TMB Documentation  v1.9.2
// Random walk with multivariate correlated increments and measurement noise.
#include <TMB.hpp>
/* Parameter transform */
template <class Type>
Type f(Type x){return Type(2)/(Type(1) + exp(-Type(2) * x)) - Type(1);}
template<class Type>
Type objective_function<Type>::operator() ()
DATA_ARRAY(obs); /* timeSteps x stateDim */
PARAMETER_ARRAY(u); /* State */
int timeSteps=obs.dim[1];
int stateDim=obs.dim[0];
Type rho=f(transf_rho);
vector<Type> sds=exp(logsds);
vector<Type> sdObs=exp(logsdObs);
// Setup object for evaluating multivariate normal likelihood
matrix<Type> cov(stateDim,stateDim);
for(int i=0;i<stateDim;i++)
for(int j=0;j<stateDim;j++)
using namespace density;
MVNORM_t<Type> neg_log_density(cov);
/* Define likelihood */
Type ans=0;
for(int i=1;i<timeSteps;i++)
ans += neg_log_density(u.col(i)-u.col(i-1)); // Process likelihood
for(int i=0; i<timeSteps; i++)
ans -= dnorm(obs.col(i).vec(), u.col(i).vec(), sdObs, true).sum(); // Data likelihood
return ans;
License: GPL v2