# Vaccine Efficacy Estimation Package

## Documentation for package ‘PoDBAY’ version 1.4.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

assignPoD | Assign probability of disease (PoD)
BlindSampling | Immunogenicity subset: vaccinated, control, non-diseased
ClinicalTrial | Clinical trial: estimation of case-count efficacy
ClinicalTrialCoverage | Clinical trial function expanded for usage in simulations when the calculation of coverage probability is needed for three confidence intervals: 80%, 90%, and user-defined
control | Dataset containing the information for control subjects
cppMLE | Maximum likelihood estimation: cpp
cppPoD | Probability of disease calculation
diseased | Dataset containing the information for diseased subjects
EfficacyCI | PoDBAY efficacy summary: mean, median, confidence intervals
EfficacyCICoverage | PoDBAY efficacy summary at three confidence levels
efficacyComputation | PoDBAY efficacy equation
efficacySet | Estimated PoDBAY efficacies
efficacySquaredError | Optimization objective function: efficacy squared error
estimatedParameters | Estimated PoD curve parameters
ExpectedPoD | Expected probability of disease
ExtractDiseased | Diseased subjects extraction
ExtractNondiseased | Non-diseased subjects extraction
fitPoD | PoD curve: fitting function
GenerateNondiseased | Generation of upsampled non-diseased subjects titers
generatePopulation | Population class object generation
getDiseasedCount | Diseased count
getDiseasedTiters | Diseased titers
getNondiseasedCount | Non-diseased count
getNondiseasedTiters | Non-diseased titers
getTiters | Subject level titers
getUnknown | Generate unknown
ImmunogenicitySubset | Immunogenicity subset
incorrectInput | Error message
incorrectPopulationInput | Population class error message
JitterMean | Population mean jittering
MLE | Maximum Likelihood estimation
nondiseased | Dataset containing the information for non-diseased subjects
numToBool | Numeric to boolean
PmaxEstimation | PoD curve paramater, pmax, estimation
PoD | Probability of disease calculation
PoDBAY | PoDBAY
PoDBAYEfficacy | PoDBAY efficacy estimation
PoDCI | PoD curve confidence ribbon
PoDCurvePlot | PoD curve: plot
PoDEfficacySquaredError | Optimization function: finds PoD curve paramaters (et50, slope)
PoDMLE | Setup for the maximum likelihood estimation (MLE)
PoDParamEstimation | PoD curve parameters estimation
PoDParamPointEstimation | PoD curve point estimate
PoDParams | PoD curve parameters
PoDParamsCI | Confidence intervals of PoD curve parameters
PoDParamsCICoverage | Confidence intervals of PoD curve parameters at three confidence levels
popFun | Population function
population | Population class
Population-class | Population class
popX | Add noise to population titers
vaccinated | Dataset containing the information for vaccinated subjects
waldCI | Wald confidence interval estimation