polynomial_model: Polynomial models

In serosv: Model Infectious Disease Parameters from Serosurveys

Polynomial models

Description

Either 'status' (treated as line-listing dataset) or 'pos' & 'tot' (treated as aggregated dataset) must be provided

Usage

polynomial_model(
  age,
  k,
  type,
  pos = NULL,
  tot = NULL,
  status = NULL,
  link = "log"
)

Arguments

age	the age vector.
k	degree of the model.
type	name of method (Muench, Giffith, Grenfell).
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).
link	link function.

Details

Refers to section 6.1.1

Value

a list of class polynomial_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

Examples

data <- parvob19_fi_1997_1998[order(parvob19_fi_1997_1998$age), ]
aggregated <- transform_data(data$age, data$seropositive)

# fit with aggregated data
model <- polynomial_model(aggregated$t, pos = aggregated$pos, tot = aggregated$tot, type = "Muench")
# fit with linelisting data
model <- polynomial_model(data$age, status = data$seropositive, type = "Muench")
plot(model)

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