rSRD

• plotCrossValidation no longer row-binds the precomputed summary statistics (min, xx1, Q1, median, Q3, xx19, max) together with the fold-wise SRD values into a single sample for ggplot to recompute quartiles and whiskers from. Previously, this mixture of real and derived values distorted the boxplot, especially when number_of_folds was small. The box geometry (min, Q1, median, Q3, max) is now taken directly from boxplot_values, and the mean is computed directly from the fold-wise SRD values; neither is derived from a contaminated sample (see also the related ordering simplification under Improvements).

New features

• calculateSRDDistribution() and calculateCrossValidation() gain a new seed parameter for reproducible results. When seed = NULL (the default), the original stochastic behaviour is preserved, ensuring full backward compatibility.
• Three example datasets are now bundled with the package and accessible via system.file("extdata", "<filename>", package = "rSRD"). The following three files use a semicolon separator and include a header row (read.csv(..., header = TRUE, sep = ";")).
• mep_profiles.csv: voting profiles of Members of the European Parliament.
• bundesliga20_21.csv: team performance data from the 2020/21 Bundesliga season.
• movies1994.csv: ratings and rankings of films released in 1994.
• Added a vignette, "Getting Started with rSRD", covering the full analysis workflow: data preprocessing, computing SRD values, the permutation test for significance, cross-validation, and pairwise visualisation via heatmaps. Access it with vignette("rSRD-introduction", package = "rSRD").

Improvements

• plotCrossValidation no longer re-derives a column ordering from boxplot_values. The columns of SRD_values_of_different_folds already arrive ordered by median, Q1, Q3, min, and max, since this ordering is performed in the C++ layer (Cross_Validation::Wilcoxon/Alpaydin/ Dietterich) and preserved unchanged by calculateCrossValidation(), which only attaches solution names to the already-ordered columns. The redundant re-ordering step has been removed, simplifying the function and removing its dependency on boxplot_values for this purpose (plotCrossValidation still uses boxplot_values directly for box geometry; see Bug fixes).
• Deprecated ggplot2::aes_string() calls in plotPermTest replaced with ggplot2::aes() using the .data pronoun.
• plotPermTest now places solution labels at the interpolated y-value of the distribution curve at each solution's SRD value, replacing a random placement that changed on every call. The x- and y-axes now carry informative labels ("Normalised SRD value" and "Relative frequency" or "Cumulative relative frequency" depending on the densityToDistr argument), replacing auto-generated labels that exposed internal implementation details.
• Broad import() directives for dplyr, ggplot2, tibble, janitor, rlang, and stringr replaced with specific importFrom() calls. stringr removed as an unused dependency.
• utilsColorPalette is now generated via grDevices::colorRampPalette() instead of a 250-element hard-coded vector.
• Added package-level documentation, accessible via ?rSRD.
• All %>% pipe operators replaced with the native R pipe |>.

Testing

• Added a comprehensive unit test suite using testthat (edition 3), covering calculateSRDValues(), calculateCrossValidation(), utilsMaxSRD(), utilsTieProbability(), utilsCalculateRank(), utilsCreateReference(), utilsPreprocessDF() and many other functions.