Fast Kalman log-likelihood for prevalence observations

Compiled counterpart of sird_ga_loglik() (same model and observation equation, RK4 transition quantities).

Usage

sird_ga_loglik_prev(theta, y, N, Delta = 1, nsub = 10L)

Arguments

theta

Named numeric vector with elements lambda, gamma, alpha, s0, i0, r0, p, tau2 (all strictly positive except r0, which may be zero; p in (0,1)).

y

Numeric vector of observed infectious head counts \(y_0, y_1, \ldots, y_n\) (not normalised; normalisation by N is performed internally, matching the \(O_N(t_k)=O(t_k)/N\) observation model of the manuscript).

N

Population size.

Delta

Time step between consecutive observations (default 1).

nsub

RK4 steps per interval.