary statistics such as means and variances can be recorded in place of the full ensemble, allowing for a reduction in the amount of memory used--an important consideration for models including large numbers of individual subpopulations or demes. In the case of population size histories, the resulting simulation output is written to disk in the flexible JSON format, which is easily read into numerical analysis environments such as R for visualization or further processing. Simulated phylogenetic trees can be recorded using the standard Newick or NEXUS formats, with extensions to these formats used for non-tree-like inheritance relationships.

Show MeSH