Vaccine Efficacy Estimation Package
Assign probability of disease (PoD)
Immunogenicity subset: vaccinated, control, non-diseased
Clinical trial: estimation of case-count efficacy
Clinical trial function expanded for usage in simulations when the cal...
Maximum likelihood estimation: cpp
Probability of disease calculation
PoDBAY efficacy summary: mean, median, confidence intervals
PoDBAY efficacy summary at three confidence levels
PoDBAY efficacy equation
Optimization objective function: efficacy squared error
Expected probability of disease
Diseased subjects extraction
Non-diseased subjects extraction
PoD curve: fitting function
Generation of upsampled non-diseased subjects titers
Population class object generation
Diseased count
Diseased titers
Non-diseased count
Non-diseased titers
Subject level titers
Generate unknown
Immunogenicity subset
Error message
Population class error message
Population mean jittering
Maximum Likelihood estimation
Numeric to boolean
PoD curve paramater, pmax, estimation
Probability of disease calculation
PoDBAY
PoDBAY efficacy estimation
PoD curve confidence ribbon
PoD curve: plot
Optimization function: finds PoD curve paramaters (et50, slope)
Setup for the maximum likelihood estimation (MLE)
PoD curve parameters estimation
PoD curve point estimate
Confidence intervals of PoD curve parameters
Confidence intervals of PoD curve parameters at three confidence level...
Population function
Population class
Add noise to population titers
Wald confidence interval estimation
Set of functions that implement the PoDBAY method, described in the publication 'A method to estimate probability of disease and vaccine efficacy from clinical trial immunogenicity data' by Julie Dudasova, Regina Laube, Chandni Valiathan, Matthew C. Wiener, Ferdous Gheyas, Pavel Fiser, Justina Ivanauskaite, Frank Liu and Jeffrey R. Sachs (NPJ Vaccines, 2021), <doi:10.1038/s41541-021-00377-6>.