Skip to contents

Estimate Vaccine Effectiveness Decay Parameters

Source: R/est_vaccine_effectiveness.R
est_vaccine_effectiveness.Rd

This function estimates oral cholera vaccine (OCV) effectiveness decay by fitting exponential decay models to meta-regression effectiveness data from Xu et al (2024). It estimates decay parameters (omega) and initial effectiveness (phi) for both one-dose and two-dose regimens using non-linear least squares with the Levenberg-Marquardt algorithm.

Usage

est_vaccine_effectiveness(PATHS)

Arguments

PATHS

A list containing the paths where data and parameters are saved. Typically generated by the get_paths() function and should include:

  • MODEL_INPUT: Path to the directory where parameter files, data, and predictions will be saved.

Value

The function does not return values but saves three CSV files:

  • data_vaccine_effectiveness.csv: Original meta-regression data points from Xu et al

  • pred_vaccine_effectiveness.csv: Predicted effectiveness over 10 years with confidence intervals

  • param_vaccine_effectiveness.csv: Parameter estimates with distributional parameters for uncertainty

Details

The function performs the following steps:

  1. Creates vaccine effectiveness data from Xu et al (2024) meta-regression results

  2. Fits exponential decay models VE(t) = phi * exp(-omega * t) separately for one-dose and two-dose regimens

  3. Estimates parameters for mean effectiveness and confidence intervals using constrained optimization

  4. Infers beta distributions for initial effectiveness (phi) and gamma distributions for decay rates (omega)

  5. Saves data points, predictions, and parameter distributions to CSV files

The model parameters are:

  • phi_1, phi_2: Initial vaccine effectiveness for one-dose and two-dose regimens

  • omega_1, omega_2: Daily decay rates for one-dose and two-dose regimens

References

Xu et al. (2024). Effectiveness of Oral Cholera Vaccines: A Systematic Review and Meta-Analysis. medRxiv. https://doi.org/10.1101/2024.08.13.24311930v2

Examples

if (FALSE) { # \dontrun{
# Assuming PATHS is generated from get_paths()
PATHS <- get_paths()
est_vaccine_effectiveness(PATHS)
} # }