README.md

EmpiricalCalibration

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EmpiricalCalibration is part of the OHDSI Methods Library.

Introduction

This R package contains 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, as described in the paper Interpreting observational studies: why empirical calibration is needed to correct p-values.

Also supported is empirical calibration of confidence intervals, based on the results for a set of negative and positive controls, as described in the paper Empirical confidence interval calibration for population-level effect estimation studies in observational healthcare data.

Features

Screenshots and examples

Calibration effect plot

data(sccs) #Load one of the included data sets
negatives <- sccs[sccs$groundTruth == 0,] #Select the negative controls
null <- fitNull(logRr = negatives$logRr, seLogRr = negatives$seLogRr) #Fit the null distribution
positive <- sccs[sccs$groundTruth == 1,]  #Select the positive control

#Create the plot above:
plotCalibrationEffect(logRrNegatives = negatives$logRr,
                      seLogRrNegatives = negatives$seLogRr,
                      logRrPositives = positive$logRr,
                      seLogRrPositives = positive$seLogRr,
                      null = null)

#Compute the calibrated p-value:
calibrateP(null = null, logRr = positive$logRr, seLogRr = positive$seLogRr) #Compute calibrated p-value
[1] 0.8390598

Technology

This is a pure R package.

System requirements

Requires R (version 3.1.0 or newer).

Installation

In R, use the following commands to install the latest stable version from CRAN:

install.packages("EmpiricalCalibration")

To install the latest development version directly from GitHub, use:

install.packages("devtools")
library(devtools)
install_github("ohdsi/EmpiricalCalibration")

User Documentation

Support

License

EmpiricalCalibration is licensed under Apache License 2.0

Development

This package has been developed in RStudio.

Development status

This package is ready for use.

Acknowledgements

Martijn Schuemie is the author of this package.



OHDSI/EmpiricalCalibration documentation built on Nov. 28, 2018, 1:03 p.m.