| Type: | Package |
| Title: | Value Added Receiver Operating Characteristics Curve |
| Version: | 0.4.0 |
| Date: | 2025-06-20 |
| Description: | A continuous version of the receiver operating characteristics (ROC) curve to assess both classification and continuity performances of biomarkers, diagnostic tests, or risk prediction models. |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| Depends: | R (≥ 4.2.0), pROC, corrplot, grDevices, graphics, stats, utils |
| NeedsCompilation: | no |
| Packaged: | 2025-06-21 14:39:28 UTC; ychung36 |
| Author: | Yunro Chung  [aut,
cre] |
| Maintainer: | Yunro Chung <yunro.chung@asu.edu> |
| Repository: | CRAN |
| Date/Publication: | 2025-06-21 15:00:02 UTC |
VAROC: value added receiver operating characteristics (ROC) curve
Description
ROC curve to visualize classification and continuity performances of biomarkers, diagnostic tests, or risk prediction models.
Usage
varoc(y,x,tmd.range=NULL,legend="right",lwd=3,digits=2)
Arguments
y |
binary outcome, where y=1 if disease (or case) and y=0 if non-disease (or control). |
x |
continuous score, e.g. biomarker, diagnostic test, risk score. |
tmd.range |
minimum and maximum values of TMD, displayed on the plot. |
legend |
legend location, "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right" and "center". |
lwd |
line width. |
digits |
number of decimals. |
Details
The varoc function summarizes a continuity performance of x at each cutoff c using two key metrics: (i) tail mean difference (TMD) and (ii) intergrated TMD (ITMD). For (i), TMD(c) is true positive mean(TPM)(c) minus false positive mean(FPM)(c), where TPM(c) is E(x>c|y=1) and FPM(c) is E(x>c|y=0). For (ii), ITMD is a global measure of evaluating continuity performance of x over all thresholds.
These measures are continuous versions of ROC curve-based measures. Specifically, TPM(c) and FPM(c) are continuous versions of true positive fraction (TPF)(c) and false positive fraction (FPF)(c), where TPF(c)=P(x>c|y=1) and FPF(c)=P(x>c|y=0). Thus, the useful (or useless) x has TPF(c)-FPF(c)>0 and TMD(c)>0 (or TPF(c)-FPF(c)=0 and TMD(c)=0); and useful (or useless) x has area under the ROC curve (AUC)>0.5 and ITMD(c)>0 (or AUC=0.5 and ITMD(c)=0).
Value
th |
Threshold values. |
tpf |
True positive fraction at each threshold. |
fpf |
False positive fraction at each th. |
tpm |
True positive mean at each th. |
fpm |
False positive fraction at each th. |
tmd |
Tail mean difference, i.e., tpm-fpm, at each th. |
auc |
Area under the ROC curve. |
itmd |
Integrated tmd over all theresholds. |
Author(s)
Yunro Chung [aut, cre]
References
Danielle Brister and Yunro Chung, Value added receiver operating characteristics curve (in-progress)
Examples
set.seed(100)
n1=100
n0=100
y=c(rep(1,n1),rep(0,n0))
#1. useless marker
x1=abs(c(rnorm(n1,0,1),rnorm(n0,0,1)))
fit1=varoc(y=y,x=x1)
#2. useful marker
x2=abs(c(rnorm(n1,2,1),rnorm(n0,0,1)))
fit2=varoc(y=y,x=x2)
#4. markers 1 vs 2
opar=par(mfrow=c(1,2))
tmd.range=range(c(fit1$tmd,fit2$tmd))
fit1=varoc(y=y,x=x1,tmd.range=tmd.range)
fit2=varoc(y=y,x=x2,tmd.range=tmd.range)
on.exit(par(opar))