auc: Area Under the Curve and Receiving Operating Curve

In USCbiostats/phylogenetic: Statistical Inference and Prediction of Annotations in Phylogenetic Trees

Area Under the Curve and Receiving Operating Curve

Description

The AUC values are computed by approximation using the area of the polygons formed under the ROC curve.

Usage

auc(pred, labels, nc = 200L, nine_na = TRUE)

## S3 method for class 'aphylo_auc'
print(x, ...)

## S3 method for class 'aphylo_auc'
plot(x, y = NULL, ...)

Arguments

pred	A numeric vector with the predictions of the model. Values must range between 0 and 1.
labels	An integer vector with the labels (truth). Values should be either 0 or 1.
nc	Integer. Number of cutoffs to use for computing the rates and AUC.
nine_na	Logical. When TRUE, 9 is treated as NA.
x	An object of class aphylo_auc.
...	Further arguments passed to the method.
y	Ignored.

Value

A list:

• tpr A vector of length nc with the True Positive Rates.

• tnr A vector of length nc with the True Negative Rates.

• fpr A vector of length nc with the False Positive Rates.

• fnr A vector of length nc with the False Negative Rates.

• auc A numeric value. Area Under the Curve.

• cutoffs A vector of length nc with the cutoffs used.

Examples

set.seed(8381)
x   <- rdrop_annotations(raphylo(50), .3)
ans <- aphylo_mcmc(x ~ mu_d + mu_s + Pi)
ans_auc <- auc(predict(ans, loo = TRUE), x[,1,drop=TRUE])
print(ans_auc)
plot(ans_auc)

USCbiostats/phylogenetic documentation built on Oct. 28, 2023, 7:23 a.m.