varoc (version 1.0.0)

varoc3d: VAROC: value added receiver operating characteristics (ROC) curve

Description

Three-dimensional VAROC curve.

Usage

varoc3d(y,x,zlim=NULL,plot=TRUE,digits=2,pval="no",B=2000)

Value

res1

Metrics at each th (threshold): tpf, fpf, tmd=tpm-fpm, pvalue (alternative hypothesis: tpm>fpm (or tpm>0))

res2

Global metrics: auc, iptm, ifpm, itmd=itpm-ifpm, pvalue (alternative hypothesis: itpm>ifpm (or itmd>0))

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.

zlim

minimum and maximum values of TMD, useful when comparing more than two scores (see Examples below).

plot

TRUE if three-dimensional VAROC curve is displayed.

digits

number of decimals.

pval

Bootstrap one-sided p-value if pval="yes".

B

Number of bootstrap samples.

Author

Yunro Chung [aut, cre]

Details

Three-dimensional version of the VAROC curve. See the varoc function in details.

References

Danielle Brister and Yunro Chung, Value added receiver operating characteristics curve, Journal of Data Science (under review)

Examples

set.seed(10)

n1=n0=25
y=c(rep(1,n1),rep(0,n0))

#1. useless marker
x1=abs(c(rnorm(n1,0,1),rnorm(n0,0,1)))
fit1=varoc3d(y=y,x=x1,plot=FALSE)

#2. useful marker
x2=abs(c(rnorm(n1,2,1),rnorm(n0,0,1)))
fit2=varoc3d(y=y,x=x2,plot=FALSE)

#3. markers 1 vs 2
opar=par(mfrow=c(1,2))
zlim=range(c(fit1$res1$tmd,fit2$res1$tmd))
fit1=varoc3d(y=y,x=x1,zlim=zlim)
fit2=varoc3d(y=y,x=x2,zlim=zlim)
on.exit(par(opar))