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_()
• The full ROC curve can now be used for metric functions. It is passed as the parameter .roc_curve.

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

cutpointr 1.1.1

This release was published on CRAN on 2021-06-29, mainly to add the citation, as requested by JSS, to the article describing cutpointr (https://www.jstatsoft.org/article/view/v098i11, DOI: 10.18637/jss.v098.i11).

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 (printed
  output is still rounded).
• 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", because this is already clear
  from the legend, and to save space.

Fixes

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

cutpointr 1.0.32

Version 1.0.32 brings some minor internal changes for compatibility with some updated packages of the tidyverse and for CRAN.

• Reduce size of tarball for CRAN by removing some superfluous files
• Accelerate tests and vignette building to lower runtime on CRAN
• 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 the non-exported utility function sanitize_metric.

cutpointr 1.0.0

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

News

cutpointr 0.7.6 is on CRAN now.

Changes and Enhancements in comparison to 0.7.4

• 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
• 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
• Add constrainable metrics, e.g. sens_constrain to calculate sensitivity given
  a minimum value for specificity
• Add a check to ensure that the metric function does not return only missing
  values

Fixes after 0.7.4

• Fix fetching of method name if the method was called using :: or :::
• Make test of summary printing more tolerant after problems with tidyr 0.8.3
• Fix a bug where dot-arguments were not passed to the metric function in
  cutpointr_internal
• Fix a few typos in the Readme and help pages

cutpointr 0.7.4

cutpointr 0.7.4 is on CRAN now.

News

• 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

cutpointr 0.7.3 is on CRAN now.

News

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