PoDParamEstimation: PoD curve parameters estimation

Description Usage Arguments Details Value Examples

View source: R/FunctionsPoDParameters.R

Description

Function estimates the PoD curve parameters (pmax, slope, et50) using PoDMLE function. Number of PoD curves estimated equals to the repeatCount input parameter.

The estimation is performed using provided diseased and non-diseased subject level data.

Usage

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PoDParamEstimation(diseasedTiters,
                   nondiseasedTiters,
                   nondiseasedGenerationCount,
                   repeatCount = 500,
                   adjustTiters = FALSE,
                   adjustFrom = log2(10),
                   adjustTo = log2(5))

Arguments

diseasedTiters

numeric vector: all diseased titers, subject level data

nondiseasedTiters

numeric vector: non-diseased titers from immunogenicity subset, subject level data

nondiseasedGenerationCount

numeric: total number of non-diseased subjects in the clinical trial

repeatCount

numeric: how many times is the dataset bootstrapped and the PoD curve parameter estimation performed

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

diseasedTiters: subject level titers of all diseased in the clinical trial

nondiseasedTiters: subject level titers of non-diseased subjects in the immunogenicity subset

There are two possible scenarios

nondiseasedGenerationCount: number of all non-diseased subjects in the clinical trial

NOTE: Number of estimated parameters can be lower than repeatCount as MLE does not necessary converge in all estimations; failcount (number of iterations in which MLE failed to converge) is also returned; for details see MLE function.

Function steps

Value

results: PoD curve parameters after resetting the disease status, named data.frame of estimated PoD curve parameters (pmax, slope, et50); see details for more information

resultsPriorReset: PoD curve parameters prior to resetting the status, named data.frame of estimated PoD curve parameters (pmax, slope, et50); see details for more information

failcount: number of iterations in which MLE failed to converge; see details for more information

Examples

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

## Example 1
# Creating imunogenicity subset, method = "Full"
NondiseasedImmunogenicitySubset <- 
    ImmunogenicitySubset(diseased, 
                         nondiseased, 
                         method = list(name = "Full", 
                                       value = "NA"))

# Number of all non-diseased subjects in the clinical trial
nondiseasedGenerationCount <- nondiseased$N

PoDParamEstimation(diseased$titers,
                   NondiseasedImmunogenicitySubset$titers,
                   nondiseasedGenerationCount,
                   repeatCount = 10)

## Example 2
# Creating imunogenicity subset, method = "Ratio", value = 4
NondiseasedImmunogenicitySubset <- 
    ImmunogenicitySubset(diseased, 
                         nondiseased, 
                         method = list(name = "Ratio", 
                                       value = 4))
                                       
# Number of all non-diseased subjects in the clinical trial
nondiseasedGenerationCount <- nondiseased$N

PoDParamEstimation(diseased$titers,
                   NondiseasedImmunogenicitySubset$titers,
                   nondiseasedGenerationCount,
                   repeatCount = 10)

PoDBAY documentation built on Sept. 21, 2021, 5:08 p.m.