Generate a list of objects governing the measurement process for a stochastic epidemic model.

stem_measure(emissions, dynamics, data = NULL, messages = FALSE)

Arguments

emissions: list of emmision lists, each generated by a call to the emission function.
dynamics: processed list of objects governing the model dynamics, returned by the stem_dynamics function.
data: matrix/data frame, or a list of matrices/data frames. All columns must be named according to which compartment_strata are measured. The first column must consist of observation times, t_1,...,t_L. If data on all measured compartments are accrued at the same observation times, a single matrix or data frame may be provided. If each compartment in the data was measured at different observation times, a list of matrices or data frames must be provided. Again, the first column of each matrix must consist of observation times, while subsequent columns must be labeled according to which compartment being measured.
messages: should compilation messages be printed? defaults to true.

list with evaluated measurement process functions and objects. The list contains the following objects:

meas_pointers: external pointers to compiled functions to simulate from and evaluate the density of the measurement process
obstimes: complete vector of observation times
obstime_inds: list of indices (C++) of observation times for each of the measurement variables
obsmat: either a template for an observation matrix, or an observation matrix that combines the supplied list of observation matrices
obscomp_codes: named numeric vector of measurement variable codes
measproc_indmat: indicator matrix for which measurement variables are measured at which observation times
meas_inds: indices (C++) of elements in the observation matrix that correspond to measurements (non-NAs)
censusmat: template matrix for storing the compartment counts at observation times
tcovar_censmat: matrix with time-varying coviates censused at observation times
lna_prevalence: indicator for whether prevalence is computed in the LNA
lna_incidence: indicator for whether incidence is computed in the LNA
incidence_codes_lna: C++ column indices for LNA count processes on transition events for which incidence is to be computed