R: A function that calculates the area under a curve constructed...
survivAURC
R Documentation
A function that calculates the area under a curve constructed from plotting the area under a ROC curve at the corresponding time point at which it was generated.
Description
This function plots the individual area under the ROC curves of different time points against the time at which they were evaluated, and calculates the area under that curve.
The censoring status of the patient. 1 for a censored patient, and 0 for a patient who has an event.
marker
The predicted survival time of the patients.
entry
The time of entry of the patients, set to NULL by default.
cut.values
The cut off values for which the ROC curves are to be constructed.
time.max
The maximum time point for which the area under a ROC curve is to be plotted.
by
The step size between every ROC curve estimated and the next.
Details
The calculations for the Area under the ROC curves at each time point is done according to Patrick Heagerty's survivalROC function in the survivalROC package in R. It is a
value indicating the performance of the predictor when used on the results of both functions STpredictor.BLH and STpredictor.xv.BLH.
Value
AUC
The value of the area under the curve generated
AUeachROC
A vector with the values of the area under the individual ROC curves
A plot of the Area under the ROC curves against their corresponding time points.
Author(s)
Douaa Mugahid
References
Heagerty,P., Lumely T. & Pepe M.(2000). Time-dependent ROC curves for censored survival data & a diagnostic marker. Biometrics, 56(2), 337-344.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(RCASPAR)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RCASPAR/survivAURC.Rd_%03d_medium.png", width=480, height=480)
> ### Name: survivAURC
> ### Title: A function that calculates the area under a curve constructed
> ### from plotting the area under a ROC curve at the corresponding time
> ### point at which it was generated.
> ### Aliases: survivAURC
> ### Keywords: ROC curves Area under ROC curves
>
> ### ** Examples
>
> True_STs <- c(1.416667,2.75,2.416667,2.583333,2.166667,2.5,2.5,1.833333,1.25,0.6666667,1,6.583333,6.5,6.666667,2.75,1.666667,1.166667,2.833333,3.583333,6.166667,6.166667,
+ 3.416667,6.083333,1.833333,5.583333,0.75,5.75,5.5,0.5833333,7.666667,5,2.833333,1.333333,5.083333,0.8333333,1.5,4.75,3.416667,4.666667,1.916667,4.666667,7.416667,0.9166667,
+ 1.083333,3.75,3.25,3,2.416667,2.75,2.5,2.666667,4.5,4.416667,1.5,0.8333333,3.166667,3.833333,3.833333,0.4166667,3.333333,2.75,3.083333,0.3333333,0.25,0.6666667,1.833333,
+ 2.333333,3.416667,3.416667,3,0.6666667,0.75,2.166667,1,1.416667,1.333333,1.166667,1.166667,0.4166667,1.25,1.166667,1.083333)
> Predicted_STs <- c(6.030591,6.014457,3.545584,5.414229,6.41576,9.393992,5.542331,6.890859,8.090213,4.98545,2.77357,6.275699,9.163978,7.511511,9.531218,7.63715,10.08977,
+ 11.12364,3.982502,5.441881,12.61404,12.21851,17.05850,12.78141,16.22795,21.48544,6.281354,13.83925,8.859929,6.104142,8.255909,2.335526,6.564962,2.335761,9.33772,12.62540,
+ 10.97276,15.63089,8.01967,5.817267,5.59897,4.340784,32.40319,33.74123,27.45024,26.31024,26.88833,24.34707,32.06541,38.90473,17.37102,15.11059,8.772035,14.24816,7.852889,
+ 7.79996,5.601459,2.802408,35.77047,24.34717,30.65796,25.93927,20.64544,22.04807,19.15037,23.83430,1.876557,3.937208,6.526354,5.886377,9.301074,12.4657,14.49783,15.41502,
+ 2.860931,2.541947,4.543111,4.525553,4.148272,3.986912,6.246755,6.89523)
> censored <- c(0,1,1,1,1,0,1,1,0,1,0,1,1,1,1,0,0,0,0,1,1,1,1,0,1,0,1,1,0,1,1,0,0,1,0,0,1,0,1,0,1,1,0,0,1,1,1,0,1,1,1,1,1,0,1,1,1,1,0,1,1,1,1,0,0,0,1,1,1,1,0,0,1,0,1,1,1,1,1,1,1,
+ 1)
> survivAURC(Stime=True_STs,status=censored, marker=Predicted_STs,time.max=5)
$AUC
[1] 2.16072
$AUeachROC
[1] 1.0000000 0.3000696 0.3558260 0.3893873 0.4102913 0.4102913
>
>
>
>
>
> dev.off()
null device
1
>