Plot Vaccine Effectiveness Decay and the Distributions Fitted to It
Source:R/plot_vaccine_effectiveness.R
plot_vaccine_effectiveness.RdThis function generates comprehensive plots showing vaccine effectiveness decay over time and
the distributions of initial effectiveness and waning rate fitted to the Xu et al. (2024)
effectiveness estimates by est_vaccine_effectiveness, for both one-dose and
two-dose OCV regimens. These are data fits, not the model priors. It creates three sets of
figures: one for one-dose OCV, one for two-dose OCV, and a combined figure showing both regimens.
Arguments
- PATHS
A list containing the paths where the figures will be saved. Typically generated by the
get_paths()function and should include:MODEL_INPUT: Path to the directory containing the vaccine effectiveness data and parameters
DOCS_FIGURES: Path to the directory where the figures will be saved
Value
Invisibly, a list with the three combined figures (one_dose,
two_dose, all) and the six panels (panels, named
A to F).
Details
The function creates the following plots:
One-dose OCV (A-C): Decay curve, fitted phi_1 distribution, fitted omega_1 distribution (blue theme)
Two-dose OCV (D-F): Decay curve, fitted phi_2 distribution, fitted omega_2 distribution (green theme)
Every panel is read from the est_vaccine_effectiveness() outputs in
PATHS$MODEL_INPUT: the decay fit and its 95% band
(pred_vaccine_effectiveness.csv), the Xu et al. (2024) estimates
(data_vaccine_effectiveness.csv), and the Beta and Gamma distributions with
the mode and 95% interval (param_vaccine_effectiveness.csv) drawn in panels
B, C, E and F, each of which is subtitled as a data fit. They are not the phi and
omega priors in priors_default: the priors builder
(data-raw/make_priors_default.R) moves each fitted 95% bound outward (by 5%
of the bound for phi, by 5% of the interval width for omega) and refits, so the
shipped omega_1 and omega_2 priors are about 10-20% wider (SD) than these curves and
the phi_1 and phi_2 priors about 2.3 and 4.9 times wider.
Three PDF files are saved:
vaccine_one_dose_combined.pdf: One-dose vaccine effectiveness plotsvaccine_two_dose_combined.pdf: Two-dose vaccine effectiveness plotsvaccine_all_combined.pdf: Both regimens combined in a single figure