EmpiricalCalibration

https://ohdsi.github.io/EmpiricalCalibration/
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EmpiricalCalibration is an R package that provides routines for performing empirical calibration of...
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### Install from CRAN

Source: https://ohdsi.github.io/EmpiricalCalibration/index.html

Use this command to install the latest stable version of the package from CRAN.

```R
install.packages("EmpiricalCalibration")
```

--------------------------------

### Install from GitHub

Source: https://ohdsi.github.io/EmpiricalCalibration/index.html

Use these commands to install the latest development version directly from the OHDSI GitHub repository.

```R
install.packages("remotes")
library(remotes)
install_github("ohdsi/EmpiricalCalibration", ref = "develop")
```

--------------------------------

### Example usage of computeTraditionalCi

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/computeTraditionalCi.html

An example demonstrating how to use computeTraditionalCi with the sccs dataset.

```R
data(sccs)
positive <- sccs[sccs$groundTruth == 1, ]
computeTraditionalCi(positive$logRr, positive$seLogRr)
#>         rr       lb       ub
#> 1 2.080532 1.800637 2.403934
```

--------------------------------

### plotMcmcTrace example usage

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/plotMcmcTrace.html

An example showing how to fit an MCMC null distribution and plot the trace.

```R
if (FALSE) { # \dontrun{
data(sccs)
negatives <- sccs[sccs$groundTruth == 0, ]
null <- fitMcmcNull(negatives$logRr, negatives$seLogRr)
plotMcmcTrace(null)
} # }
```

--------------------------------

### calibrateP usage example

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/calibrateP.html

Example demonstrating how to fit a null distribution and calibrate p-values for positive control estimates.

```R
data(sccs)
negatives <- sccs[sccs$groundTruth == 0, ]
null <- fitNull(negatives$logRr, negatives$seLogRr)
positive <- sccs[sccs$groundTruth == 1, ]
calibrateP(null, positive$logRr, positive$seLogRr)
#> [1] 0.8389142
```

--------------------------------

### fitNull example usage

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/fitNull.html

Example showing how to filter negative controls from a dataset and fit the null distribution.

```R
data(sccs)
negatives <- sccs[sccs$groundTruth == 0, ]
null <- fitNull(negatives$logRr, negatives$seLogRr)
null
#> Estimated null distribution
#> 
#>      Estimate
#> Mean   0.7922
#> SD     0.2834
```

--------------------------------

### Example usage of computeTraditionalP

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/computeTraditionalP.html

An example demonstrating how to compute the p-value using the sccs dataset.

```R
data(sccs)
positive <- sccs[sccs$groundTruth == 1, ]
computeTraditionalP(positive$logRr, positive$seLogRr)
#> [1] 0
```

--------------------------------

### Example usage of plotCiCoverage

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/plotCiCoverage.html

A basic example demonstrating how to simulate controls and generate a confidence interval coverage plot.

```R
if (FALSE) { # \dontrun{
data <- simulateControls(n = 50 * 3, mean = 0.25, sd = 0.25, trueLogRr = log(c(1, 2, 4)))
plotCiCoverage(data$logRr, data$seLogRr, data$trueLogRr)
} # }
```

--------------------------------

### Comparing EASE of two methods

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/compareEase.html

Example demonstrating how to simulate two sets of negative control results and compare their EASE using compareEase.

```R
# Simulate results of first method:
ncs1 <- simulateControls(n = 50)

# Simulate second method to be more biased:
ncs2 <- ncs1
ncs2$logRr <- ncs2$logRr + rnorm(nrow(ncs2), mean = 0.1, sd = 0.1)

delta <- compareEase(
  logRr1 = ncs1$logRr,
  seLogRr1 = ncs1$seLogRr,
  logRr2 = ncs2$logRr,
  seLogRr2 = ncs2$seLogRr
)
delta
#>         delta       ciLb        ciUb p
#> 1 -0.09135734 -0.1215314 -0.06221161 0
attr(delta, "ease1")
#>         ease       ciLb      ciUb
#> 1 0.06262257 0.04643558 0.0785099
attr(delta, "ease2")
#>        ease      ciLb      ciUb
#> 1 0.1539799 0.1208099 0.1869629
```

--------------------------------

### calibrateLlr example usage

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/calibrateLlr.html

Example demonstrating how to fit a null distribution using negative controls and then calibrate the log likelihood ratio for a positive control.

```R
data(sccs)
negatives <- sccs[sccs$groundTruth == 0, ]
null <- fitNull(negatives$logRr, negatives$seLogRr)
positive <- sccs[sccs$groundTruth == 1, ]
calibrateLlr(null, positive)
#> Detected data following normal distribution
#> [1] 0
```

--------------------------------

### plotForest usage example

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/plotForest.html

Example showing how to generate a forest plot using data from the sccs dataset.

```R
data(sccs)
negatives <- sccs[sccs$groundTruth == 0, ]
plotForest(negatives$logRr, negatives$seLogRr, negatives$drugName)
```

--------------------------------

### fitSystematicErrorModel example usage

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/fitSystematicErrorModel.html

Example showing how to simulate controls and fit a systematic error model.

```R
controls <- simulateControls(n = 50 * 3, mean = 0.25, sd = 0.25, trueLogRr = log(c(1, 2, 4)))
model <- fitSystematicErrorModel(controls$logRr, controls$seLogRr, controls$trueLogRr)
model
#> meanIntercept     meanSlope   sdIntercept       sdSlope 
#>    0.24339542    1.01498772    0.18418950    0.04939429 
#> attr(,"class")
#> [1] "systematicErrorModel"
```

--------------------------------

### fitMcmcNull usage example

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/fitMcmcNull.html

Example demonstrating how to fit the null distribution using negative control data and calibrate p-values for positive controls.

```R
if (FALSE) { # \dontrun{
data(sccs)
negatives <- sccs[sccs$groundTruth == 0, ]
null <- fitMcmcNull(negatives$logRr, negatives$seLogRr)
null
plotMcmcTrace(null)
positive <- sccs[sccs$groundTruth == 1, ]
calibrateP(null, positive$logRr, positive$seLogRr)
} # }
```

--------------------------------

### evaluateCiCalibration usage example

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/evaluateCiCalibration.html

An example demonstrating how to simulate controls and evaluate confidence interval calibration using the evaluateCiCalibration function.

```R
if (FALSE) { # \dontrun{
data <- simulateControls(n = 50 * 3, mean = 0.25, sd = 0.25, trueLogRr = log(c(1, 2, 4)))
eval <- evaluateCiCalibration(data$logRr, data$seLogRr, data$trueLogRr)
} # }
```

--------------------------------

### Example usage of plotCiCalibration

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/plotCiCalibration.html

An example demonstrating how to simulate control data and generate a confidence interval calibration plot.

```R
if (FALSE) { # \dontrun{
data <- simulateControls(n = 50 * 3, mean = 0.25, sd = 0.25, trueLogRr = log(c(1, 2, 4)))
plotCiCalibration(data$logRr, data$seLogRr, data$trueLogRr)
} # }
```

--------------------------------

### calibrateConfidenceInterval example usage

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/calibrateConfidenceInterval.html

Example demonstrating the simulation of control data, fitting a systematic error model, and calibrating confidence intervals for new data.

```R
data <- simulateControls(n = 50 * 3, mean = 0.25, sd = 0.25, trueLogRr = log(c(1, 2, 4)))
model <- fitSystematicErrorModel(data$logRr, data$seLogRr, data$trueLogRr)
newData <- simulateControls(n = 15, mean = 0.25, sd = 0.25, trueLogRr = log(c(1, 2, 4)))
result <- calibrateConfidenceInterval(newData$logRr, newData$seLogRr, model)
result
#>         logRr  logLb95Rr logUb95Rr   seLogRr
#> 1   0.3633442 -0.2215560 0.9160445 0.2902095
#> 2   0.7721447  0.1459751 1.3463734 0.3062297
#> 3   1.1476296  0.5005040 1.7445525 0.3173651
#> 4  -0.0978154 -0.6475848 0.4608360 0.2827656
#> 5   1.1071717  0.4268373 1.7371203 0.3342620
#> 6   1.4525291  0.9184392 1.9378269 0.2600527
#> 7  -0.1621166 -0.7149772 0.4053362 0.2857995
#> 8   0.3809725 -0.2428391 0.9731956 0.3102186
#> 9   1.1543678  0.5655266 1.6930417 0.2876367
#> 10  0.1361149 -0.4309147 0.6909088 0.2861847
#> 11  0.6254329 -0.0715306 1.2756716 0.3436803
#> 12  1.3846512  0.7810774 1.9391390 0.2954293
#> 13  0.1129226 -0.4440026 0.6595497 0.2815236
#> 14  0.3980328 -0.2251682 0.9882119 0.3095414
#> 15  1.4982276  0.8546360 2.0932464 0.3159778
```

--------------------------------

### Perform Empirical Calibration Analysis

Source: https://ohdsi.github.io/EmpiricalCalibration/index.html

This example demonstrates loading a dataset, fitting a null distribution using negative controls, plotting the calibration effect, and computing a calibrated p-value.

```R
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
```

--------------------------------

### Simulate MaxSPRT data example

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/simulateMaxSprtData.html

An example of generating simulated data with 1000 subjects and displaying the first few rows of the resulting data frame.

```R
data <- simulateMaxSprtData(n = 1000)
head(data)
#>        time outcome exposure lookTime outcomeId
#> 5  8.661996       0     TRUE       10         1
#> 11 9.386998       0     TRUE       10         1
#> 20 0.498716       0    FALSE       10         1
#> 22 7.061753       0     TRUE       10         1
#> 85 3.030036       0     TRUE       10         1
#> 98 2.959496       0     TRUE       10         1
```

--------------------------------

### Example usage of fitNullNonNormalLl

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/fitNullNonNormalLl.html

Example demonstrating how to fit the null distribution using negative control data from the sccs dataset.

```R
data(sccs)
negatives <- sccs[sccs$groundTruth == 0, ]
null <- fitNullNonNormalLl(negatives)
#> Detected data following normal distribution
null
#> Estimated null distribution
#> 
#>      Estimate
#> Mean   0.7922
#> SD     0.2834
```

--------------------------------

### computeCvPoisson usage example

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/computeCvPoisson.html

An example demonstrating how to call computeCvPoisson with a vector of group sizes and the resulting output including the selected alpha and critical value.

```R
groupSizes <- rep(1, 10)
computeCvPoisson(groupSizes)
#> Selected alpha: 0.044 (least conservative value below 0.05)
#> [1] 2.545177
#> attr(,"alpha")
#> [1] 0.044113
```

--------------------------------

### computeCvPoissonRegression usage example

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/computeCvPoissonRegression.html

An example demonstrating how to compute the critical value for a sequence of 10 groups with a control-to-risk time ratio of 4.

```R
groupSizes <- rep(1, 10)
computeCvPoissonRegression(groupSizes, z = 4)
#> Selected alpha: 0.049 (least conservative value below 0.05)
#> [1] 2.677723
#> attr(,"alpha")
#> [1] 0.049444
```

--------------------------------

### Example usage of plotCalibration

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/plotCalibration.html

A basic example demonstrating how to generate a calibration plot using negative control data from the sccs dataset.

```R
data(sccs)
negatives <- sccs[sccs$groundTruth == 0, ]
plotCalibration(negatives$logRr, negatives$seLogRr)
```

--------------------------------

### Example usage of plotCiCalibrationEffect

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/plotCiCalibrationEffect.html

An example demonstrating how to simulate control data and generate a CI calibration effect plot.

```R
data <- simulateControls(n = 50 * 3, mean = 0.25, sd = 0.25, trueLogRr = log(c(1, 2, 4)))
plotCiCalibrationEffect(data$logRr, data$seLogRr, data$trueLogRr)
```

--------------------------------

### Example usage of plotErrorModel

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/plotErrorModel.html

An example demonstrating how to simulate control data and visualize the systematic error model using plotErrorModel.

```R
data <- simulateControls(n = 50 * 3, mean = 0.25, sd = 0.25, trueLogRr = log(c(1, 2, 4)))
plotErrorModel(data$logRr, data$seLogRr, data$trueLogRr)
```

--------------------------------

### plotTrueAndObserved example usage

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/plotTrueAndObserved.html

An example demonstrating how to simulate control data and plot the true versus observed effect sizes.

```R
data <- simulateControls(n = 50 * 3, mean = 0.25, sd = 0.25, trueLogRr = log(c(1, 2, 4)))
plotTrueAndObserved(data$logRr, data$seLogRr, data$trueLogRr)
```

--------------------------------

### Example usage with sccs data

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/computeExpectedAbsoluteSystematicError.html

Shows how to fit a null distribution using the sccs dataset and compute the expected absolute systematic error.

```R
data(sccs)
negatives <- sccs[sccs$groundTruth == 0, ]
null <- fitNull(negatives$logRr, negatives$seLogRr)
computeExpectedAbsoluteSystematicError(null)
#> [1] 0.792597
```

--------------------------------

### computeCvBinomial usage example

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/computeCvBinomial.html

An example demonstrating how to call computeCvBinomial with a vector of group sizes and a specified z value, including the expected output.

```R
groupSizes <- rep(1, 10)
computeCvBinomial(groupSizes, z = 4)
#> Selected alpha: 0.049 (least conservative value below 0.05)
#> [1] 3.064954
#> attr(,"alpha")
#> [1] 0.049321
```

--------------------------------

### Example of calibrating confidence intervals

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/convertNullToErrorModel.html

A complete workflow demonstrating fitting a null distribution, converting it to a systematic error model, and using that model to calibrate confidence intervals for positive controls.

```R
data(sccs)
negatives <- sccs[sccs$groundTruth == 0, ]
null <- fitNull(negatives$logRr, negatives$seLogRr)
model <- convertNullToErrorModel(null)
positive <- sccs[sccs$groundTruth == 1, ]
calibrateConfidenceInterval(positive$logRr, positive$seLogRr, model)
#>         logRr  logLb95Rr logUb95Rr   seLogRr
#> 1 -0.05953451 -0.6335409 0.5144719 0.2928658
```

--------------------------------

### Example usage of plotExpectedType1Error

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/plotExpectedType1Error.html

A basic example demonstrating how to prepare negative and positive control data from the sccs dataset and generate the expected type 1 error plot.

```R
data(sccs)
negatives <- sccs[sccs$groundTruth == 0, ]
positive <- sccs[sccs$groundTruth == 1, ]
plotExpectedType1Error(negatives$logRr, negatives$seLogRr, positive$seLogRr)
```

--------------------------------

### compareEase(logRr1, seLogRr1, logRr2, seLogRr2, alpha = 0.05, sampleSize = 1000)

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/compareEase.html

Compares the expected absolute systematic error (EASE) of two sets of effect estimates for the same set of negative controls. Returns a data frame with the difference in EASE, confidence interval, and p-value, along with attributes containing EASE estimates for each set.

```APIDOC
## compareEase(logRr1, seLogRr1, logRr2, seLogRr2, alpha = 0.05, sampleSize = 1000)

### Description
Compares the expected absolute systematic error (EASE) of two sets of estimates for the same set of negative controls. The two sets of estimates must be in identical order.

### Usage
```r
compareEase(
  logRr1,
  seLogRr1,
  logRr2,
  seLogRr2,
  alpha = 0.05,
  sampleSize = 1000
)
```

### Arguments
- **logRr1** (numeric vector) - Required - A numeric vector of effect estimates generated using the first method on the log scale.
- **seLogRr1** (numeric vector) - Required - The standard error of the log of the effect estimates generated using the first method.
- **logRr2** (numeric vector) - Required - A numeric vector of effect estimates generated using the second method on the log scale.
- **seLogRr2** (numeric vector) - Required - The standard error of the log of the effect estimates generated using the second method.
- **alpha** (numeric) - Optional - The expected type I error for computing confidence intervals and p-values. Default is 0.05.
- **sampleSize** (integer) - Optional - The number of samples in the bootstraps. Default is 1000.

### Value
A data frame with 4 columns: the point estimate, confidence interval lower bound, and upper bound for the difference between EASE in the two sets of negative controls, and a p value against the null hypothesis that the EASE is the same for the two sets. The data frame has two attributes: ease1 and ease2, providing the EASE estimates (and confidence intervals) for the two sets, computed using bootstrapping.

### Details
Compare the expected absolute systematic error (EASE) of two sets of estimates for the same set of negative controls. Important: the two sets of estimates (logRr1 + seLogRr1 and logRr2 + seLogRr2) should be in identical order, so that for example the first item in each vector corresponds to the same negative control.

### Example
```r
# Simulate results of first method:
ncs1 <- simulateControls(n = 50)

# Simulate second method to be more biased:
ncs2 <- ncs1
ncs2$logRr <- ncs2$logRr + rnorm(nrow(ncs2), mean = 0.1, sd = 0.1)

delta <- compareEase(
  logRr1 = ncs1$logRr,
  seLogRr1 = ncs1$seLogRr,
  logRr2 = ncs2$logRr,
  seLogRr2 = ncs2$seLogRr
)
delta
#>         delta       ciLb        ciUb p
#> 1 -0.09135734 -0.1215314 -0.06221161 0
attr(delta, "ease1")
#>         ease       ciLb      ciUb
#> 1 0.06262257 0.04643558 0.0785099
attr(delta, "ease2")
#>        ease      ciLb      ciUb
#> 1 0.1539799 0.1208099 0.1869629
```
```

--------------------------------

### compareEase()

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/index.html

Compares the EASE (Expected Absolute Systematic Error) of correlated sets of estimates.

```APIDOC
## compareEase()

### Description
Compares EASE of correlated sets of estimates.

### Usage
compareEase(logRr1, seLogRr1, logRr2, seLogRr2)

### Arguments
- **logRr1** (numeric) - Required - Log effect estimates for the first set.
- **seLogRr1** (numeric) - Required - Standard errors for the first set.
- **logRr2** (numeric) - Required - Log effect estimates for the second set.
- **seLogRr2** (numeric) - Required - Standard errors for the second set.

### Value
A data frame with the EASE comparison.
```

--------------------------------

### Example: plotCalibrationEffect with sccs data

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/plotCalibrationEffect.html

Example usage of plotCalibrationEffect with negative and positive controls from the sccs dataset. The output includes a warning about a removed row containing missing values.

```R
data(sccs)
negatives <- sccs[sccs$groundTruth == 0, ]
positive <- sccs[sccs$groundTruth == 1, ]
plotCalibrationEffect(negatives$logRr, negatives$seLogRr, positive$logRr, positive$seLogRr)
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_vline()`).
```

--------------------------------

### Basic usage of computeExpectedAbsoluteSystematicError

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/computeExpectedAbsoluteSystematicError.html

Demonstrates the basic syntax for calling the function with a null object and an optional alpha parameter.

```R
computeExpectedAbsoluteSystematicError(null, alpha = 0.05)
```

--------------------------------

### Load and inspect SCCS study data

Source: https://ohdsi.github.io/EmpiricalCalibration/articles/EmpiricalPCalibrationVignette.html

Loads the example SCCS study results from the EmpiricalCalibration package and filters for the drug of interest.

```R
data(sccs)
drugOfInterest <- sccs[sccs$groundTruth == 1, ]
drugOfInterest
```

--------------------------------

### Load cohortMethod dataset

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/cohortMethod.html

Load the cohortMethod dataset into the R environment.

```R
data(cohortMethod)
```

--------------------------------

### simulateControls()

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/index.html

Simulates (negative) controls for testing and demonstration purposes.

```APIDOC
## simulateControls()

### Description
Simulates (negative) controls.

### Usage
simulateControls(n = 100)

### Arguments
- **n** (numeric) - Optional - The number of controls to simulate. Default is 100.

### Value
A data frame with simulated controls.
```

--------------------------------

### Retrieve package citation

Source: https://ohdsi.github.io/EmpiricalCalibration/articles/EmpiricalCiCalibrationVignette.html

Displays the citation information for the EmpiricalCalibration package.

```R
citation("EmpiricalCalibration")
```

```R
## To cite EmpiricalCalibration in publications use:
## 
##   Schuemie MJ, Ryan PB, DuMouchel W, Suchard MA, Madigan D (2013).
##   "Interpreting observational studies: why empirical calibration is
##   needed to correct p-values." _Statistics in Medicine_, *33*(2),
##   209-218. <http://dx.doi.org/10.1002/sim.5925>.
## 
##   Schuemie MJ, Hripcsak G, Ryan PB, Madigan D, Suchard MA (2018).
##   "Empirical confidence interval calibration for population-level
##   effect estimation studies in observational healthcare data." _Proc.
##   Natl. Acad. Sci. U.S.A._, *115*(11), 2571-2577.
##   <https://doi.org/10.1073/pnas.1708282114>.
## 
## To see these entries in BibTeX format, use 'print(<citation>,
## bibtex=TRUE)', 'toBibtex(.)', or set
## 'options(citation.bibtex.max=999)'.
```

--------------------------------

### Load caseControl dataset

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/caseControl.html

Loads the caseControl dataset into the R environment.

```R
data(caseControl)
```

--------------------------------

### simulateMaxSprtData()

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/index.html

Simulates survival data for MaxSPRT computation.

```APIDOC
## simulateMaxSprtData()

### Description
Simulates survival data for MaxSPRT computation.

### Usage
simulateMaxSprtData(n = 100)

### Arguments
- **n** (numeric) - Optional - The number of observations to simulate. Default is 100.

### Value
A data frame with simulated survival data.
```

--------------------------------

### calibrateP function signatures

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/calibrateP.html

Function signatures for calibrateP, including S3 methods for null and mcmcNull classes.

```R
calibrateP(null, logRr, seLogRr, twoSided = TRUE, upper = TRUE, ...)

# S3 method for class 'null'
calibrateP(null, logRr, seLogRr, twoSided = TRUE, upper = TRUE, ...)

# S3 method for class 'mcmcNull'
calibrateP(
  null,
  logRr,
  seLogRr,
  twoSided = TRUE,
  upper = TRUE,
  pValueOnly,
  ...
)
```

--------------------------------

### fitNull(logRr, seLogRr)

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/fitNull.html

Fits the null distribution to a set of negative controls. Returns an object containing the parameters of the null distribution.

```APIDOC
## fitNull(logRr, seLogRr)

### Description
Fits a Gaussian function to the negative control estimates as described in Schuemie et al (2014). Returns an object containing the parameters of the null distribution.

### Usage
fitNull(logRr, seLogRr)

### Arguments
- **logRr** (numeric vector) - Required - A numeric vector of effect estimates on the log scale.
- **seLogRr** (numeric vector) - Required - The standard error of the log of the effect estimates. Hint: often the standard error = (log(<lower bound 95 percent confidence interval>) - log(<effect estimate>))/qnorm(0.025).

### Value
An object containing the parameters of the null distribution.

### Details
This function fits a Gaussian function to the negative control estimates as described in Schuemie et al (2014).

### References
Schuemie MJ, Ryan PB, Dumouchel W, Suchard MA, Madigan D. Interpreting observational studies: why empirical calibration is needed to correct p-values. Statistics in Medicine 33(2):209-18,2014

### Examples
```r
data(sccs)
negatives <- sccs[sccs$groundTruth == 0, ]
null <- fitNull(negatives$logRr, negatives$seLogRr)
null
#> Estimated null distribution
#> 
#>      Estimate
#> Mean   0.7922
#> SD     0.2834
```
```

--------------------------------

### calibrateLlr()

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/index.html

Calibrates the log likelihood ratio (LLR) for MaxSPRT-based sequential testing.

```APIDOC
## calibrateLlr()

### Description
Calibrates the log likelihood ratio.

### Usage
calibrateLlr(llr, seLogRr, model)

### Arguments
- **llr** (numeric) - Required - The log likelihood ratio.
- **seLogRr** (numeric) - Required - The standard error of the log effect estimate.
- **model** (systematicErrorModel) - Required - An object of class 'systematicErrorModel'.

### Value
The calibrated log likelihood ratio.
```

--------------------------------

### Function signature for computeTraditionalCi

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/computeTraditionalCi.html

The basic syntax for calling the computeTraditionalCi function.

```R
computeTraditionalCi(logRr, seLogRr, ciWidth = 0.95)
```

--------------------------------

### calibrateP(null, logRr, seLogRr, twoSided = TRUE, upper = TRUE, ...)

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/calibrateP.html

Computes calibrated p-values using the fitted null distribution. This is the main function signature for the S3 generic.

```APIDOC
## calibrateP(null, logRr, seLogRr, twoSided = TRUE, upper = TRUE, ...)

### Description
Computes calibrated p-values using the fitted null distribution.

### Usage
```r
calibrateP(null, logRr, seLogRr, twoSided = TRUE, upper = TRUE, ...)
```

### Arguments
- **null** - An object of class `null` created using the `fitNull` function or an object of class `mcmcNull` created using the `fitMcmcNull` function.
- **logRr** - A numeric vector of one or more effect estimates on the log scale.
- **seLogRr** - The standard error of the log of the effect estimates. Hint: often the standard error = (log(<lower bound 95 percent confidence interval>) - log(<effect estimate>))/qnorm(0.025).
- **twoSided** - Compute two-sided (TRUE) or one-sided (FALSE) p-value? Default is TRUE.
- **upper** - If one-sided: compute p-value for upper (TRUE) or lower (FALSE) bound? Default is TRUE.
- **...** - Any additional parameters (currently none).

### Value
The calibrated p-value.

### Details
This function computes a calibrated two-sided p-value as described in Schuemie et al (2014).

### Methods (by class)
- `calibrateP(null)`: Computes the calibrated P-value using asymptotic assumptions.
- `calibrateP(mcmcNull)`: Computes the calibrated P-value and 95 percent credible interval using Markov Chain Monte Carlo (MCMC).

### References
Schuemie MJ, Ryan PB, Dumouchel W, Suchard MA, Madigan D. Interpreting observational studies: why empirical calibration is needed to correct p-values. Statistics in Medicine 33(2):209-18,2014

### Examples
```r
data(sccs)
negatives <- sccs[sccs$groundTruth == 0, ]
null <- fitNull(negatives$logRr, negatives$seLogRr)
positive <- sccs[sccs$groundTruth == 1, ]
calibrateP(null, positive$logRr, positive$seLogRr)
#> [1] 0.8389142
```
```

--------------------------------

### calibrateP(null, logRr, seLogRr, twoSided = TRUE, upper = TRUE, ...) S3 method for class 'null'

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/calibrateP.html

S3 method for class 'null' that computes the calibrated P-value using asymptotic assumptions.

```APIDOC
## calibrateP(null, logRr, seLogRr, twoSided = TRUE, upper = TRUE, ...) S3 method for class 'null'

### Description
Computes the calibrated P-value using asymptotic assumptions.

### Usage
```r
calibrateP(null, logRr, seLogRr, twoSided = TRUE, upper = TRUE, ...)
```

### Arguments
- **null** - An object of class `null` created using the `fitNull` function.
- **logRr** - A numeric vector of one or more effect estimates on the log scale.
- **seLogRr** - The standard error of the log of the effect estimates. Hint: often the standard error = (log(<lower bound 95 percent confidence interval>) - log(<effect estimate>))/qnorm(0.025).
- **twoSided** - Compute two-sided (TRUE) or one-sided (FALSE) p-value? Default is TRUE.
- **upper** - If one-sided: compute p-value for upper (TRUE) or lower (FALSE) bound? Default is TRUE.
- **...** - Any additional parameters (currently none).

### Value
The calibrated p-value.

### Details
This method computes the calibrated P-value using asymptotic assumptions.

### References
Schuemie MJ, Ryan PB, Dumouchel W, Suchard MA, Madigan D. Interpreting observational studies: why empirical calibration is needed to correct p-values. Statistics in Medicine 33(2):209-18,2014

### Examples
```r
data(sccs)
negatives <- sccs[sccs$groundTruth == 0, ]
null <- fitNull(negatives$logRr, negatives$seLogRr)
positive <- sccs[sccs$groundTruth == 1, ]
calibrateP(null, positive$logRr, positive$seLogRr)
#> [1] 0.8389142
```
```

--------------------------------

### fitMcmcNull()

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/index.html

Fits the null distribution using Markov Chain Monte Carlo (MCMC) methods. This is an alternative to fitNull() that may be more robust in certain scenarios.

```APIDOC
## fitMcmcNull()

### Description
Fits the null distribution using MCMC.

### Usage
fitMcmcNull(logRr, seLogRr)

### Arguments
- **logRr** (numeric) - Required - A numeric vector of log effect estimates.
- **seLogRr** (numeric) - Required - The standard error of the log effect estimates.

### Value
An object of class 'mcmcNull' containing the MCMC samples and fitted null distribution.
```

--------------------------------

### plotCalibration()

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/index.html

Creates a calibration plot showing the relationship between traditional and calibrated p-values.

```APIDOC
## plotCalibration()

### Description
Creates a calibration plot.

### Usage
plotCalibration(null, logRr, seLogRr)

### Arguments
- **null** (null) - Required - An object of class 'null'.
- **logRr** (numeric) - Required - A numeric vector of log effect estimates.
- **seLogRr** (numeric) - Required - The standard error of the log effect estimates.

### Value
A ggplot object.
```

--------------------------------

### plotForest(logRr, seLogRr, names, xLabel, title, fileName)

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/plotForest.html

Creates a forest plot of effect size estimates. Estimates significantly different from 1 (alpha = 0.05) are marked in orange, others in blue.

```APIDOC
## plotForest(logRr, seLogRr, names, xLabel, title, fileName)

### Description
Creates a forest plot of effect size estimates (ratios). Estimates that are significantly different from 1 (alpha = 0.05) are marked in orange, others are marked in blue.

### Usage
```r
plotForest(
  logRr,
  seLogRr,
  names,
  xLabel = "Relative risk",
  title,
  fileName = NULL
)
```

### Arguments
- **logRr** (numeric vector) - Required - A numeric vector of effect estimates on the log scale.
- **seLogRr** (numeric vector) - Required - The standard error of the log of the effect estimates. Hint: often the standard error = (log(<lower bound 95 percent confidence interval>) - log(<effect estimate>))/qnorm(0.025).
- **names** (character vector) - Required - A vector containing the names of the drugs or outcomes.
- **xLabel** (character) - Optional - The label on the x-axis: the name of the effect estimate. Default is "Relative risk".
- **title** (character) - Optional - The main title for the plot.
- **fileName** (character) - Optional - Name of the file where the plot should be saved, for example 'plot.png'. See the function `ggsave` in the ggplot2 package for supported file formats.

### Value
A Ggplot object. Use the `ggsave` function to save to file.

### Examples
```r
data(sccs)
negatives <- sccs[sccs$groundTruth == 0, ]
plotForest(negatives$logRr, negatives$seLogRr, negatives$drugName)
```
```

--------------------------------

### plotCiCalibration()

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/index.html

Creates a confidence interval calibration plot.

```APIDOC
## plotCiCalibration()

### Description
Creates a confidence interval calibration plot.

### Usage
plotCiCalibration(logRr, seLogRr, trueLogRr)

### Arguments
- **logRr** (numeric) - Required - A numeric vector of log effect estimates.
- **seLogRr** (numeric) - Required - The standard error of the log effect estimates.
- **trueLogRr** (numeric) - Required - The true log effect estimates.

### Value
A ggplot object.
```

--------------------------------

### calibrateP(null, logRr, seLogRr, twoSided = TRUE, upper = TRUE, pValueOnly, ...) S3 method for class 'mcmcNull'

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/calibrateP.html

S3 method for class 'mcmcNull' that computes the calibrated P-value and 95 percent credible interval using Markov Chain Monte Carlo (MCMC).

```APIDOC
## calibrateP(null, logRr, seLogRr, twoSided = TRUE, upper = TRUE, pValueOnly, ...) S3 method for class 'mcmcNull'

### Description
Computes the calibrated P-value and 95 percent credible interval using Markov Chain Monte Carlo (MCMC).

### Usage
```r
calibrateP(
  null,
  logRr,
  seLogRr,
  twoSided = TRUE,
  upper = TRUE,
  pValueOnly,
  ...
)
```

### Arguments
- **null** - An object of class `mcmcNull` created using the `fitMcmcNull` function.
- **logRr** - A numeric vector of one or more effect estimates on the log scale.
- **seLogRr** - The standard error of the log of the effect estimates. Hint: often the standard error = (log(<lower bound 95 percent confidence interval>) - log(<effect estimate>))/qnorm(0.025).
- **twoSided** - Compute two-sided (TRUE) or one-sided (FALSE) p-value? Default is TRUE.
- **upper** - If one-sided: compute p-value for upper (TRUE) or lower (FALSE) bound? Default is TRUE.
- **pValueOnly** - If true, will return only the calibrated P-value itself, not the credible interval.
- **...** - Any additional parameters (currently none).

### Value
The calibrated p-value.

### Details
This method computes the calibrated P-value and 95 percent credible interval using Markov Chain Monte Carlo (MCMC).

### References
Schuemie MJ, Ryan PB, Dumouchel W, Suchard MA, Madigan D. Interpreting observational studies: why empirical calibration is needed to correct p-values. Statistics in Medicine 33(2):209-18,2014
```

--------------------------------

### fitMcmcNull(logRr, seLogRr, iter = 1e+05)

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/fitMcmcNull.html

Fits the null distribution to a set of negative controls using Markov Chain Monte Carlo (MCMC). This is an experimental function for computing the 95 percent credible interval of a calibrated p-value.

```APIDOC
## fitMcmcNull(logRr, seLogRr, iter = 1e+05)

### Description
Fits the null distribution to a set of negative controls using Markov Chain Monte Carlo (MCMC). This is an experimental function for computing the 95 percent credible interval of a calibrated p-value.

### Usage
fitMcmcNull(logRr, seLogRr, iter = 1e+05)

### Arguments
- **logRr** (numeric vector) - Required - A numeric vector of effect estimates on the log scale.
- **seLogRr** (numeric vector) - Required - The standard error of the log of the effect estimates. Hint: often the standard error = (log(<lower bound 95 percent confidence interval>) - log(<effect estimate>))/qnorm(0.025).
- **iter** (numeric) - Optional - Number of iterations of the MCMC. Default is 1e+05.

### Value
An object of type `mcmcNull` containing the mean and standard deviation (both on the log scale) of the null distribution, as well as the MCMC trace.

### Details
This is an experimental function for computing the 95 percent credible interval of a calibrated p-value using Markov-Chain Monte Carlo (MCMC).

### Examples
```r
if (FALSE) { # \dontrun{
data(sccs)
negatives <- sccs[sccs$groundTruth == 0, ]
null <- fitMcmcNull(negatives$logRr, negatives$seLogRr)
null
plotMcmcTrace(null)
positive <- sccs[sccs$groundTruth == 1, ]
calibrateP(null, positive$logRr, positive$seLogRr)
} # }
```
```

--------------------------------

### calibrateLlr(null, likelihoodApproximation, twoSided = FALSE, upper = TRUE)

Source: https://ohdsi.github.io/EmpiricalCalibration/reference/calibrateLlr.html

Computes the calibrated log likelihood ratio using the fitted null distribution. The function accepts a null object and likelihood approximations, with options for one- or two-sided p-values.

```APIDOC
## calibrateLlr(null, likelihoodApproximation, twoSided = FALSE, upper = TRUE)

### Description
Computes calibrated log likelihood ratio using the fitted null distribution.

### Usage
calibrateLlr(null, likelihoodApproximation, twoSided = FALSE, upper = TRUE)

### Arguments
- **null** - An object of class `null` created using the `fitNull` function or an object of class `mcmcNull` created using the `fitMcmcNull` function.
- **likelihoodApproximation** - Either a data frame containing normal, skew-normal, or custom parametric likelihood approximations, or a list of (adaptive) grid likelihood profiles.
- **twoSided** - Compute two-sided (TRUE) or one-sided (FALSE) p-value?
- **upper** - If one-sided: compute p-value for upper (TRUE) or lower (FALSE) bound?

### Value
The calibrated log likelihood ratio.

### Examples
```r
data(sccs)
negatives <- sccs[sccs$groundTruth == 0, ]
null <- fitNull(negatives$logRr, negatives$seLogRr)
positive <- sccs[sccs$groundTruth == 1, ]
calibrateLlr(null, positive)
#> Detected data following normal distribution
#> [1] 0
```
```

--------------------------------

### Plot MCMC Trace

Source: https://ohdsi.github.io/EmpiricalCalibration/articles/EmpiricalPCalibrationVignette.html

Visualizes the MCMC trace to ensure the null distribution estimation is reliable. The trace should resemble random noise without significant auto-correlation.

```R
plotMcmcTrace(null)
```
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