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
EfficacyCI              PoDBAY efficacy summary: mean, median,
                        confidence intervals
EfficacyCICoverage      PoDBAY efficacy summary at three confidence
                        levels
ExpectedPoD             Expected probability of disease
ExtractDiseased         Diseased subjects extraction
ExtractNondiseased      Non-diseased subjects extraction
GenerateNondiseased     Generation of upsampled non-diseased subjects
                        titers
ImmunogenicitySubset    Immunogenicity subset
JitterMean              Population mean jittering
MLE                     Maximum Likelihood estimation
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
Population-class        Population class
assignPoD               Assign probability of disease (PoD)
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
efficacyComputation     PoDBAY efficacy equation
efficacySet             Estimated PoDBAY efficacies
efficacySquaredError    Optimization objective function: efficacy
                        squared error
estimatedParameters     Estimated PoD curve parameters
fitPoD                  PoD curve: fitting function
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
incorrectInput          Error message
incorrectPopulationInput
                        Population class error message
nondiseased             Dataset containing the information for
                        non-diseased subjects
numToBool               Numeric to boolean
popFun                  Population function
popX                    Add noise to population titers
vaccinated              Dataset containing the information for
                        vaccinated subjects
waldCI                  Wald confidence interval estimation
