plotSmoothCalibration: Plot the smooth calibration as detailed in Calster et al. "A...

In quinterpriest/PatientLevelPrediction: Developing patient level prediction using data in the OMOP Common Data Model

Plot the smooth calibration as detailed in Calster et al. "A calibration heirarchy for risk models was defined: from utopia to empirical data" (2016)

Description

Plot the smooth calibration as detailed in Calster et al. "A calibration heirarchy for risk models was defined: from utopia to empirical data" (2016)

Usage

plotSmoothCalibration(
  plpResult,
  smooth = "loess",
  span = 0.75,
  nKnots = 5,
  scatter = FALSE,
  bins = 20,
  sample = TRUE,
  typeColumn = "evaluation",
  saveLocation = NULL,
  fileName = "smoothCalibration.pdf"
)

Arguments

plpResult	The result of running runPlp function. An object containing the model or location where the model is save, the data selection settings, the preprocessing and training settings as well as various performance measures obtained by the model.
smooth	options: 'loess' or 'rcs'
span	This specifies the width of span used for loess. This will allow for faster computing and lower memory usage.
nKnots	The number of knots to be used by the rcs evaluation. Default is 5
scatter	plot the decile calibrations as points on the graph. Default is False
bins	The number of bins for the histogram. Default is 20.
sample	If using loess then by default 20,000 patients will be sampled to save time
typeColumn	The name of the column specifying the evaluation type
saveLocation	Directory to save plot (if NULL plot is not saved)
fileName	Name of the file to save to plot, for example 'plot.png'. See the function ggsave in the ggplot2 package for supported file formats.

Details

Create a plot showing the smoothed calibration #'

Value

A ggplot object.

quinterpriest/PatientLevelPrediction documentation built on April 20, 2022, 12:50 a.m.