Create DiscuitModel

Source: R/DiscuitModel.R

Returns an object of type DiscuitModel. Available models: SI, SIS, SIR, SEI, SEIR, SEIRa (SEIR and SEIRa are for modelling systems with permanent and temporary immunity, respectively). Custom models can be created by accesing the library directly via C++.

DiscuitModel(modelName, initialCondition, rateFunction, transitionMatrix,
  observationFunction, priorDensity, observationModel, t0Index = 0)

Arguments

modelName

model name (e.g. "SIS", "SEIR", etc)
initialCondition

initial condition.
rateFunction

string representing the event rate function, e.g. "output1 = parameters1 * population1 * population2".
transitionMatrix

transition matrix.
observationFunction

observation function.
priorDensity

prior density function.
observationModel

observation model likelihood function.
t0Index

index of the parameter that represents the initial time. 0 if fixed at 0.0.

Examples

DiscuitModel("SI", c(100, 1), "output[1] = parameters[1] * population[1] * population[2]", c(-1, 1)
, "return population", "return parameters[1] > 0 ? 1 : 0")
#> Julia version 1.0.0 at location /home/martin/dev/julia/julia-1.0.0-linux-x86_64/julia-1.0.0/bin will be used.
#> Loading setup script for JuliaCall...
#> Finish loading setup script for JuliaCall.
#> rf (generic function with 1 method)
#>   
#> of (generic function with 1 method)
#>   
#> prior (generic function with 1 method)
#>   
#> Error in paste("function om(y::Array{Int64, 1}, population::Array{Int64, 1})",     observationModel, "end", sep = "\n"): argument "observationModel" is missing, with no default