Additional CRAN feedback addressed in resubmission:
The \dontrun{} block in the sarscov2_variants dataset example that calls References$display() (which requires DT, in Suggests) was missed in the prior audit. The block is now wrapped in if (interactive() && requireNamespace("DT", quietly = TRUE)), the CRAN-recommended pattern for examples that depend on Suggests packages and are intended for interactive use.
ViralEntropR 0.6.1
Additional fixes discovered during local verification of the resubmission:
Fix spurious “windows will be empty” warnings in partition_time_windows(). The warning predicate previously compared end_date against max(data$Date) directly, which fires whenever end_date is at all past max(data$Date) — even when the last window correctly contains the trailing data. The fix compares against the left boundary of the last window instead, so the warning fires only when one or more trailing windows would actually be empty. Mirror logic applies to start_date. The function’s partition output was always correct; only the warning fires more accurately now.
Update detect_changepoints_ecp() example: last example referenced $cpLoc[[1]], which is the zero-change-point case (always empty under ks.cp3o’s indexing). The example line has been removed to avoid user confusion.
Improve example clarity for tabulate_site_evolution(): display the underlying data frame ($table) rather than the kableExtra HTML object ($styled), which prints as raw HTML text outside R Markdown contexts. The styled HTML still renders correctly in vignettes and interactive use.
Redesign the examples for plot_entropy_trajectories() and plot_site_class_trajectory() to use three-period synthetic datasets with distinct trajectory shapes and visible class changes across partitions, producing more pedagogically useful reference output. Added expansion(add = 0.6) to the plot_entropy_trajectories() x-axis scale so rotated tick labels at the leftmost partition are no longer clipped.
ViralEntropR 0.6.1
Address CRAN initial-review feedback:
Expand “NCBI” on first use in DESCRIPTION.
Remove @examples blocks from internal functions (get_site_counts, build_distance_matrix, get_variants), which eliminates the ::: usage previously required to call them.