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cutpointr (version 1.0.2)

Determine and Evaluate Optimal Cutpoints in Binary Classification Tasks

Description

Estimate cutpoints that optimize a specified metric in binary classification tasks and validate performance using bootstrapping. Some methods for more robust cutpoint estimation and various plotting functions are included.

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Install

install.packages('cutpointr')

Monthly Downloads

1,770

Version

1.0.2

License

GPL-3

Issues

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Repository

https://github.com/thie1e/cutpointr

Maintainer

Christian Thiele

Last Published

April 14th, 2020

Functions in cutpointr (1.0.2)

Extract the cutpoints from a ROC curve generated by cutpointr

Calculate number of knots to use in spline smoothing

abs_d_sens_spec

Calculate the absolute difference of sensitivity and specificity

false_omission_rate

Calculate the false omission and false discovery rate

misclassification_cost

Calculate the misclassification cost

Plot a metric over all possible cutoffs from a cutpointr object

metric_constrain

Metrics that are constrained by another metric

plot_metric_boot

Plot the bootstrapped metric distribution from a cutpointr object

maximize_gam_metric

Optimize a metric function in binary classification after smoothing via generalized additive models

Calculate recall

print.multi_cutpointr

Print multi_cutpointr objects

Nodal involvement and acid phosphatase levels in 53 prostate cancer patients

print.cutpointr

Print cutpointr objects

maximize_loess_metric

Optimize a metric function in binary classification after LOESS smoothing

maximize_metric

Optimize a metric function in binary classification

maximize_spline_metric

Optimize a metric function in binary classification after spline smoothing

Determine and evaluate optimal cutpoints

maximize_boot_metric

Optimize a metric function in binary classification after bootstrapping

Plot ROC curve from a cutpointr or roc_cutpointr object

oc_youden_kernel

Determine an optimal cutpoint maximizing the Youden-Index based on kernel smoothed densities

plot_precision_recall

Precision recall plot from a cutpointr object

Calculate the positive predictive value

Calculate the positive or negative likelihood ratio

Use the sample median as cutpoint

Calculate the distance between points on the ROC curve and (0,1)

Calculate sensitivity

Calculate the Youden-Index

Calculate the total utility

The standard evaluation version of cutpointr (deprecated)

multi_cutpointr

Calculate optimal cutpoints and further statistics for multiple predictors

Extract number true / false positives / negatives

oc_youden_normal

Determine an optimal cutpoint for the Youden-Index assuming normal distributions

Calculate the product of positive and negative predictive value

General purpose plotting function for cutpointr or roc_cutpointr objects

Calculate the product of sensitivity and specificity

Plot the bootstrapped distribution of optimal cutpoints from a cutpointr object

Calculate the odds ratio

Calculate the negative predictive value

Calculate the sum of positive and negative predictive value

Calculate the p-value of a chi-squared test

Calculate the sum of sensitivity and specificity

Plot cutpointr objects

predict.cutpointr

Predict using a cutpointr object

Calculate the risk ratio (relative risk)

Calculate precision

Use the sample mean as cutpoint

Calculate a ROC curve

plot.multi_cutpointr

Plotting multi_cutpointr objects is currently not supported

Set a manual cutpoint for use with cutpointr

plot.roc_cutpointr

Plot ROC curve from a cutpointr or roc_cutpointr object

Calculate specificity

plot_sensitivity_specificity

Sensitivity and specificity plot from a cutpointr object

Plot the distribution of the independent variable per class from a cutpointr object

user_span_cutpointr

Calculate bandwidth for LOESS smoothing of metric functions by rule of thumb

Calculate true / false positive / negative rate

Suicide attempts and DSI sum scores of 532 subjects

Calculate the Jaccard Index

Test for equivalence of a metric

Calculate the absolute difference of positive and negative predictive value

Calculate accuracy

Calculate bootstrap confidence intervals from a cutpointr object

Calculate AUC from a roc_cutpointr or cutpointr object

Calculate Cohen's Kappa

Calculate the F1-score

Add metrics to a cutpointr or roc_cutpointr object