PoDBAYEfficacy {PoDBAY}

PoDBAY efficacy estimation

Description

Function calculates the PoDBAY efficacy based on the set of PoD curve parameters calculated in PoDParamEstimation function, vaccinated and control immunogenicity subset means and standard deviations.

Usage

PoDBAYEfficacy(estimatedParameters,
              blindVaccinated,
              blindControl,
              adjustTiters = FALSE,
              adjustFrom = log2(10),
              adjustTo = log2(5))

Arguments

estimatedParameters

named data frame ("pmax", "slope", "et50"): set of estimated PoD curve parameters

blindVaccinated

Population-class object: vaccinated subjects from immunogenicity subset, containing N, mean, standard deviation information

blindControl

Population-class object: control subjects from immunogenicity subset, containing N, mean, standard deviation information

adjustTiters

boolean: set to TRUE if titer values should be adjusted, for details see PoD function

adjustFrom

numeric: value specifying the detection limit, all values below the detection limit will be adjusted to adjustTo value

adjustTo

numeric: value to which titers below the detection limit will be adjusted

Details

Application of efficacyComputation function to the all PoD curves (each characterized by three PoD parameters) estimated by PoDParamEstimation function.

Inputs into the efficacyComputation are:

• PoDParameters: i'th estimated PoD parameters from PoDParamEstimation. i = 1, ..., N, where N = number of estimations in which MLE converges. See PoDMLE for details.

• means: jittered means of immunogenicity subset. See JitterMeans for details.

• standardDeviations: standard deviations of the vaccinated and control subjects from the immunogenicity subset.

Value

efficacySet, set of PoDBAY effficacies corresponding to estimated set of PoD curve parameters

Examples

## Data preparation
data(diseased)
data(nondiseased)
data(estimatedParameters)

## Example 1
# Creating imunogenicity subset, method = "Ratio", value = 4
ImmunogenicitySubset <- 
  BlindSampling(diseased, 
                nondiseased, 
                method = list(name = "Ratio", 
                              value = 4))
                              
# Estimating PoD curve parameters
nondiseasedGenerationCount <- nondiseased$N

estimatedParameters <- PoDParamEstimation(diseased$titers,
                       ImmunogenicitySubset$ImmunogenicityNondiseased$titers,
                       nondiseasedGenerationCount,
                       repeatCount = 10)
                       
# Estimating PoDBAY efficacy  
PoDBAYEfficacy(estimatedParameters$results,
              ImmunogenicitySubset$ImmunogenicityVaccinated,
              ImmunogenicitySubset$ImmunogenicityControl)