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1.  Direct Estimation of the Area Under the Receiver Operating Characteristic Curve in the Presence of Verification Bias 
Statistics in medicine  2009;28(3):361-376.
SUMMARY
The area under a receiver operating characteristic (ROC) curve (AUC) is a commonly used index for summarizing the ability of a continuous diagnostic test to discriminate between healthy and diseased subjects. If all subjects have their true disease status verified, one can directly estimate the AUC nonparametrically using the Wilcoxon statistic. In some studies, verification of the true disease status is performed only for a subset of subjects, possibly depending on the result of the diagnostic test and other characteristics of the subjects. Because estimators of the AUC based only on verified subjects are typically biased, it is common to estimate the AUC from a bias-corrected ROC curve. The variance of the estimator, however, does not have a closed-form expression and thus resampling techniques are used to obtain an estimate. In this paper, we develop a new method for directly estimating the AUC in the setting of verification bias based on U-statistics and inverse probability weighting. Closed-form expressions for the estimator and its variance are derived. We also show that the new estimator is equivalent to the empirical AUC derived from the bias-corrected ROC curve arising from the inverse probability weighting approach.
doi:10.1002/sim.3388
PMCID: PMC2626141  PMID: 18680124
Diagnostic test; Inverse probability weighting; Missing at random; U-statistic
2.  Covariate adjustment in estimating the area under ROC curve with partially missing gold standard 
Biometrics  2013;69(1):91-100.
Summary
In ROC analysis, covariate adjustment is advocated when the covariates impact the magnitude or accuracy of the test under study. Meanwhile, for many large scale screening tests, the true condition status may be subject to missingness because it is expensive and/or invasive to ascertain the disease status. The complete-case analysis may end up with a biased inference, also known as “verification bias”. To address the issue of covariate adjustment with verification bias in ROC analysis, we propose several estimators for the area under the covariate-specific and covariate-adjusted ROC curves (AUCx and AAUC). The AUCx is directly modelled in the form of binary regression, and the estimating equations are based on the U statistics. The AAUC is estimated from the weighted average of AUCx over the covariate distribution of the diseased subjects. We employ reweighting and imputation techniques to overcome the verification bias problem. Our proposed estimators are initially derived assuming that the true disease status is missing at random (MAR), and then with some modification, the estimators can be extended to the not-missing-at-random (NMAR) situation. The asymptotic distributions are derived for the proposed estimators. The finite sample performance is evaluated by a series of simulation studies. Our method is applied to a data set in Alzheimer's disease research.
doi:10.1111/biom.12001
PMCID: PMC3622116  PMID: 23410529
Alzheimer's disease; area under ROC curve; covariate adjustment; U statistics; verification bias; weighted estimating equations
3.  A model for adjusting for nonignorable verification bias in estimation of ROC curve and its area with likelihood-based approach 
Biometrics  2010;66(4):1119-1128.
Summary
In estimation of the ROC curve, when the true disease status is subject to nonignorable missingness, the observed likelihood involves the missing mechanism given by a selection model. In this paper, we proposed a likelihood-based approach to estimate the ROC curve and the area under ROC curve when the verification bias is nonignorable. We specified a parametric disease model in order to make the nonignorable selection model identifiable. With the estimated verification and disease probabilities, we constructed four types of empirical estimates of the ROC curve and its area based on imputation and reweighting methods. In practice, a reasonably large sample size is required to estimate the nonignorable selection model in our settings. Simulation studies showed that all the four estimators of ROC area performed well, and imputation estimators were generally more efficient than the other estimators proposed. We applied the proposed method to a data set from research in the Alzheimer’s disease.
doi:10.1111/j.1541-0420.2010.01397.x
PMCID: PMC3618959  PMID: 20222937
Alzheimer’s disease; nonignorable missing data; ROC curve; verification bias
4.  ROC curve estimation under test-result-dependent sampling 
Biostatistics (Oxford, England)  2012;14(1):160-172.
The receiver operating characteristic (ROC) curve is often used to evaluate the performance of a biomarker measured on continuous scale to predict the disease status or a clinical condition. Motivated by the need for novel study designs with better estimation efficiency and reduced study cost, we consider a biased sampling scheme that consists of a SRC and a supplemental TDC. Using this approach, investigators can oversample or undersample subjects falling into certain regions of the biomarker measure, yielding improved precision for the estimation of the ROC curve with a fixed sample size. Test-result-dependent sampling will introduce bias in estimating the predictive accuracy of the biomarker if standard ROC estimation methods are used. In this article, we discuss three approaches for analyzing data of a test-result-dependent structure with a special focus on the empirical likelihood method. We establish asymptotic properties of the empirical likelihood estimators for covariate-specific ROC curves and covariate-independent ROC curves and give their corresponding variance estimators. Simulation studies show that the empirical likelihood method yields good properties and is more efficient than alternative methods. Recommendations on number of regions, cutoff points, and subject allocation is made based on the simulation results. The proposed methods are illustrated with a data example based on an ongoing lung cancer clinical trial.
doi:10.1093/biostatistics/kxs020
PMCID: PMC3577107  PMID: 22723502
Binormal model; Covariate-independent ROC curve; Covariate-specific ROC curve; Empirical likelihood method; Test-result-dependent sampling
5.  A Unified Approach to Nonparametric Comparison of Receiver Operating Characteristic Curves for Longitudinal and Clustered Data 
We present a unified approach to nonparametric comparisons of receiver operating characteristic (ROC) curves for a paired design with clustered data. Treating empirical ROC curves as stochastic processes, their asymptotic joint distribution is derived in the presence of both between-marker and within-subject correlations. A Monte Carlo method is developed to approximate their joint distribution without involving nonparametric density estimation. The developed theory is applied to derive new inferential procedures for comparing weighted areas under the ROC curves, confidence bands for the difference function of ROC curves, confidence intervals for the set of specificities at which one diagnostic test is more sensitive than the other, and multiple comparison procedures for comparing more than two diagnostic markers. Our methods demonstrate satisfactory small-sample performance in simulations. We illustrate our methods using clustered data from a glaucoma study and repeated-measurement data from a startle response study.
PMCID: PMC2832229  PMID: 20209021
Area under the receiver operating characteristic curve; Clustered data; Confidence band; Intersection-union tests; Longitudinal data; Multiple comparison; Paired design; Partial area under the receiver operating characteristic curve; Quantile process; Repeated measurement
6.  Compare diagnostic tests using transformation-invariant smoothed ROC curves⋆ 
Receiver operating characteristic (ROC) curve, plotting true positive rates against false positive rates as threshold varies, is an important tool for evaluating biomarkers in diagnostic medicine studies. By definition, ROC curve is monotone increasing from 0 to 1 and is invariant to any monotone transformation of test results. And it is often a curve with certain level of smoothness when test results from the diseased and non-diseased subjects follow continuous distributions. Most existing ROC curve estimation methods do not guarantee all of these properties. One of the exceptions is Du and Tang (2009) which applies certain monotone spline regression procedure to empirical ROC estimates. However, their method does not consider the inherent correlations between empirical ROC estimates. This makes the derivation of the asymptotic properties very difficult. In this paper we propose a penalized weighted least square estimation method, which incorporates the covariance between empirical ROC estimates as a weight matrix. The resulting estimator satisfies all the aforementioned properties, and we show that it is also consistent. Then a resampling approach is used to extend our method for comparisons of two or more diagnostic tests. Our simulations show a significantly improved performance over the existing method, especially for steep ROC curves. We then apply the proposed method to a cancer diagnostic study that compares several newly developed diagnostic biomarkers to a traditional one.
doi:10.1016/j.jspi.2010.05.026
PMCID: PMC3358774  PMID: 22639484
ROC curve; Smoothing spline; Bootstrap
7.  Youden Index and Optimal Cut-Point Estimated from Observations Affected by a Lower Limit of Detection 
Summary
The receiver operating characteristic (ROC) curve is used to evaluate a biomarker’s ability for classifying disease status. The Youden Index (J), the maximum potential effectiveness of a biomarker, is a common summary measure of the ROC curve. In biomarker development, levels may be unquantifiable below a limit of detection (LOD) and missing from the overall dataset. Disregarding these observations may negatively bias the ROC curve and thus J. Several correction methods have been suggested for mean estimation and testing; however, little has been written about the ROC curve or its summary measures. We adapt non-parametric (empirical) and semi-parametric (ROC-GLM [generalized linear model]) methods and propose parametric methods (maximum likelihood (ML)) to estimate J and the optimal cut-point (c*) for a biomarker affected by a LOD. We develop unbiased estimators of J and c* via ML for normally and gamma distributed biomarkers. Alpha level confidence intervals are proposed using delta and bootstrap methods for the ML, semi-parametric, and non-parametric approaches respectively. Simulation studies are conducted over a range of distributional scenarios and sample sizes evaluating estimators’ bias, root-mean square error, and coverage probability; the average bias was less than one percent for ML and GLM methods across scenarios and decreases with increased sample size. An example using polychlorinated biphenyl levels to classify women with and without endometriosis illustrates the potential benefits of these methods. We address the limitations and usefulness of each method in order to give researchers guidance in constructing appropriate estimates of biomarkers’ true discriminating capabilities.
doi:10.1002/bimj.200710415
PMCID: PMC2515362  PMID: 18435502
Youden Index; ROC curve; Sensitivity and Specificity; Optimal Cut-Point
8.  Estimation of AUC or Partial AUC under Test-Result-Dependent Sampling 
The area under the ROC curve (AUC) and partial area under the ROC curve (pAUC) are summary measures used to assess the accuracy of a biomarker in discriminating true disease status. The standard sampling approach used in biomarker validation studies is often inefficient and costly, especially when ascertaining the true disease status is costly and invasive. To improve efficiency and reduce the cost of biomarker validation studies, we consider a test-result-dependent sampling (TDS) scheme, in which subject selection for determining the disease state is dependent on the result of a biomarker assay. We first estimate the test-result distribution using data arising from the TDS design. With the estimated empirical test-result distribution, we propose consistent nonparametric estimators for AUC and pAUC and establish the asymptotic properties of the proposed estimators. Simulation studies show that the proposed estimators have good finite sample properties and that the TDS design yields more efficient AUC and pAUC estimates than a simple random sampling (SRS) design. A data example based on an ongoing cancer clinical trial is provided to illustrate the TDS design and the proposed estimators. This work can find broad applications in design and analysis of biomarker validation studies.
doi:10.1080/19466315.2012.692514
PMCID: PMC3564679  PMID: 23393612
Area under ROC curve (AUC); Empirical likelihood; Nonparametric; Partial area under ROC curve (pAUC); Simple random sampling; Test-result-dependent sampling
9.  Generalized ROC curve inference for a biomarker subject to a limit of detection and measurement error‡ 
Statistics in medicine  2009;28(13):1841-1860.
SUMMARY
The receiver operating characteristic (ROC) curve is a tool commonly used to evaluate biomarker utility in clinical diagnosis of disease, especially during biomarker development research. Emerging biomarkers are often measured with random measurement error and subject to limits of detection that hinder their potential utility or mask an ability to discriminate by negatively biasing the estimates of ROC curves and subsequent area under the curve. Methods have been developed to correct the ROC curve for each of these types of sources of bias but here we develop a method by which the ROC curve is corrected for both simultaneously through replicate measures and maximum likelihood. Our method is evaluated via simulation study and applied to two potential discriminators of women with and without preeclampsia.
doi:10.1002/sim.3575
PMCID: PMC2754222  PMID: 19340817
ROC curve; limit of detection; measurement error; area under the curve; replicates
10.  Nonparametric ROC Based Evaluation for Survival Outcomes 
Statistics in medicine  2012;31(23):2660-2675.
SUMMARY
For censored survival outcomes, it can be of great interest to evaluate the predictive power of individual markers or their functions. Compared with alternative evaluation approaches, the time-dependent ROC (receiver operating characteristics) based approaches rely on much weaker assumptions, can be more robust, and hence are preferred. In this article, we examine evaluation of markers’ predictive power using the time-dependent ROC curve and a concordance measure which can be viewed as a weighted area under the time-dependent AUC (area under the ROC curve) profile. This study significantly advances from existing time-dependent ROC studies by developing nonparametric estimators of the summary indexes and, more importantly, rigorously establishing their asymptotic properties. It reinforces the statistical foundation of the time-dependent ROC based evaluation approaches for censored survival outcomes. Numerical studies, including simulations and application to an HIV clinical trial, demonstrate the satisfactory finite-sample performance of the proposed approaches.
doi:10.1002/sim.5386
PMCID: PMC3743052  PMID: 22987578
time-dependent ROC; concordance measure; inverse-probability-of-censoring weighting; marker evaluation; survival outcomes
11.  Bias in trials comparing paired continuous tests can cause researchers to choose the wrong screening modality 
Background
To compare the diagnostic accuracy of two continuous screening tests, a common approach is to test the difference between the areas under the receiver operating characteristic (ROC) curves. After study participants are screened with both screening tests, the disease status is determined as accurately as possible, either by an invasive, sensitive and specific secondary test, or by a less invasive, but less sensitive approach. For most participants, disease status is approximated through the less sensitive approach. The invasive test must be limited to the fraction of the participants whose results on either or both screening tests exceed a threshold of suspicion, or who develop signs and symptoms of the disease after the initial screening tests.
The limitations of this study design lead to a bias in the ROC curves we call paired screening trial bias. This bias reflects the synergistic effects of inappropriate reference standard bias, differential verification bias, and partial verification bias. The absence of a gold reference standard leads to inappropriate reference standard bias. When different reference standards are used to ascertain disease status, it creates differential verification bias. When only suspicious screening test scores trigger a sensitive and specific secondary test, the result is a form of partial verification bias.
Methods
For paired screening tests with bivariate normally distributed scores, we give formulae and programs to quantify the effect of paired screening trial bias on a paired comparison of area under the curves. We fix the prevalence of disease, and the chance a diseased subject manifests signs and symptoms. We derive the formulas for true sensitivity and specificity, and those for the sensitivity and specificity observed by the study investigator.
Results
The observed area under the ROC curves is quite different from the true area under the ROC curves. The typical direction of the bias is a strong inflation in sensitivity, paired with a concomitant slight deflation of specificity.
Conclusion
In paired trials of screening tests, when area under the ROC curve is used as the metric, bias may lead researchers to make the wrong decision as to which screening test is better.
doi:10.1186/1471-2288-9-4
PMCID: PMC2657218  PMID: 19154609
12.  Statistical methods to correct for verification bias in diagnostic studies are inadequate when there are few false negatives: a simulation study 
Background
A common feature of diagnostic research is that results for a diagnostic gold standard are available primarily for patients who are positive for the test under investigation. Data from such studies are subject to what has been termed "verification bias". We evaluated statistical methods for verification bias correction when there are few false negatives.
Methods
A simulation study was conducted of a screening study subject to verification bias. We compared estimates of the area-under-the-curve (AUC) corrected for verification bias varying both the rate and mechanism of verification.
Results
In a single simulated data set, varying false negatives from 0 to 4 led to verification bias corrected AUCs ranging from 0.550 to 0.852. Excess variation associated with low numbers of false negatives was confirmed in simulation studies and by analyses of published studies that incorporated verification bias correction. The 2.5th – 97.5th centile range constituted as much as 60% of the possible range of AUCs for some simulations.
Conclusion
Screening programs are designed such that there are few false negatives. Standard statistical methods for verification bias correction are inadequate in this circumstance.
doi:10.1186/1471-2288-8-75
PMCID: PMC2600821  PMID: 19014457
13.  Interval Estimation for the Difference in Paired Areas under the ROC Curves in the Absence of a Gold Standard Test 
Statistics in medicine  2009;28(25):3108-3123.
Summary
Receiver operating characteristic (ROC) curves can be used to assess the accuracy of tests measured on ordinal or continuous scales. The most commonly used measure for the overall diagnostic accuracy of diagnostic tests is the area under the ROC curve (AUC). A gold standard test on the true disease status is required to estimate the AUC. However, a gold standard test may sometimes be too expensive or infeasible. Therefore, in many medical research studies, the true disease status of the subjects may remain unknown. Under the normality assumption on test results from each disease group of subjects, using the expectation-maximization (EM) algorithm in conjunction with a bootstrap method, we propose a maximum likelihood based procedure for construction of confidence intervals for the difference in paired areas under ROC curves in the absence of a gold standard test. Simulation results show that the proposed interval estimation procedure yields satisfactory coverage probabilities and interval lengths. The proposed method is illustrated with two examples.
doi:10.1002/sim.3661
PMCID: PMC2812057  PMID: 19691022
Area under the ROC curve; EM algorithm; bootstrap method; gold standard test; maximum likelihood estimation
14.  A robust method using propensity score stratification for correcting verification bias for binary tests 
Sensitivity and specificity are common measures of the accuracy of a diagnostic test. The usual estimators of these quantities are unbiased if data on the diagnostic test result and the true disease status are obtained from all subjects in an appropriately selected sample. In some studies, verification of the true disease status is performed only for a subset of subjects, possibly depending on the result of the diagnostic test and other characteristics of the subjects. Estimators of sensitivity and specificity based on this subset of subjects are typically biased; this is known as verification bias. Methods have been proposed to correct verification bias under the assumption that the missing data on disease status are missing at random (MAR), that is, the probability of missingness depends on the true (missing) disease status only through the test result and observed covariate information. When some of the covariates are continuous, or the number of covariates is relatively large, the existing methods require parametric models for the probability of disease or the probability of verification (given the test result and covariates), and hence are subject to model misspecification. We propose a new method for correcting verification bias based on the propensity score, defined as the predicted probability of verification given the test result and observed covariates. This is estimated separately for those with positive and negative test results. The new method classifies the verified sample into several subsamples that have homogeneous propensity scores and allows correction for verification bias. Simulation studies demonstrate that the new estimators are more robust to model misspecification than existing methods, but still perform well when the models for the probability of disease and probability of verification are correctly specified.
doi:10.1093/biostatistics/kxr020
PMCID: PMC3276270  PMID: 21856650
Diagnostic test; Model misspecification; Propensity score; Sensitivity; Specificity
15.  ROC curve regression analysis: the use of ordinal regression models for diagnostic test assessment. 
Environmental Health Perspectives  1994;102(Suppl 8):73-78.
Diagnostic tests commonly are characterized by their true positive (sensitivity) and true negative (specificity) classification rates, which rely on a single decision threshold to classify a test result as positive. A more complete description of test accuracy is given by the receiver operating characteristic (ROC) curve, a graph of the false positive and true positive rates obtained as the decision threshold is varied. A generalized regression methodology, which uses a class of ordinal regression models to estimate smoothed ROC curves has been described. Data from a multi-institutional study comparing the accuracy of magnetic resonance (MR) imaging with computed tomography (CT) in detecting liver metastases, which are ideally suited for ROC regression analysis, are described. The general regression model is introduced and an estimate for the area under the ROC curve and its standard error using parameters of the ordinal regression model is given. An analysis of the liver data that highlights the utility of the methodology in parsimoniously adjusting comparisons for covariates is presented.
PMCID: PMC1566538  PMID: 7851336
16.  Regularized binormal ROC method in disease classification using microarray data 
BMC Bioinformatics  2006;7:253.
Background
An important application of microarrays is to discover genomic biomarkers, among tens of thousands of genes assayed, for disease diagnosis and prognosis. Thus it is of interest to develop efficient statistical methods that can simultaneously identify important biomarkers from such high-throughput genomic data and construct appropriate classification rules. It is also of interest to develop methods for evaluation of classification performance and ranking of identified biomarkers.
Results
The ROC (receiver operating characteristic) technique has been widely used in disease classification with low dimensional biomarkers. Compared with the empirical ROC approach, the binormal ROC is computationally more affordable and robust in small sample size cases. We propose using the binormal AUC (area under the ROC curve) as the objective function for two-sample classification, and the scaled threshold gradient directed regularization method for regularized estimation and biomarker selection. Tuning parameter selection is based on V-fold cross validation. We develop Monte Carlo based methods for evaluating the stability of individual biomarkers and overall prediction performance. Extensive simulation studies show that the proposed approach can generate parsimonious models with excellent classification and prediction performance, under most simulated scenarios including model mis-specification. Application of the method to two cancer studies shows that the identified genes are reasonably stable with satisfactory prediction performance and biologically sound implications. The overall classification performance is satisfactory, with small classification errors and large AUCs.
Conclusion
In comparison to existing methods, the proposed approach is computationally more affordable without losing the optimality possessed by the standard ROC method.
doi:10.1186/1471-2105-7-253
PMCID: PMC1513612  PMID: 16684357
17.  Which method of estimating renal function is the best predictor of mortality after coronary artery bypass grafting? 
Netherlands Heart Journal  2011;19(11):464-469.
Objectives
Definitions of renal function in patients undergoing coronary artery bypass graft surgery (CABG) vary in the literature. We sought to investigate which method of estimating renal function is the best predictor of mortality after CABG.
Methods
We analysed the preoperative and postoperative renal function data from all patients undergoing isolated CABG from January 1998 through December 2007. Preoperative and postoperative renal function was estimated using serum creatinine (SeCr) levels, creatinine clearance (CrCl) determined by the Cockcroft-Gault formula and the glomerular filtration rate (e-GFR) estimated by the Modification of Diet in Renal Disease (MDRD) formula. Receiver operator characteristic (ROC) curves and area under the ROC curves were calculated.
Results
In 9987 patients, CrCl had the best discriminatory power to predict early as well as late mortality, followed by e-GFR and finally SeCr. The odds ratios for preoperative parameters for early mortality were closer to 1 than those of the postoperative parameters.
Conclusions
Renal function determined by the Cockcroft-Gault formula is the best predictor of early and late mortality after CABG. The relationship between renal function and mortality is non-linear. Renal function as a variable in risk scoring systems such as the EuroSCORE needs to be reconsidered.
doi:10.1007/s12471-011-0184-3
PMCID: PMC3203983  PMID: 21847773
Coronary artery bypass grafts, CABG; Kidney, renal function; Statistics, regression analysis
18.  Receiver Operating Characteristic (ROC) Curve Analysis Using Microcomputer Spreadsheets 
As medical technology proliferates, we must have useful methods for evaluating that technology. One method - ROC curves - allows us to examine the spectrum of a test's usefulness. This paper discusses the concept of ROC curves and presents a simple method for estimating the area under the ROC curve. This measurement - the area under the ROC curve (AUC) - gives a useful estimate of a test's discriminatory ability. One can easily estimate the AUC using microcomputer spreadsheet software. The paper demonstrates how to develop the program and suggests that spreadsheets be adopted for other simple statistical uses.
PMCID: PMC2578036
19.  Estimation and Comparison of Receiver Operating Characteristic Curves 
The Stata journal  2009;9(1):1.
The receiver operating characteristic (ROC) curve displays the capacity of a marker or diagnostic test to discriminate between two groups of subjects, cases versus controls. We present a comprehensive suite of Stata commands for performing ROC analysis. Non-parametric, semiparametric and parametric estimators are calculated. Comparisons between curves are based on the area or partial area under the ROC curve. Alternatively pointwise comparisons between ROC curves or inverse ROC curves can be made. Options to adjust these analyses for covariates, and to perform ROC regression are described in a companion article. We use a unified framework by representing the ROC curve as the distribution of the marker in cases after standardizing it to the control reference distribution.
PMCID: PMC2774909  PMID: 20161343
20.  Receiver Operating Characteristics (ROC) Curve Area Analysis Using the ROC ANALYZER 
ROC analysis occupies an increasingly important role in technology assessment.[1] ROC curves allow one to compare a set of ordinal estimates over the entire range of estimates. Sources of such estimates may include subjective probabilities, mathematical prediction models and empiric prediction models (like the APGAR score). The area under the ROC curve measures the ability of the estimation method to discriminate between two states (usually disease and non-disease). This paper discusses how one constructs ROC curves, what the area under the curve means, and how and why one compares two ROC curves. The computer program (ROC ANALYZER) allows easy performance of these analyses on MS-DOS compatible machines.
PMCID: PMC2245768
21.  Receiver Operating Characteristic (ROC) Curve Analysis for Medical Diagnostic Test Evaluation  
This review provides the basic principle and rational for ROC analysis of rating and continuous diagnostic test results versus a gold standard. Derived indexes of accuracy, in particular area under the curve (AUC) has a meaningful interpretation for disease classification from healthy subjects. The methods of estimate of AUC and its testing in single diagnostic test and also comparative studies, the advantage of ROC curve to determine the optimal cut off values and the issues of bias and confounding have been discussed.
PMCID: PMC3755824  PMID: 24009950
Sensitivity; Specificity; ROC curve; Area under the curve (AUC); Parametric; Nonparametric; Bias
22.  pROC: an open-source package for R and S+ to analyze and compare ROC curves 
BMC Bioinformatics  2011;12:77.
Background
Receiver operating characteristic (ROC) curves are useful tools to evaluate classifiers in biomedical and bioinformatics applications. However, conclusions are often reached through inconsistent use or insufficient statistical analysis. To support researchers in their ROC curves analysis we developed pROC, a package for R and S+ that contains a set of tools displaying, analyzing, smoothing and comparing ROC curves in a user-friendly, object-oriented and flexible interface.
Results
With data previously imported into the R or S+ environment, the pROC package builds ROC curves and includes functions for computing confidence intervals, statistical tests for comparing total or partial area under the curve or the operating points of different classifiers, and methods for smoothing ROC curves. Intermediary and final results are visualised in user-friendly interfaces. A case study based on published clinical and biomarker data shows how to perform a typical ROC analysis with pROC.
Conclusions
pROC is a package for R and S+ specifically dedicated to ROC analysis. It proposes multiple statistical tests to compare ROC curves, and in particular partial areas under the curve, allowing proper ROC interpretation. pROC is available in two versions: in the R programming language or with a graphical user interface in the S+ statistical software. It is accessible at http://expasy.org/tools/pROC/ under the GNU General Public License. It is also distributed through the CRAN and CSAN public repositories, facilitating its installation.
doi:10.1186/1471-2105-12-77
PMCID: PMC3068975  PMID: 21414208
23.  Reliable and computationally efficient maximum-likelihood estimation of “proper” binormal ROC curves 
Academic radiology  2007;14(7):814-829.
Rationale and Objectives
Estimation of ROC curves and their associated indices from experimental data can be problematic, especially in multi-reader, multi-case (MRMC) observer studies. Wilcoxon estimates of area under the curve (AUC) can be strongly biased with categorical data, whereas the conventional binormal ROC curve-fitting model may produce unrealistic fits. The “proper” binormal model (PBM) was introduced by Metz and Pan (1) to provide acceptable fits for both sturdy and problematic datasets, but other investigators found that its first software implementation was numerically unstable in some situations (2). Therefore, we created an entirely new algorithm to implement the PBM.
Materials and Methods
This paper describes in detail the new PBM curve-fitting algorithm, which was designed to perform successfully in all problematic situations encountered previously. Extensive testing was conducted also on a broad variety of simulated and real datasets. Windows, Linux, and Apple Macintosh OS X versions of the algorithm are available online at http://xray.bsd.uchicago.edu/krl/.
Results
Plots of fitted curves as well as summaries of AUC estimates and their standard errors are reported. The new algorithm never failed to converge and produced good fits for all of the several million datasets on which it was tested. For all but the most problematic datasets, the algorithm also produced very good estimates of AUC standard error. The AUC estimates compared well with Wilcoxon estimates for continuously -distributed data and are expected to be superior for categorical data.
Conclusion
This implementation of the PBM is reliable in a wide variety of ROC curve-fitting tasks.
doi:10.1016/j.acra.2007.03.012
PMCID: PMC2693394  PMID: 17574132
Receiver operating characteristic (ROC) analysis; receiver operating characteristic (ROC) curves; proper binormal model; maximum likelihood estimation (MLE); multi-reader; multi-case (MRMC) analysis
24.  Multicategory reclassification statistics for assessing improvements in diagnostic accuracy 
Biostatistics (Oxford, England)  2012;14(2):382-394.
In this paper, we extend the definitions of the net reclassification improvement (NRI) and the integrated discrimination improvement (IDI) in the context of multicategory classification. Both measures were proposed in Pencina and others (2008. Evaluating the added predictive ability of a new marker: from area under the receiver operating characteristic (ROC) curve to reclassification and beyond. Statistics in Medicine 27, 157–172) as numeric characterizations of accuracy improvement for binary diagnostic tests and were shown to have certain advantage over analyses based on ROC curves or other regression approaches. Estimation and inference procedures for the multiclass NRI and IDI are provided in this paper along with necessary asymptotic distributional results. Simulations are conducted to study the finite-sample properties of the proposed estimators. Two medical examples are considered to illustrate our methodology.
doi:10.1093/biostatistics/kxs047
PMCID: PMC3695653  PMID: 23197381
Area under the ROC curve; Integrated discrimination improvement; Multicategory classification; Multinomial logistic regression; Net reclassification improvement
25.  ROC Analysis in Biomarker Combination with Covariate Adjustment 
Academic radiology  2013;20(7):874-882.
Rational and Objectives
Receiver operating characteristic analysis (ROC) is often used to find the optimal combination of biomarkers. When the subject level covariates affect the magnitude and/or accuracy of the biomarkers, the combination rule should take into account of the covariate adjustment. The authors propose two new biomarker combination methods that make use of the covariate information.
Materials and Methods
The first method is to maximize the area under covariate-adjusted ROC curve (AAUC). To overcome the limitations of the AAUC measure, the authors further proposed the area under covariate standardized ROC curve (SAUC), which is an extension of the covariate-specific ROC curve. With a series of simulation studies, the proposed optimal AAUC and SAUC methods are compared with the optimal AUC method that ignores the covariates. The biomarker combination methods are illustrated by an example from Alzheimer's disease research.
Results
The simulation results indicate that the optimal AAUC combination performs well in the current study population. The optimal SAUC method is flexible to choose any reference populations, and allows the results to be generalized to different populations.
Conclusions
The proposed optimal AAUC and SAUC approaches successfully address the covariate adjustment problem in estimating the optimal marker combination. The optimal SAUC method is preferred for practical use, because the biomarker combination rule can be easily evaluated for different population of interest.
doi:10.1016/j.acra.2013.03.009
PMCID: PMC3682803  PMID: 23747153
Biomarker combination; covariate adjustment; AUC; covariate standardization

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