plotCiCalibration {EmpiricalCalibration}

Create a confidence interval calibration plot

Description

plotCalibration creates a plot showing the calibration of our confidence interval calibration procedure

Usage

plotCiCalibration(
  logRr,
  seLogRr,
  trueLogRr,
  strata = as.factor(trueLogRr),
  crossValidationGroup = 1:length(logRr),
  legacy = FALSE,
  evaluation,
  legendPosition = "top",
  title,
  fileName = NULL
)

Arguments

logRr

A numeric vector of 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).

trueLogRr

The true log relative risk.

strata

Variable used to stratify the plot. Set strata = NULL for no stratification.

crossValidationGroup

What should be the unit for the cross-validation? By default the unit is a single control, but a different grouping can be provided, for example linking a negative control to synthetic positive controls derived from that negative control.

legacy

If true, a legacy error model will be fitted, meaning standard deviation is linear on the log scale. If false, standard deviation is assumed to be simply linear.

evaluation

A data frame as generated by the evaluateCiCalibration function. If provided, the logRr, seLogRr, trueLogRr, strata, and legacy arguments will be ignored.

legendPosition

Where should the legend be positioned? ("none", "left", "right", "bottom", "top").

title

Optional: the main title for the plot

fileName

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.

Details

Creates a calibration plot showing the fraction of effects within the confidence interval. The empirical calibration is performed using a leave-one-out design: The confidence interval of an effect is computed by fitting a null using all other controls. Ideally, the calibration line should approximate the diagonal. The plot shows the coverage for both theoretical (traditional) and empirically calibrated confidence intervals.

Value

A Ggplot object. Use the ggsave function to save to file.

Examples

## Not run: 
data <- simulateControls(n = 50 * 3, mean = 0.25, sd = 0.25, trueLogRr = log(c(1, 2, 4)))
plotCiCalibration(data$logRr, data$seLogRr, data$trueLogRr)

## End(Not run)