Routines for performing empirical calibration of observational study estimates. By using a set of negative control hypotheses we can estimate the empirical null distribution of a particular observational study setup. This empirical null distribution can be used to compute a calibrated p-value, which reflects the probability of observing an estimated effect size when the null hypothesis is true taking both random and systematic error into account.

Author | Martijn Schuemie, Marc Suchard |

Date of publication | 2016-08-16 19:47:12 |

Maintainer | Martijn Schuemie <schuemie@ohdsi.org> |

License | Apache License 2.0 |

Version | 1.2.0 |

https://github.com/OHDSI/EmpiricalCalibration |

**calibrateConfidenceInterval:** Calibrate confidence intervals

**calibrateP:** Calibrate the p-value

**caseControl:** Odds ratios from a case-control design

**cohortMethod:** Relative risks from a new-user cohort design

**computeTraditionalP:** Compute the (traditional) p-value

**EmpiricalCalibration:** EmpiricalCalibration

**fitMcmcNull:** Fit the null distribution using MCMC

**fitNull:** Fit the null distribution

**fitSystematicErrorModel:** Fit a systematic error model

**plotCalibration:** Create a calibration plot

**plotCalibrationEffect:** Plot the effect of the calibration

**plotCiCalibration:** Create a confidence interval calibration plot

**plotForest:** Create a forest plot

**plotMcmcTrace:** Plot the MCMC trace

**plotTrueAndObserved:** Plot true and observed values

**sccs:** Incidence rate ratios from Self-Controlled Case Series

**simulateControls:** Simulate (negative) controls

EmpiricalCalibration

EmpiricalCalibration/inst

EmpiricalCalibration/inst/CITATION

EmpiricalCalibration/inst/doc

EmpiricalCalibration/inst/doc/EmpiricalCalibrationVignette.R

EmpiricalCalibration/inst/doc/EmpiricalCalibrationVignette.pdf

EmpiricalCalibration/inst/doc/EmpiricalCalibrationVignette.Rmd

EmpiricalCalibration/NAMESPACE

EmpiricalCalibration/NEWS

EmpiricalCalibration/data

EmpiricalCalibration/data/caseControl.rda

EmpiricalCalibration/data/sccs.rda

EmpiricalCalibration/data/cohortMethod.rda

EmpiricalCalibration/R

EmpiricalCalibration/R/Data.R
EmpiricalCalibration/R/EmpiricalCalibration.R
EmpiricalCalibration/R/Simulation.R
EmpiricalCalibration/R/EmpiricalCalibrationUsingAsymptotics.R
EmpiricalCalibration/R/Plots.R
EmpiricalCalibration/R/EmpiricalCalibrationUsingMcmc.R
EmpiricalCalibration/R/ConfidenceIntervalCalibration.R
EmpiricalCalibration/R/EmpiricalCalibrationUsingPLikelihood.R
EmpiricalCalibration/vignettes

EmpiricalCalibration/vignettes/EmpiricalCalibrationVignette.Rmd

EmpiricalCalibration/README.md

EmpiricalCalibration/MD5

EmpiricalCalibration/build

EmpiricalCalibration/build/vignette.rds

EmpiricalCalibration/DESCRIPTION

EmpiricalCalibration/man

EmpiricalCalibration/man/plotCiCalibration.Rd
EmpiricalCalibration/man/calibrateConfidenceInterval.Rd
EmpiricalCalibration/man/simulateControls.Rd
EmpiricalCalibration/man/plotCalibration.Rd
EmpiricalCalibration/man/computeTraditionalP.Rd
EmpiricalCalibration/man/caseControl.Rd
EmpiricalCalibration/man/fitMcmcNull.Rd
EmpiricalCalibration/man/fitNull.Rd
EmpiricalCalibration/man/fitSystematicErrorModel.Rd
EmpiricalCalibration/man/plotTrueAndObserved.Rd
EmpiricalCalibration/man/plotForest.Rd
EmpiricalCalibration/man/plotMcmcTrace.Rd
EmpiricalCalibration/man/EmpiricalCalibration.Rd
EmpiricalCalibration/man/plotCalibrationEffect.Rd
EmpiricalCalibration/man/cohortMethod.Rd
EmpiricalCalibration/man/sccs.Rd
EmpiricalCalibration/man/calibrateP.Rd
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