Estimate cutpoints that optimize a specified metric in binary classification tasks
and validate performance using bootstrapping. Some methods for more robust cutpoint
estimation are supported, e.g. a parametric method assuming normal distributions,
bootstrapped cutpoints, and smoothing of the metric values per cutpoint using
Generalized Additive Models. Various plotting functions are included. For an overview
of the package see Thiele and Hirschfeld (2021)

- Add
`sigfig`

argument to`print.cutpointr`

to allow for specifying the number of significant digits to be printed - Add
`add_metric()`

function to add further metrics to the output of`cutpointr()`

- Add
`roc01`

metric function to calculate the distance of points on the ROC curve to the point (0,1) on ROC space - Fix
`plot_sensitivity_specificity()`

if`boot_runs = 0`

- Fix display of bootstrap results in summary
- Update benchmarks in Readme

- More tests and modified two tests that led to errors when CRAN checked
the package (
`spar = NULL`

in`maximize_spline_metric`

) - Add links to the documentation of all method, plotting, main and metric functions to all other functions of the same family
- Add some checks to predict.cutpointr to prevent improper
`cutpoint_nr`

- The
`boot`

column is now always returned and`NA`

, if no bootstrapping was run, so that the number of returned columns is constant

- Fix a bug in check_method_cols that occurred when a user-supplied method function returned a metric column but no roc_curve
- Add chapters to the Readme about GAM, kernel and normal methods
- Fix bug in bootstrapping that allowed resamples with only one class to be sampled
`use_midpoints`

is now also passed to`method`

by`cutpointr`

to allow for the calculation of midpoints within`maximize_boot_metric`

and`minimize_boot_metric`

, which before happened in`cutpointr`

, leading to slightly biased cutpoints in certain scenarios

- Change defaults in spline smoothing:
`nknots`

is now calculated by`stats::.nknots_smspl`

and`spar = 1`

- Add
`cutpoint_tol`

argument to define a tolerance around the optimized metric, so that multiple cutpoints in the vicinity of the target metric can be returned and to avoid not returning other "optimal" cutpoints due to floating-point problems - Change default value to
`break_ties = c`

- If multiple optimal cutpoints are found and they are summarized using
`break_ties`

, the returned main metric is now not the optimal one but the one corresponding to the summarized cutpoint (thus may be worse than the optimal one) - Add
`maximize_gam_metric`

and`minimize_gam_metric`

for smoothing via generalized additive models - All plots with
`geom_ribbon`

now use`size = 0`

to plot no lines around the (transparent) areas

- Return multiple optimal cutpoints
- Add spline smoothing method

- Reformat docs
- Remove superfluous check in
`plot_cutpointr`

- Add metrics
`plr`

(positive likelihood ratio),`nlr`

(negative likelihood ratio),`false_discovery_rate`

, and`false_omission_rate`

- In preparation for a new version of tibble that will restore the old printing behaviour and in order to pass the CRAN check the print method for cutpointr has been altered depending on the loaded version of tibble.
`silent`

argument for roc().- Reformat docs to include better formatted equations
- Remove superfluous check in plot_cutpointr

`cutpointr_`

now accepts functions instead of character strings as`method`

or`metric`

- Fix naming the metric in the bootstrap if the supplied function returns an unnamed vector
- Fix help for the
`use_midpoints`

parameter. If TRUE (default FALSE) the returned optimal cutpoint will be the mean of the optimal cutpoint and the next lowest observation (for`direction = ">="`

) or the next highest observation (for`direction = "<="`

) - Rename
`sum_ppvnpv`

,`prod_ppvnpv`

, and`abs_d_ppvnpv`

to`sum_ppv_npv`

,`prod_ppv_npv`

, and`abs_d_ppvnpv`

to match the naming scheme to the names of the metrics that optimize sensitivity and specificity - Also all metric names that are returned by the metric functions are now lower case
- The
`summary_sd`

function now also returns 5% and 95% percentiles that are included in the output of`summary`

- The default number of bootstrap repeats in
`minimize_boot_metric`

and`maximize_boot_metric`

was changed from 200 to 50 - The message "Running bootstrap..." is now displayed before executing the bootstrap so that possible messages or warnings can be attributed to the main cutpoint estimation or cutpoint estimation during the bootstrapping
- The
`summary`

function now returns a data.frame instead of a list, also the printing method for`summary_cutpointr`

has been slightly modified - Add
`plot_sensitivity_specificity`

for plotting cutpoints vs. sensitivity and specificity on the y-axis - Remove
`oc_optimalCutpoints`

function - Remove dependencies
`ROCR`

and`OptimalCutpoints`

by rewriting tests and storing benchmark results

- cutpointr() now also works on vectors of raw data, that is without the
`data`

argument. Thus, it can be used as before by specifying`data`

,`x`

, and`class`

or alternatively without specifying`data`

and directly supplying the vectors of predictions and outcomes as`x`

and`class`

. `silent`

argument for optionally suppressing messages (e.g. which class is assumed to be the positive one)- Parts of the code were rewritten using Rcpp which leads to roughly a threefold speedup with larger n (n > 1e5)
- The automatic determination of the positive / negative classes and direction now uses the median of the predictor values per class instead of the mean so that the AUC is always >= 0.5
- The bootstrapping now also returns the in-bag main metric, the out-of-bag ROC curve, and the out-of-bag AUC

- Add multi_cutpointr for running cutpointr_ on multiple predictor variables
- Add metric risk_ratio
- Use geom_bar instead of geom_histogram if all cutpoints are integer in plot_x and plot_cut_boot or if there is just one unique value
- If bootstrapping is run, a bootstrapped confidence interval can be displayed in plot_metric
- Add methods for median and mean as cutpoint
- Fix display of cutpoint in ROC curve (use get_opt_ind in plot.cutpoint and plot_roc)
- Fix picking correct metric in plot_metric_boot