Determine and Evaluate Optimal Cutpoints in Binary Classification Tasks


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Documentation for package ‘cutpointr’ version 1.1.0

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abs_d_ppv_npv Calculate the absolute difference of positive and negative predictive value
abs_d_sens_spec Calculate the absolute difference of sensitivity and specificity
accuracy Calculate accuracy
acc_constrain Metrics that are constrained by another metric
add_metric Add metrics to a cutpointr or roc_cutpointr object
add_metric.cutpointr Add metrics to a cutpointr or roc_cutpointr object
add_metric.multi_cutpointr Add metrics to a cutpointr or roc_cutpointr object
add_metric.roc_cutpointr Add metrics to a cutpointr or roc_cutpointr object
auc Calculate AUC from a roc_cutpointr or cutpointr object
auc.cutpointr Calculate AUC from a roc_cutpointr or cutpointr object
auc.roc_cutpointr Calculate AUC from a roc_cutpointr or cutpointr object
boot_ci Calculate bootstrap confidence intervals from a cutpointr object
boot_test Test for equivalence of a metric
cohens_kappa Calculate Cohen's Kappa
cutpoint Extract the cutpoints from a ROC curve generated by cutpointr
cutpointr Determine and evaluate optimal cutpoints
cutpointr.default Determine and evaluate optimal cutpoints
cutpointr.numeric Determine and evaluate optimal cutpoints
cutpointr_ The standard evaluation version of cutpointr (deprecated)
cutpoints Extract the cutpoints from a ROC curve generated by cutpointr
cutpoint_knots Calculate number of knots to use in spline smoothing
F1_score Calculate the F1-score
false_discovery_rate Calculate the false omission and false discovery rate
false_omission_rate Calculate the false omission and false discovery rate
fn Extract number true / false positives / negatives
fnr Calculate true / false positive / negative rate
fp Extract number true / false positives / negatives
fpr Calculate true / false positive / negative rate
Jaccard Calculate the Jaccard Index
maximize_boot_metric Optimize a metric function in binary classification after bootstrapping
maximize_gam_metric Optimize a metric function in binary classification after smoothing via generalized additive models
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
metric_constrain Metrics that are constrained by another metric
minimize_boot_metric Optimize a metric function in binary classification after bootstrapping
minimize_gam_metric Optimize a metric function in binary classification after smoothing via generalized additive models
minimize_loess_metric Optimize a metric function in binary classification after LOESS smoothing
minimize_metric Optimize a metric function in binary classification
minimize_spline_metric Optimize a metric function in binary classification after spline smoothing
misclassification_cost Calculate the misclassification cost
multi_cutpointr Calculate optimal cutpoints and further statistics for multiple predictors
nlr Calculate the positive or negative likelihood ratio
npv Calculate the negative predictive value
oc_manual Set a manual cutpoint for use with cutpointr
oc_mean Use the sample mean as cutpoint
oc_median Use the sample median as cutpoint
oc_youden_kernel Determine an optimal cutpoint maximizing the Youden-Index based on kernel smoothed densities
oc_youden_normal Determine an optimal cutpoint for the Youden-Index assuming normal distributions
odds_ratio Calculate the odds ratio
plot.cutpointr Plot cutpointr objects
plot.multi_cutpointr Plotting multi_cutpointr objects is currently not supported
plot.roc_cutpointr Plot ROC curve from a cutpointr or roc_cutpointr object
plot_cutpointr General purpose plotting function for cutpointr or roc_cutpointr objects
plot_cut_boot Plot the bootstrapped distribution of optimal cutpoints from a cutpointr object
plot_metric Plot a metric over all possible cutoffs from a cutpointr object
plot_metric_boot Plot the bootstrapped metric distribution from a cutpointr object
plot_precision_recall Precision recall plot from a cutpointr object
plot_roc Plot ROC curve from a cutpointr or roc_cutpointr object
plot_roc.cutpointr Plot ROC curve from a cutpointr or roc_cutpointr object
plot_roc.roc_cutpointr Plot ROC curve from a cutpointr or roc_cutpointr object
plot_sensitivity_specificity Sensitivity and specificity plot from a cutpointr object
plot_x Plot the distribution of the independent variable per class from a cutpointr object
plr Calculate the positive or negative likelihood ratio
ppv Calculate the positive predictive value
precision Calculate precision
predict.cutpointr Predict using a cutpointr object
print.cutpointr Print cutpointr objects
print.multi_cutpointr Print multi_cutpointr objects
prod_ppv_npv Calculate the product of positive and negative predictive value
prod_sens_spec Calculate the product of sensitivity and specificity
prostate_nodal Nodal involvement and acid phosphatase levels in 53 prostate cancer patients
p_chisquared Calculate the p-value of a chi-squared test
recall Calculate recall
risk_ratio Calculate the risk ratio (relative risk)
roc Calculate a ROC curve
roc01 Calculate the distance between points on the ROC curve and (0,1)
sensitivity Calculate sensitivity
sens_constrain Metrics that are constrained by another metric
specificity Calculate specificity
spec_constrain Metrics that are constrained by another metric
suicide Suicide attempts and DSI sum scores of 532 subjects
sum_ppv_npv Calculate the sum of positive and negative predictive value
sum_sens_spec Calculate the sum of sensitivity and specificity
tn Extract number true / false positives / negatives
tnr Calculate true / false positive / negative rate
total_utility Calculate the total utility
tp Extract number true / false positives / negatives
tpr Calculate true / false positive / negative rate
user_span_cutpointr Calculate bandwidth for LOESS smoothing of metric functions by rule of thumb
youden Calculate the Youden-Index