epilike: Calculates the log likelihood

Description Usage Arguments References Examples

Description

Calculates the log likelihood for the specified individual level model and data set

Usage

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epilike (type, x = NULL, y = NULL, inftime, infperiod = NULL, tmin = NULL, tmax, alpha, 

         beta, spark = NULL, Sformula = NULL, contact = NULL)

Arguments

type

Type of compartment framework, with the choice of "SI" for Susceptible-Infectious diseases and "SIR" for Susceptible-Infectious-Removed

x

X coordinates of individuals

y

Y coordinates of individuals

inftime

Infection times

infperiod

Length of infectious period for each individual

tmin

The first time point at which data is observed, default value is one

tmax

The last time point at which data is observed

alpha

Susceptibility parameter(>0)

beta

Spatial parameter(s) (>0) or network parameter (s) (>0) if contact is used

spark

Sparks parameter(>=0), representing infections unexplained by other parts of the model or infections coming in from outside the observed population, default value is zero

Sformula

An object of class formula. See formula

Individual-level covariate information passable through this argument. An expression of the form ~ model is interpreted as a specification that the susceptibility function, Ω_s(i) is modelled by a linear predictor specified symbolically by the model term. Such a model consists of a series of terms separated by + and - operators. If there is no covariate information, Sformula is null

contact

Contact network matrix (matrices)

References

Deardon R, Brooks, S. P., Grenfell, B. T., Keeling, M. J., Tildesley, M. J., Savill, N. J., Shaw, D. J., Woolhouse, M. E. (2010). Inference for individual level models of infectious diseases in large populations. Statistica Sinica, 20, 239-261.

Examples

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## Example 1:  spatial SI model 
# generate 100 individuals 
## Not run: 
x <- runif(100, 0, 10)

y <- runif(100, 0, 10)

covariate <- runif(100, 0, 2)

out <- epidata(type = "SI", n = 100, Sformula = ~covariate, tmax = 15, 
              alpha = c(0.1, 0.3), beta = 5.0, x = x, y = y)

epilike(type = "SI", x = x, y = y, inftime = out$inftime, tmax = 15, 
         alpha = c(0.1, 0.3), beta = 5, Sformula = ~covariate)

## End(Not run)
## Example 2: spatial SIR model 
# generate infectious period (=3) for 100 individuals 
## Not run: 
lambda <- rep(3, 100)

out <- epidata(type = "SIR", n = 100, tmax = 15, alpha  =0.3, beta = 5.0,
              infperiod = lambda, x = x, y = y)

epilike(type = "SIR", x = x, y = y, infperiod = lambda, inftime = out$inftime, 
        tmax = 15, alpha = 0.3, beta = 5.0)


## End(Not run)

EpiILM documentation built on May 2, 2019, 12:20 p.m.