[lwaldron]

Prepares the manuscript figures and tables for re-running on the next bugphyzz release. No rendered output is included; the pkgdown site is rebuilt once the final export and Zenodo deposit exist.

• Every article takes params$bugphyzz_version (a Zenodo DOI or devel, default devel for now) and calls importBugphyzz(version = ...). The old importBugphyzz(v = 0.5) no longer matches the function signature, and the in-article MCC/R2 filters are redundant since bugphyzzExports applies them at export (bugphyzzExports#67).
• data_integration_and_stats also takes params$validation_tsv (path or URL of a taxPProValidation validation_summary.tsv; empty uses the installed package's copy), so Figure 2 can be rendered for an older validation version. It writes Supplementary Table 1 (sources) and a new Supplementary Table 2 (one row per attribute: type, sources, curated/IBD/ASR counts, taxa, per-value MCC or R2 at rank all) as TSVs next to the output.
• enrichment_dbbact and inst/rmd/bsdb_signatures read Uberon from a pinned release (v2024-05-13) with ontologyIndex; bugsigdbr::getOntology() fails on its download step here. nychanes pins BugSigDB to v1.2.1 like the other articles.

Rendered locally against release v1.0.3 and devel: Figures 1 and 2, the supplementary counts figure, both supplementary tables, the gingival-plaque and NYC-HANES articles; the dbBact article is running.

Drafted with Claude Code.

[claude]

Without validation_tsv, the validation table comes from the installed bugphyzz via the internal bugphyzz:::.validationData(), not from the release named by bugphyzz_version. If you pass a DOI and leave validation_tsv empty, Figure 2 and the new Supplementary Table 2 can show MCC/R2 values from a different version than the annotation counts next to them. Nothing warns about this.

Suggested fixes:

• Make validation_tsv required whenever bugphyzz_version != "devel", or stop() / warning() when the two are inconsistent.
• Replace ::: with an exported accessor. Bioconductor guidelines discourage :::, and an internal rename would silently break the vignette. If no accessor exists, export one in bugphyzz.

[claude]

This chunk writes TSVs to the knit working directory. That is a side effect on the source tree when built with R CMD build/BiocCheck, and the location varies with how the article is rendered (rmarkdown::render vs pkgdown). It also uses an unnamed relative path, and supplementary_table_sources.tsv is not mentioned in the PR's table list.

Fix: take an output directory from a param (e.g. params$out_dir, defaulting to tempdir()), build the path with file.path(), and use readr::write_tsv (readr is already in Imports). Also add *.tsv outputs to .gitignore/.Rbuildignore if they can land in the repo.

[claude]

The new supplementary table has no test or check. Total is n() while Curated + IBD + ASR counts only specific Evidence codes, so any other or NA Evidence value makes the columns stop summing to Total without notice. The join to validation is by tolower(Attribute), so a mismatch gives silent NA in the validation column.

Suggested fixes:

• Add stopifnot(with(supp_attr_tbl, all(Curated + IBD + ASR == Total))) after the table is built.
• Assert that every row has a validation string, or document which attributes are expected to be NA.
• Note that Sources / Type use unique(...)[1], which hides inconsistent values within an attribute.

[claude]

Main points, most important first:

1. Validation/version mismatch (data_integration_and_stats.Rmd). With the default empty validation_tsv, the validation table comes from the installed bugphyzz through internal :::.validationData(). It does not come from the release set by bugphyzz_version, so Figure 2 and Supplementary Table 2 can mix versions silently. Require or warn on this, and use an exported accessor rather than :::.
2. No checks on the new Supplementary Table 2. Curated + IBD + ASR need not equal Total, and the tolower() join to validation can give silent NAs. Add stopifnot assertions.
3. TSVs are written to the knit working directory with a hard-coded relative path. Add an output-directory param (default tempdir()) and use file.path().
4. Unrelated to the diff lines but worth tracking: the default bugphyzz_version = "devel" makes the articles non-reproducible. Pin a DOI before the pkgdown rebuild.

[lwaldron]

1. Added a warning when bugphyzz_version is not devel and validation_tsv is empty, naming the installed bugphyzz version. Kept bugphyzz:::.validationData() because bugphyzz exports no accessor for that table; worth adding there.
2. stopifnot(): Curated + IBD + ASR equals Total for every attribute, and every attribute with ASR annotations has a validation string. The join is by lowercased name because the export lowercases attribute names.
3. New out_dir param (default tempdir()), file.path(), readr::write_tsv(); the sources TSV is now mentioned in the description.
4. Agreed; the default moves to the new Zenodo DOI before the pkgdown rebuild.

Drafted with Claude Code.