TMB Documentation  v1.9.0
// Inference in a linear scalar stochastic differential equation.
// dX = - lambda*X*dt + sigmaX*dB
// based on discrete observations
// Y(i) = X(t(i)) + e(i)
// where e(i) is N(0,sigmaY^2)
// Latent variables are the states.
// We use Euler approximation to evalaute transition densities. The time mesh for this
// discretization is finer than the sample interval, i.e. some (many) states are unobserved.
#include <TMB.hpp>
template<class Type>
Type objective_function<Type>::operator() ()
DATA_VECTOR(tsim); // Time points where X is simulated
DATA_VECTOR(iobs); // Indeces into tsim where X is observed
DATA_VECTOR(Y); // Observations taken. Must have same length as iobs.
PARAMETER_VECTOR(X); // States at tsim. Length = length(tsim)
PARAMETER(lambda); // Rate parameter in the SDE
PARAMETER(logsX); // log(sigmaX) where sigmaX is noise intensity in the SDE
PARAMETER(logsY); // log(sigmaY) where sigmaY is on measurement error
Type sX=exp(logsX);
Type sY=exp(logsY);
Type ans=0; // ans will be the resulting likelihood
vector<Type> dt(tsim.size()-1);
for(int i=0;i<dt.size();i++)
dt(i) = tsim(i+1)-tsim(i);
// Include likelihood contributions from state transitions
for(int i=0;i<dt.size();i++){
ans -= dnorm(X(i+1),X(i) + lambda*X(i)*dt(i),sX*sqrt(dt(i)),1);
// Include likelihood contributions from measurements
for(int i=0;i<Y.size(); ++i){
int j=CppAD::Integer(iobs(i));
return ans;
License: GPL v2