show.demographic.process: Show demographic process

In emvolz-phylodynamics/phydynR: Model-based coalescent simulation and likelihood for phylodynamic inference

Show demographic process

Description

Shows a graphical representation of the demographic process given values for each parameter of interest, and initial population sizes. The user should also provide the initial size for the population of interest in the their model.

Usage

show.demographic.process(
  demo.model,
  theta,
  x0,
  t0,
  t1,
  res = 1000,
  integrationMethod = "lsoda",
  legend_position = "bottomright",
  ...
)

Arguments

demo.model	An object of class demographic.process, which is a function that can be used to simulate the model.
theta	A named numeric vector or named list of parameter values used by the demographic model
x0	A named vector of initial conditions required by the model. This includes demes and any other dynamic variables.
t0	Initial time for the simulation (to show the demographic process)
t1	Final time for tge simulation (to show the demographic process)
res	Integer number of time steps to use when simulating model.
integrationMethod	If simulating an ODE model, this provides the integration routine corresponding to options in deSolve.
legend_position	String for position of legend in final plot. Default is set to "bottomright"
...	Additional arguments that can be passed to the function, such as graphical parameters.

See Also

build.demographic.process

Examples

# A simple exponential growth model with birth rates beta and death rates gamma:
# I is the number of infected individuals.
dm <- build.demographic.process(births=c(I = 'parms$beta * I'),
                                deaths = c(I = 'parms$gamma * I'),
                                parameterNames=c('beta', 'gamma'),
                                rcpp=FALSE,
                                sde = TRUE)
# Do a simulation and plot the trajectory:
show.demographic.process(dm,
                         theta = list(beta = 1.5, gamma = 1),
                         x0  = c(I = 1),
                         t0 = 0,
                         t1 = 10)

emvolz-phylodynamics/phydynR documentation built on July 28, 2023, 6:06 a.m.