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.] (http://dx.doi.org/10.1002/sim.5925).

- Estimate the empirical null distribution given the effect estimates of a set of negative controls
- Estimate the calibrated p-value of a given hypothesis given the estimated empirical null distribution
- Produce various plots for evaluating the empirical calibration
- Contains the data sets from the paper for illustration

```
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
```

This is a pure R package.

Requires R (version 3.1.0 or newer).

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")
```

- Vignette: Empirical calibration of p-values
- Vignette: Empirical calibration of confidence intervals
- Package manual: EmpiricalCalibration.pdf
- Developer questions/comments/feedback: OHDSI Forum
- We use the GitHub issue tracker for all bugs/issues/enhancements

EmpiricalCalibration is licensed under Apache License 2.0

This package has been developed in RStudio.

This package is ready for use.

Martijn Schuemie is the author of this package.

OHDSI/EmpiricalCalibration documentation built on June 26, 2018, 7:12 a.m.

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