miclust 1.3.0

Minor changes:

• Dependences:
  • The package is now completely independent of the irr package, which was previously used to internally calculate Cohen’s Kappa (irr::kappa2). Now, Cohen’s Kappa is calculated using a native base implementation to improve stability and maintainability. In addition, the Cohen’s Kappa calculation is now faster.
• Documentation:
  • Updated source code documentation to comply with the latest roxygen2 (v8.0.0) standards.
  • Improved README.Rmd plot rendering.
  • Integrated documentation for miclust() and its related methods print.miclust() and plot.miclust() into a single help page for a more fluid usage.
  • Integrated documentation for methods summary.miclust() and print.summary.miclust().
• miclust:
  • The width of the verbose message has been reduced (now, breaks line each 20 imputations).
• print.miclust:
  • Fix erratum in labels of the output of print.miclust.
• plot.miclust:
  • New parameter metric, to select which metric is displayed. Defaults to "all", maintaining compatibility with the output from versions 1.2.8 and earlier. Other options are: "nclfreq" (percentage of times each number of clusters has been selected); "critcf" (critCF distribution for each number of clusters); "nvarfreq" (distribution of the number of selected variables), and "varsel" (percentage of appearance of the variables that remained in the final set of selected variables).
  • New parameters col.nclfreq, col.critcf, col.nvarfreq, and col.varsel, to customize the color used in the plots for metrics, "nclfreq", "critcf", "nvarfreq", and "varsel", respectively. Default values are consistent with results under versions 1.2.8 and earlier.
  • New parameter col.all. When specified, it overrides col.nclfreq, col.critcf, col.nvarfreq, and col.varsel, and applies that color across the entire panel. Default (NULL) is consistent with results under versions 1.2.8 and earlier.
• summary.miclust:
  • Fix output errors related to within-cluster missingness of the selected variables.
  • Fix an internal error in summary.miclust() (originally triggered during kcca() execution inside assignprobandkappas()) that occurred when a specific imputation or the final assigned clustering result contained an empty cluster. Specifically, add a validation check in summary.miclust() to detect empty clusters across all imputations and the assigned cluster for the given k. The function now prints the affected cases and halts execution with a detailed error message.
  • An internal error in summary.miclust() (originally triggered during kcca() execution inside assignprobandkappas()) occurs when the final clustering for a given k and the set of selected variables results in an empty cluster within specific imputed datasets. This indicates that such a combination of k and selected variables is unable to find as many clusters as requested. A validation check has been added in summary.miclust() to detect these scenarios and halt execution with a detailed error message.
• print.summary.miclust:
  • The Within-cluster summary section of the output has changed. To reduce the output width, the columns for missingness, mean, and standard deviation have been collapsed into a single column. The section label has been changed to Within-cluster summary [%miss.;mean;sd]. Separated columns (version <= 1.2.8 style) are still available in the summarybycluster element of the object.

miclust 1.2.8

Minor changes:

• Update deprecated code in CITATION.

miclust 1.2.7

Minor changes:

• Fix two missed figures in README.

miclust 1.2.6

• First version on R CRAN