Age-time varying seroprevalence Fit age-stratified seroprevalence across multiple time points. Also try to monotonize age (or cohort) - specific seroprevalence.

Age-time varying seroprevalence Fit age-stratified seroprevalence across multiple time points. Also try to monotonize age (or cohort) - specific seroprevalence.

Usage

age_time_model(
  data,
  time_col = "date",
  grouping_col = "group",
  age_correct = F,
  le = 512,
  ci = 0.95
)

Arguments

data

- input data, must have`age`, `status`, time, group columns, where group column determines how data is aggregated

time_col

- name of the column for time (default to `date`)

grouping_col

- name of the column for time (default to `group`)

age_correct

- a boolean, if `TRUE`, monotonize age-specific prevalence. Monotonize birth cohort-specific seroprevalence otherwise.

le

- number of bins to generate age grid, used when monotonizing data

ci

- confidence interval for smoothing

Value

a list of class time_age_model with 3 items

out

a data.frame with dimension n_group x 9, where columns `info`, `sp`, `foi` store output for non-monotonized data and `monotonized_info`, `monotonized_sp`, `monotonized_foi`, `monotonized_ci_mod` store output for monotnized data

grouping_col

name of the column for grouping

age_correct

a boolean indicating whether the data is monotonized across age or cohort