Before revision:  To address these issues, we first develop a compartmental model for non-communicable infections, which are especially common with NS. Then, we develop a novel optimal linear filterfor Poisson observations, characteristic of infectious diseases, which model the number of patients recorded as presenting each day at hospitals. The classical Linear Quadratic Regulator is generalized to nonautonomous linear dynamics with mixed linear and quadratic cost functions, which better model real world costs. At each step we apply our methods to  a case study of NS and PIH , using parameters estimated from publicly available data for Uganda.
After revision:  To address these issues, we first develop a compartmental model for non-communicable infections, which are especially common with NS. Then, we develop a novel optimal linear filterfor Poisson observations, characteristic of infectious diseases, which model the number of patients recorded as presenting each day to a case study of NS and PIH , using parameters estimated from publicly available data for Uganda.