stratify_data: Split data by stratum

In serocalculator: Estimating Infection Rates from Serological 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")
)

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

Value

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

Examples

## Not run: 
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
   )

## End(Not run)

serocalculator documentation built on April 3, 2025, 7:35 p.m.