## ----echo = FALSE, message = FALSE, warning = FALSE---------------------------
library(EmpiricalCalibration)

## -----------------------------------------------------------------------------
data(southworthReplication)

## -----------------------------------------------------------------------------
outcomeOfInterest <- southworthReplication[is.na(southworthReplication$trueLogRr), ]
outcomeOfInterest
computeTraditionalCi(outcomeOfInterest$logRr, outcomeOfInterest$seLogRr)

## -----------------------------------------------------------------------------
negatives <- southworthReplication[southworthReplication$trueLogRr == 0 &
                                     !is.na(southworthReplication$trueLogRr), ]
head(negatives)

## -----------------------------------------------------------------------------
data(southworthReplication)
positives <- southworthReplication[southworthReplication$trueLogRr != 0 &
                                     !is.na(southworthReplication$trueLogRr), ]
head(positives)

## ----fig.height=7-------------------------------------------------------------
controls <- southworthReplication[!is.na(southworthReplication$trueLogRr), ]
plotTrueAndObserved(controls$logRr, controls$seLogRr, controls$trueLogRr)

## -----------------------------------------------------------------------------
null <- fitNull(negatives$logRr, negatives$seLogRr)
model <- convertNullToErrorModel(null)

## -----------------------------------------------------------------------------
model <- fitSystematicErrorModel(controls$logRr, controls$seLogRr, controls$trueLogRr)
model

## -----------------------------------------------------------------------------
plotErrorModel(controls$logRr, controls$seLogRr, controls$trueLogRr)

## ----fig.width=13, fig.height=2.8, out.width="100%"---------------------------
plotCiCalibrationEffect(controls$logRr, controls$seLogRr, controls$trueLogRr)

## -----------------------------------------------------------------------------
plotCiCoverage(controls$logRr,
               controls$seLogRr,
               controls$trueLogRr,
               crossValidationGroup = controls$outcomeName)

## -----------------------------------------------------------------------------
ci <- calibrateConfidenceInterval(outcomeOfInterest$logRr, outcomeOfInterest$seLogRr, model)
ci
exp(ci[,1:3])

## ----eval=TRUE----------------------------------------------------------------
citation("EmpiricalCalibration")