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Changelog

Source: NEWS.md

clinstats 0.1.2

  • evaluate_model() reported 1 - AUC. The ROC curves were built with direction = ">", but pROC defines "<" as “observations are positive when they are greater than or equal to the threshold”, which is the convention a predicted probability follows. A model that ranked the data well was therefore reported as worse than chance (a true AUC of 0.78 was reported as 0.22) and the DeLong comparison tested the inverted hypothesis. The direction is now "<".
  • Added a semantic test for this: a marker that is higher in the event group must produce an AUC above 0.5. The previous test compared the result against a pROC::roc() call that used the same inverted direction, so it could not detect the defect.

clinstats 0.1.1

  • One orientation for every expression-matrix function: samples in rows, genes in columns, which is the convention inherited from gaofenglib. In 0.1.0 clean_expression() returned samples in rows while oncotype_crc() required genes in rows, so the two could not be chained without a manual transpose.
  • oncotype_crc() gains a gene_axis argument. The default "columns" matches clean_expression() and composes with it directly; "rows" keeps the previous orientation available. Declaring the wrong axis now reports which argument to use instead of listing twelve missing genes.

clinstats 0.1.0

  • Initial release. Consolidates and modernises the statistical utilities and curated colorectal cancer clinical datasets previously distributed as the separate gaofenglib and curatedClinicalData repositories.
  • Function redesign:
    • roc_summary() replaces calc_logit(), with tidy one-row output.
    • odds_ratio() replaces calc_or().
    • cox_table() replaces factor_analysis_cox().
    • logistic_table() replaces factor_analysis_logit().
    • evaluate_model() replaces eval_logit(), with train/test evaluation and a DeLong comparison between the two areas under the curve.
    • survival_cutoff() replaces calc_cutoff_survivalroc() and computes the Kaplan-Meier Youden cut point directly with survival::survfit() over a bounded quantile grid, so the long-unmaintained survivalROC package is no longer a dependency.
    • resample_cox() replaces calc_resamp_cox(), reports per-gene selection frequencies, and defaults to the sequential future plan.
    • clean_expression() replaces clean_dat(); gene identifier mapping is now an optional org.Hs.eg.db dependency.
    • oncotype_crc() replaces calc_oncotypedx_crc().
    • tcga_clinical() replaces extract_tcga_clinical().
    • survival_response() replaces get_survival().
  • Removed environment-mutating helpers init_R() and update_all().
  • All exported functions return tibbles and validate their inputs with clear error messages.
  • cox_table() and logistic_table() include every requested variable in the multivariable model by default; multivariable = "significant" reproduces the previous univariable-screening rule of the original helpers.
  • Datasets clin_crc, clin_crc_gf, and clin_crc_cell are carried over byte-identical from curatedClinicalData, with provenance documentation.
  • Added a Quarto analysis report template, testthat coverage, GitHub Actions checks, and a pkgdown site.