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Plot Vaccine Immune Decay

Source: R/est_immune_decay_vaccine.R
est_immune_decay_vaccine.Rd

Draws the documentation figure of oral cholera vaccine (OCV) effectiveness over time for the one- and two-dose regimens: the Xu et al. (2024) meta-regression points and the exponential-decay fits \(VE_k(t) = \phi_k e^{-\omega_k t}\) produced by est_vaccine_effectiveness.

Usage

est_immune_decay_vaccine(PATHS)

Arguments

PATHS

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

  • MODEL_INPUT: Directory holding data_vaccine_effectiveness.csv, pred_vaccine_effectiveness.csv and param_vaccine_effectiveness.csv from est_vaccine_effectiveness().

  • DOCS_FIGURES: Directory where vaccine_effectiveness_decay.png is saved.

Value

Invisibly, the combined plot object; the figure is written to DOCS_FIGURES.

Details

This function does not fit anything. Before v0.100.0 it re-implemented the est_vaccine_effectiveness() fit (without its \(\phi_2 \ge \phi_1\) bound and with hard-coded omega shapes), announced parameter files it did not write, and so plotted a fit that differed from the one behind the priors. It now reads the files that est_vaccine_effectiveness() writes, so the figure always shows the fit the priors use; run that function first.

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{
PATHS <- get_paths()
est_vaccine_effectiveness(PATHS)
est_immune_decay_vaccine(PATHS)
} # }