Vaccine Efficacy Estimation Package

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Documentation for package ‘PoDBAY’ version 1.4.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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