Default Log-likelihood Function

Extracts the logLikelihood value from the simulations attribute of the parMCMC argument, requires:

• parMCMC has simulations attribute

• simulations list includes logLikelihood values (omit<3)

Usage

ll(parMCMC)

Arguments

parMCMC

a numeric vector, with attributes for MCMC, specifically smmala

Value

a scalar value: log(likelihood(data|parMCMC))

Details

This function will take the log-likelihood-values claculated by the ode solver in this package, and return the sum of those values over all experiments. The value the simulator returns is calculated with the assumption of a normal distribution on measurement errors.

This function does almost no work, it merely sums up the values calculated during simulation.

Examples

m <- model_from_tsv(uqsa_example("AKAR4"))
o <- as_ode(m)
c_path(o) <- write_c_code(generate_code(o))
so_path(o) <- shlib(o)
ex <- experiments(m,o)
options(mc.cores=length(ex))
s <- simulator.c(ex,o,omit=2) # not 3
p <- values(m$Parameter)
attr(p,"simulations") <- s(p)
print(ll(p))
#> [1] -2491.245