GDILM_SEIRS_Par_Est {GDILM.SEIRS} | R Documentation |
GDILM SEIRS for Real Data
Description
This function applies the Geographically Dependent Individual Level Model (GDILM) for infectious disease transmission, incorporating reinfection dynamics within the Susceptible-Exposed-Infectious-Recovered-Susceptible (SEIRS) framework, to real data. It employs a likelihood based Monte Carlo Expectation Conditional Maximization (MCECM) algorithm for parameter estimation and AIC calculation. This function requires two dataframes, named data
and adjacency_matrix
, along with the necessary parameters. Detailed information on the structure of these two datasets is provided in the package.
Usage
GDILM_SEIRS_Par_Est(
data,
adjacency_matrix,
DimCovInf,
DimCovSus,
DimCovSusReInf,
tau0,
lambda0,
alphaS0,
delta0,
alphaT0,
InfPrd,
IncPrd,
NIterMC,
NIterMCECM
)
Arguments
data |
Dataset. The dataset should exactly match the |
adjacency_matrix |
Adjacency matrix representing the regions in the study area (0 if no connection between regions) |
DimCovInf |
Dimensions of the individual infectivity covariate |
DimCovSus |
Dimensions of the area-level susceptibility to initial infection covariate |
DimCovSusReInf |
Dimensions of the area-level susceptibility to reinfection covariate |
tau0 |
Initial value for spatial precision |
lambda0 |
Initial value for spatial dependence |
alphaS0 |
Initial value for the susceptibility intercept |
delta0 |
Initial value for the spatial decay parameter |
alphaT0 |
Initial value for the infectivity intercept |
InfPrd |
Infectious period that can be obtained either from the literature or by fitting an SEIRS model to the data |
IncPrd |
Incubation period that can be obtained either from the literature or by fitting an SEIRS model to the data |
NIterMC |
Number of MCMC iterations |
NIterMCECM |
Number of MCECM iterations |
Value
alphaS
Estimate of alpha S
BetaCovInf
Estimate of beta vector for the individual level infection covariate
BetaCovSus
Estimate of beta vector for the areal susceptibility to first infection covariate
BetaCovSusReInf
Estimate of beta vector for the areal susceptibility to reinfection covariate
alphaT
Estimate of alpha T
delta
Estimate of delta
tau1
Estimate of tau
lambda1
Estimate of lambda
AIC
AIC of the fitted GDILM SEIRS
Examples
data(data)
data(adjacency_matrix)
GDILM_SEIRS_Par_Est(data,adjacency_matrix,2,2,2,0.5, 0.5, 1, 2, 1, 1, 1, 20, 2)