Changelog • hvtiRutilities

hvtiRutilities 1.0.0.9004

read_clinical_data(): files with no extension now produce a clear error (“Cannot determine file type: … has no extension”) instead of the misleading Unsupported file type: '..' message. The unsupported-extension error also now includes the full file path for easier diagnosis.

test-read_clinical_data.R: strengthened the tibble-coercion assertion from expect_true(is.data.frame(result)) (TRUE for tibbles) to expect_equal(class(result), "data.frame") so the test actually protects against as.data.frame() being removed or bypassed.

vignettes/reproducible-seeds.qmd: section heading “Using the Seed with varpro” and narrative references to the package now use the correct CRAN casing varPro; function-name references (varpro(), unsupv.varpro()) remain lowercase as those are the exported function names.

Fixed Suggests entry for varPro: package name on CRAN is varPro (camelCase), not varpro (lowercase). The case mismatch caused pak lockfile resolution to fail with “Can’t find package called varpro”. Updated the corresponding varPro::varpro() call in vignettes/reproducible-seeds.qmd to match.

All vignettes migrated from R Markdown (.Rmd) to Quarto (.qmd). Added quarto to Suggests.

read_clinical_data(): CSV files are now read with check.names = FALSE so column names containing spaces, hyphens, or special characters are preserved exactly as written, preventing silent name mangling that could break downstream label lookups.

Added generate_survival_data(): generates a synthetic cardiac surgery survival cohort with 22 clinical variables, Weibull-distributed survival times, reoperation outcome, and variable labels

Fixed r_data_types() silently corrupting Date, POSIXct, and POSIXlt columns that had exactly 2 unique values (they were converted to logical)
Fixed r_data_types() incorrectly converting constant columns (1 unique value) to logical; binary detection now requires exactly 2 unique values
Fixed r_data_types() producing a cryptic “missing value where TRUE/FALSE needed” error when factor_size = NaN
Fixed r_data_types() giving a misleading “not found in dataset” error when skip_vars was not a character vector
Fixed generate_survival_data() producing NaN in iv_reop for patients with very short follow-up times
Fixed generate_survival_data() permanently altering the global RNG state; the session’s RNG is now saved and restored on exit

r_data_types() now validates all inputs before doing any work, so errors are raised immediately with clear messages
r_data_types() input validation now explicitly checks that dataset is a data.frame, skip_vars is a character vector, and factor_size is not NaN
generate_survival_data() now uses labelled::var_label() consistently to attach labels instead of attr() directly
Removed leftover if (interactive()) development block from generate_survival_data.R
Added new vignette survival-data demonstrating generate_survival_data() and its integration with r_data_types() and label_map()

Added 27 tests for generate_survival_data() covering structure, column types, outcome validity, reproducibility, RNG side-effect safety, and variable labels
Updated POSIXct test to verify preservation without skip_vars (the previous test only verified the skip_vars workaround)
Strengthened idempotency test to assert full value equality across sequential conversions, not just column class equality
Updated skip_vars type-error test to match the improved error message

Fixed critical bug in r_data_types() where dplyr::na_if() was called with a vector instead of scalar values
Fixed bug where character columns with 2 unique values were incorrectly converted to logical (returning all NAs)
Fixed bug in sample_data() where sample.int() parameters were reversed, causing errors for small sample sizes
Fixed column order preservation bug in r_data_types() when using skip_vars - columns now maintain original order
Fixed silent parameter mutation bug where factor_size > 50 was changed to 20 without user consent - now errors instead

Removed unused lubridate dependency that was never actually used in the package
Removed inappropriate use of invisible() from label_map() and r_data_types() functions
Implemented hvtiRutilities.news() function that was referenced but didn’t exist
Completely rewrote test suite with modern testthat 3 syntax (removed deprecated context() calls)
Expanded test coverage from 24 tests to 75 comprehensive tests
Added proper examples to label_map() documentation with @examples tag
Improved error messages for better clarity and consistency
Changed == TRUE comparisons to simpler boolean checks

Complete rewrite of README.md with actual package description and usage examples
Fixed label_map() documentation (was incomplete sentence, wrong return type)
Improved r_data_types() documentation with clearer parameter descriptions
Added comprehensive usage examples for all main functions