serocalculator (version 1.3.0)

stratify_data: Split data by stratum

Description

Split biomarker data, decay curve parameters, and noise parameters to prepare for stratified incidence estimation.

Usage

stratify_data(
  data,
  curve_params,
  noise_params,
  strata_varnames = "",
  curve_strata_varnames = NULL,
  noise_strata_varnames = NULL,
  antigen_isos = data %>% attr("antigen_isos")
)

Value

a "biomarker_data_and_params.list" object (a list with extra attributes "strata", "antigen_isos", etc)

Arguments

curve_params

a data.frame() containing MCMC samples of parameters from the Bayesian posterior distribution of a longitudinal decay curve model. The parameter columns must be named:

• antigen_iso: a character() vector indicating antigen-isotype combinations

• iter: an integer() vector indicating MCMC sampling iterations

• y0: baseline antibody level at $t=0$ ($y(t=0)$)

• y1: antibody peak level (ELISA units)

• t1: duration of infection

• alpha: antibody decay rate (1/days for the current longitudinal parameter sets)

• r: shape factor of antibody decay

noise_params

a data.frame() (or tibble::tibble()) containing the following variables, specifying noise parameters for each antigen isotype:

• antigen_iso: antigen isotype whose noise parameters are being specified on each row

• nu: biological noise

• eps: measurement noise

• y.low: lower limit of detection for the current antigen isotype

• y.high: upper limit of detection for the current antigen isotype

strata_varnames

character() vector of names of variables in data to stratify by

curve_strata_varnames

A subset of strata. Values must be variable names in curve_params. Default = "".

noise_strata_varnames

A subset of strata. Values must be variable names in noise_params. Default = "".

antigen_isos

Character vector with one or more antibody names. Values must match pop_data

Examples

if (FALSE) {
library(dplyr)

xs_data <-
  sees_pop_data_pk_100

curve <-
  typhoid_curves_nostrat_100 %>%
  filter(antigen_iso %in% c("HlyE_IgA", "HlyE_IgG"))

noise <-
  example_noise_params_pk

stratified_data =
  stratify_data(
   data = xs_data,
   curve_params = curve,
   noise_params = noise,
   strata_varnames = "catchment",
   curve_strata_varnames = NULL,
   noise_strata_varnames = NULL
   )
}