Reshape Shigella longitudinal data for serodynamics workflows

Filters a dataset to a given study and antigen column, standardizes column names, and returns a visit-ordered long dataset suitable for conversion to serodynamics::as_case_data().

Usage

process_shigella_data(data, study_filter, antigen)

Arguments

data: A data frame containing longitudinal measurements.
study_filter: Character scalar. Value of study_name to keep (e.g. "SOSAR").
antigen: Unquoted column name for the antigen measurement (e.g. n_ipab_MFI).

Value

A tibble with standardized columns:

index_id: Participant ID (copied from sid).
antigen_iso: Isotype label (copied from isotype_name).
visit: Visit label (copied from timepoint).
timeindays: Time since infection (copied from Actual day).
result: Antibody measurement (from antigen).

Examples

if (FALSE) { # \dontrun{
dat_long <- process_shigella_data(df, "SOSAR", n_ipab_MFI)
dL <- serodynamics::as_case_data(dat_long,
  id_var = "index_id", biomarker_var = "antigen_iso",
  time_in_days = "timeindays", value_var = "result"
)
} # }