NEWS.md

cutpointr 1.2.0

Changes

• Remove dependency pkgmaker
• Remove maximize_spline_metric and minimize_spline_metric
• Add boot_digits parameter to cutpointr:::print.summary_cutpointr

cutpointr 1.1.2

Changes

• The (very long) vignette has been split up into multiple vignettes, each with its own topic. @kapsner has written an additional vignette on bootstrapping.
• Update ?multi_cutpointr to say that it uses cutpointr(), not cutpointr_()

Fixes

• When using an extra parameter for the metric, such as in sens_constrain, and if bootstrapping was run, that parameter was not forwarded to the bootstrapping

cutpointr 1.1.1

Changes

• Clarified the help for the boot_stratify parameter
• Better examples for the constrained metrics
• Added reference and citation for the article about cutpointr in JSS

cutpointr 1.1.0

Changes

• boot_ci now works with multiple cutpoints (multiple cutpoints are possible if break_ties = c).
• add_metric now adds the selected metrics to the bootstrap results, too.
• Include metrics that were added with add_metric in summary().
• Change default value of subgroup in multi_cutpointr to NULL (instead of missing) to make it consistent with cutpointr.
• No rounding anymore within the internal function summary_sd so that the various summary functions now return all values without rounding.
• Descriptive statistics in summary functions are now stored with the additional first column "Data" instead of giving the class values as row names.
• Nicer printing of summary objects in Rmd documents.
• boot_stratify is now passed to the method functions so that the bootstrap within maximize_boot_metric and minimize_boot_metric can be stratified, too.
• Subtitles (such as "by class") have been removed from the plots because the subtitles should have read "by subgroup" and because this is already clear from the legend.

Fixes

• Fix a bug in multi_cutpointr that forced the class variable to be named "suicide".

cutpointr 1.0.32

• Reduce size of tarball for CRAN by removing some superfluous files

cutpointr 1.0.31

• Accelerate tests and vignette building to lower runtime on CRAN

cutpointr 1.0.3

• Some changes for vctrs 0.3.0 and dplyr 1.0.0: Unname and correctly assign classes to a few objects instead of using vctrs::df_cast and vctrs::df_ptype2 to keep compatibility with vctrs 0.2.4
• Added ORCID and article reference to Description

cutpointr 1.0.2

• Minor internal changes for compatibility with the latest updates of some packages from the tidyverse (e.g. tibble 3.0.0)

cutpointr 1.0.1

• Prepare for matrix inheriting from class "array" in R 4.0.0 by making a minor change in non-exported utility function sanitize_metric

cutpointr 1.0.0

Most important changes

• cutpointr and roc now both use tidyeval. !! can be used when an argument should be unquoted, as in dplyr, e.g. myvar <- "dsi"; cutpointr(suicide, !!myvar, suicide). cutpointr_ is now deprecated. Transforming variables directly in the call is thus no longer supported, e.g. cutpointr(suicide, dsi * 2, suicide) now throws an error.
• The object returned by multi_cutpointr does not have the cutpointr class anymore.

New functions

• A new boot_ci function is available that calculates confidence intervals (the empirical quantiles) based on the bootstrap results.
• The auc function is now exported and can be used to calculate the AUC from a cutpointr or roc_cutpointr object, e.g. auc(roc(suicide, dsi, suicide, "yes", "no"))
• boot_test is a new function for carrying out a bootstrap test for equivalence of a metric, e.g. the AUC, the Youden-Index or also the optimal cutpoint. The standard deviation is calculated as sd of the differences in metric values per bootstrap repetition, then a z-test is calculated.

Plotting

• New type argument to plot_roc for choosing line or step
• The resulting object from roc_cutpointr can now simply be plotted with plot()

Bootstrapping

• The bootstrapping no longer tries to redraw bootstrap samples if only one class is drawn. In that case the repetition is removed from the results via .errorhandling = "remove" in foreach.
• Subsequently report the number of missing values in the bootstrap results. summary.cutpointr and summary.multi_cutpointr now print an additional NAs column in the bootstrap summary and cutpointr issues a message if any bootstrap repeats failed (e.g. because only one class was drawn).
• Stratified bootstrapping is now supported via the boot_stratify argument.

Misc

• Make the printed output of summary.cutpointr and summary.multi_cutpointr more compact
• No rounding of numbers in summary.cutpointr and summary.multi_cutpointr any more. The rounding is now done in print.summary_cutpointr and print.summary_multi_cutpointr, respectively, and can be controlled via the digits argument
• plot_metric has a new add_unsmoothed argument for adding the unsmoothed metric values to the plot as a dashed line (default TRUE). Helpful to inspect the smoothing of functions like maximize_gam_metric.
• Add some mathematical details to ?oc_youden_kernel.
• The Readme and vignette have been updated and condensed a bit.
• A warning is issued if in metric_constrain or one of the other constrained metrics min_constrain can not be achieved.

Fixes

• Fix the default for break_ties in cutpointr.default by setting it to median as it was already in cutpointr.numeric and cutpointr_.

cutpointr 0.7.6

• Let roc() return a tibble instead of a data.frame
• Printing results of roc() is now possible with plot_roc()
• Extra metric columns can now be added to a roc_cutpointr object with add_metric()
• Add prostate_nodal data set of nodal involvement and acid phosphatase levels in 53 prostate cancer patients
• Fix fetching of method name if method was called using :: or :::
• Make test of summary printing more tolerant after problems with tidyr 0.8.3
• Issue an error if plot is used on a multi_cutpointr object
• Add a summary method for multi_cutpointr, a corresponding summary_multi_cutpointr class and a printing method for that class
• The column variable is not returned anymore by multi_cutpointr, because it is identical to predictor
• Run multi_cutpointr only on all numeric columns, if x = NULL

cutpointr 0.7.5

• Add constrainable metrics, e.g. sens_constrain to calculate sensitivity given a minimum value for specificity
• Fix a bug where dot-arguments were not passed to the metric function in cutpointr_internal
• Add a check to ensure that the metric function does not return only missing values
• Replace (fix) ">" by ">=" in the documentation of cutpointr().

cutpointr 0.7.4

• 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

cutpointr 0.7.3

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

cutpointr 0.7.2

• 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

cutpointr 0.7.1

• 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

cutpointr 0.7.0

• 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

cutpointr 0.6.0

• Return multiple optimal cutpoints
• Add spline smoothing method

cutpointr 0.5.2

• 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

cutpointr 0.5.1

• 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 0.5.0

• 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 0.4.0

• 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

cutpointr 0.3.2

• 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