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[manuscript] Add Supplement S4: description of the Nepal SEES typhoid use-case dataset #236

@Kwan-Jenny

Description

@Kwan-Jenny

Add a supplementary section that describes the nepal_sees dataset used in
the Use section of the manuscript. This should parallel Supplement S4
of the serocalculator paper. It should include:

  1. Brief background on the Surveillance for Enteric Fever in Asia Project
    (SEAP) and the SeroEpidemiology and Environmental Surveillance (SEES)
    sub-study (Aiemjoy et al. 2022, Garrett et al. 2022).
  2. Inclusion criteria for the longitudinal arm: blood-culture-confirmed
    enteric fever cases enrolled in Nepal.
  3. Sample size: n = 145 culture-confirmed subjects, 689 longitudinal
    HlyE IgG/IgA observations (the subset shipped as nepal_sees).
  4. Specimen schedule: baseline, 28 days, 3 months, 6 months, 12 months,
    18 months as available.
  5. Laboratory methods: ELISA for HlyE IgG and IgA.
  6. Reference to the data dictionary and CSV shipped as
    inst/extdata/SEES_Case_Nepal_ForSeroKinetics_02-13-2025.csv.

Referenced in manuscript at: Use section:

"Additional details on these data are available in Supplement [TODO]."

Once written, replace the [TODO] in the manuscript with a reference to
the supplement (e.g. "Supplement S4").

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