penalized_spline_model: Penalized Spline model

In serosv: Model Infectious Disease Parameters from Serosurveys

Penalized Spline model

Description

Penalized Spline model

Usage

penalized_spline_model(
  age,
  pos = NULL,
  tot = NULL,
  status = NULL,
  s = "bs",
  link = "logit",
  framework = "pl",
  sp = NULL
)

Arguments

age	the age vector
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).
s	smoothing basis to use
link	link function to use
framework	which approach to fit the model ("pl" for penalized likelihood framework, "glmm" for generalized linear mixed model framework)
sp	smoothing parameter

Value

a list of class penalized_spline_model with 6 attributes

datatype	type of datatype used for model fitting (aggregated or linelisting)
df	the dataframe used for fitting the model
framework	either pl or glmm
info	fitted "gam" model when framework is pl or "gamm" model when framework is glmm
sp	seroprevalence
foi	force of infection

See Also

[mgcv::gam()], [mgcv::gamm()] for more information the fitted gam and gamm model

Examples

data <- parvob19_be_2001_2003
model <- penalized_spline_model(data$age, status = data$seropositive, framework="glmm")
model$info$gam
plot(model)

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