farrington_model: The Farrington (1990) model.

In serosv: Model Infectious Disease Parameters from Serosurveys

The Farrington (1990) model.

Description

Refers to section 6.1.2.

Usage

farrington_model(
  age,
  start,
  pos = NULL,
  tot = NULL,
  status = NULL,
  fixed = list()
)

Arguments

age	the age vector.
start	Named list of vectors or single vector. Initial values for optimizer.
pos	the positive count vector (optional if status is provided).
tot	the total count vector (optional if status is provided).
status	the serostatus vector (optional if pos & tot are provided).
fixed	Named list of vectors or single vector. Parameter values to keep fixed during optimization.

Value

a list of class farrington_model with 5 items

datatype	type of datatype used for model fitting (aggregated or linelisting)
df	the dataframe used for fitting the model
info	fitted "glm" object
sp	seroprevalence
foi	force of infection

See Also

[stats::glm()] for more information on the fitted glm object

Examples

df <- rubella_uk_1986_1987
model <- farrington_model(
  df$age, pos = df$pos, tot = df$tot,
  start=list(alpha=0.07,beta=0.1,gamma=0.03)
  )
plot(model)

serosv documentation built on Oct. 18, 2024, 5:07 p.m.