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PoDBAY

The goal of PoDBAY is to provide the functions described in the methodological publication "A method to estimate probability of disease and vaccine efficacy from clinical trial immunogenicity data". Vignettes help to setup the simulation and estimation workflow.

Installation

You can install the released version of PoDBA from CRAN with:

install.packages("PoDBAY")

Example

This is a basic example which shows you how to solve a common problem:

library(PoDBAY)
## basic example code

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Version

Install

install.packages('PoDBAY')

Monthly Downloads

134

Version

1.4.3

License

GPL-3

Maintainer

Julie Dudasova (MSD)

Last Published

September 21st, 2021

Functions in PoDBAY (1.4.3)

PoDEfficacySquaredError

Optimization function: finds PoD curve paramaters (et50, slope)
PoD

Probability of disease calculation
PmaxEstimation

PoD curve paramater, pmax, estimation
PoDCurvePlot

PoD curve: plot
ExpectedPoD

Expected probability of disease
cppPoD

Probability of disease calculation
PoDCI

PoD curve confidence ribbon
cppMLE

Maximum likelihood estimation: cpp
getDiseasedTiters

Diseased titers
PoDBAY

PoDBAY
PoDBAYEfficacy

PoDBAY efficacy estimation
PoDParamsCICoverage

Confidence intervals of PoD curve parameters at three confidence levels
Population-class

Population class
popX

Add noise to population titers
assignPoD

Assign probability of disease (PoD)
diseased

Dataset containing the information for diseased subjects
PoDMLE

Setup for the maximum likelihood estimation (MLE)
control

Dataset containing the information for control subjects
getNondiseasedTiters

Non-diseased titers
getTiters

Subject level titers
getNondiseasedCount

Non-diseased count
vaccinated

Dataset containing the information for vaccinated subjects
PoDParamsCI

Confidence intervals of PoD curve parameters
generatePopulation

Population class object generation
efficacyComputation

PoDBAY efficacy equation
getDiseasedCount

Diseased count
PoDParams

PoD curve parameters
JitterMean

Population mean jittering
waldCI

Wald confidence interval estimation
estimatedParameters

Estimated PoD curve parameters
incorrectPopulationInput

Population class error message
nondiseased

Dataset containing the information for non-diseased subjects
MLE

Maximum Likelihood estimation
numToBool

Numeric to boolean
PoDParamPointEstimation

PoD curve point estimate
PoDParamEstimation

PoD curve parameters estimation
efficacySet

Estimated PoDBAY efficacies
efficacySquaredError

Optimization objective function: efficacy squared error
popFun

Population function
fitPoD

PoD curve: fitting function
getUnknown

Generate unknown
incorrectInput

Error message
EfficacyCI

PoDBAY efficacy summary: mean, median, confidence intervals
ImmunogenicitySubset

Immunogenicity subset
EfficacyCICoverage

PoDBAY efficacy summary at three confidence levels
BlindSampling

Immunogenicity subset: vaccinated, control, non-diseased
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
ClinicalTrial

Clinical trial: estimation of case-count efficacy
GenerateNondiseased

Generation of upsampled non-diseased subjects titers
ExtractDiseased

Diseased subjects extraction
ExtractNondiseased

Non-diseased subjects extraction