NonLinearModels: Modeling the Force of Infection using Non-Linear Models

In TeaKov/serostat: Modeling Infectious Disease Parameters Based on Serological and Social Contact Data R Package

Description

Models the (age-dependent) force of infection using non-linear models, given input parameters and the specification of a model (see arguments).

Usage

NonLinearModels(data, parameters, fun)

Arguments

data	Contains all input parameters: Age describes the population's age categories, Pos represents the number of seropositive individuals by age category, and Tot are the total number of individuals in each specified age category.
parameters	Specifies the parameters used in the non-linear force of infection equation: λ(a) = (aα - γ)e^{-aβ} + γ, where gamma is the long-term residual value of the force of infection (Farrington et al., 1990). In order to ensure that the force of infection satisfies λ(a) ≥ 0, the parameter space is constrained to be non-negative.
fun	This specifies which non-linear model for the force of infection you want to use: FarringtonABG is Farrington's model where alpha, beta, and gamma are used as model parameters, FarringtonAB_G is an alternative simplified model in which gamma is kept as a fixed parameter and alpha and beta are the model parameters that are estimated.

See Also

Farrington, C. P. (1990). Modelling forces of infection for measles, mumps and rubella, 9(8), 953-967.

Examples

# Load UK's Rubella data from '86-'87
data("Rubella_UK_8687")

# Prepare the data
data <- list(Tot=(Rubella_UK_8687$Pos+Rubella_UK_8687$Neg),
  Pos=Rubella_UK_8687$Pos, Age=Rubella_UK_8687$Age)

# Prepare the parameters
params <- list(alpha=0.07, beta=0.1, gamma=0.03)

# Farrington's model, with alpha, beta, and gamma as starting values for MLE
result <- NonLinearModels(data, params, FarringtonABG)
summary(result)

# Farrington's model, with alpha and beta as starting values for MLE, and gamma as a fixed parameter
params <- list(alpha=0.07, beta=0.1, gamma=0)
result <- NonLinearModels(data, params, FarringtonAB_G)
summary(result)

TeaKov/serostat documentation built on May 21, 2019, 1:21 p.m.