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Table 2 Predictive accuracy measures and the corresponding R package in which they can be computed

From: Assessing models for genetic prediction of complex traits: a comparison of visualization and quantitative methods

Predictive accuracy measure R package Version
(1) The confusion matrix
Receiver Operating Characteristic Curve and area under the curve prediction and performance in ROCR [11] performance (prediction.object, “auc”) 1.0-7
Positive predictive value and negative predictive value prediction and performance in ROCR performance (prediction.object, “ppv”) performance (prediction.object, “npv”) 1.0-7
(2) Visualization of the distribution of prediction values
Histograms of the prediction values separated by class multhist in plotrix [12] 3.5-11
Box plots boxplot in graphics Base package
Violin plots vioplot in vioplot  
Quantile-quantile plots qqplot in stats Base package
(3) Statistical tests
Hypergeometric test phyper in stats Base package
Mann–Whitney U test wilcox.test in stats Base package
Asymptotic Generalized Cochran-Mantel-Haenszel Test cmh_test in coin [13] 1.0-24