statistics.raplot: Statistical metrics

In JohnPickering/risk-assessment-plot-package: Risk Assessment Plot and reclassification metrics

Statistical metrics

Description

The function statistics.raplot calculates the reclassification metrics. Used by CI.raplot.

Usage

statistics.raplot(x1, x2, y, t = NULL, NRI_return = FALSE)

Arguments

x1	Either a logistic regression fitted using glm (base package) or lrm (rms package) or calculated probabilities (eg through a logistic regression model) of the baseline model. Must be between 0 & 1
x2	Either a logistic regression fitted using glm (base package) or lrm (rms package) or calculated probabilities (eg through a logistic regression model) of the new (alternative) model. Must be between 0 & 1
y	Binary of outcome of interest. Must be 0 or 1 (if fitted models are provided this is extracted from the fit which for an rms fit must have x = TRUE, y = TRUE).
t	The risk threshold(s) for groups. eg t<-c(0,0.1,1) is a two group scenario with a threshold of 0.1 & t<-c(0,0.1,0.3,1) is a three group scenario with thresholds at 0.1 and 0.3. Nb. If no t is provided it defaults to a single threshold at the prevalence of the cohort.
NRI_return	Flag to return NRI metrics, default is FALSE.

Value

A matrix of metrics for use within CI.raplot

JohnPickering/risk-assessment-plot-package documentation built on July 3, 2023, 8:41 a.m.