PatientLevelPrediction (version 6.4.1)

recalibratePlp: recalibratePlp

Description

Recalibrating a model using the recalibrationInTheLarge or weakRecalibration methods

Usage

recalibratePlp(
  prediction,
  analysisId,
  typeColumn = "evaluationType",
  method = c("recalibrationInTheLarge", "weakRecalibration")
)

Value

A prediction dataframe with the recalibrated predictions added

Arguments

prediction

A prediction dataframe

analysisId

The model analysisId

typeColumn

The column name where the strata types are specified

method

Method used to recalibrate ('recalibrationInTheLarge' or 'weakRecalibration' )

Details

'recalibrationInTheLarge' calculates a single correction factor for the average predicted risks to match the average observed risks. 'weakRecalibration' fits a glm model to the logit of the predicted risks, also known as Platt scaling/logistic recalibration.

Examples

prediction <- data.frame(rowId = 1:100,
                         value = runif(100),
                         outcomeCount = stats::rbinom(100, 1, 0.1),
                         evaluationType = rep("validation", 100))
attr(prediction, "metaData") <- list(modelType = "binary")
# since value is unformally distributed but outcomeCount is not (prob <- 0.1)
# the predictions are mis-calibrated
outcomeRate <- mean(prediction$outcomeCount)
observedRisk <- mean(prediction$value)
message("outcome rate is: ", outcomeRate)
message("observed risk is: ", observedRisk)
# lets recalibrate the predictions
prediction <- recalibratePlp(prediction, 
                             analysisId = "recalibration", 
                             method = "recalibrationInTheLarge")
recalibratedRisk <- mean(prediction$value)
message("recalibrated risk with recalibration in the large is: ", recalibratedRisk)
prediction <- recalibratePlp(prediction, 
                             analysisId = "recalibration", 
                             method = "weakRecalibration")
recalibratedRisk <- mean(prediction$value)
message("recalibrated risk with weak recalibration is: ", recalibratedRisk)