Prepare 0.8.0 CRAN release#294
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Consolidate NEWS, bump version 0.7.6 -> 0.8.0, and fix R CMD check NOTEs ahead of the CRAN submission (CRAN currently has 0.7.4). - NEWS.md: collapse the GitHub-only 0.7.5/0.7.6 dev sections plus the merged backend/xgboost work (#292, #293) into a single categorized 0.8.0 section; drop the duplicate Enhancements heading. - DESCRIPTION: Version 0.8.0, Date 2026-06-17. - .Rbuildignore: exclude dev/check artifacts (Rplots.pdf, Rprof.out, *.Rcheck, *.tar.gz, *.patch, *.RData, attic, agent notes) so they cannot leak into the build tarball (fixes "Non-standard files at top level" NOTE). - R/zzz.R: register gg_state_occupation() NSE column names as global variables (fixes "no visible binding" NOTE). - R/add-functions.R: qualify utils::head() in get_cif() (fixes "no visible global function" NOTE). - R/as-ped.R: document forwarded `id`/`combine` in as_ped()'s `...` instead of as orphaned @param tags, and re-home @param combine on as_ped_cr where it is a formal argument (fixes "documented arguments not in usage" NOTE). - R/sim-ic.R: add_inspections() example \dontrun -> \donttest (runs in ~2s). - man/: regenerate (also syncs previously stale Rd, e.g. the missing maintainer entry on the package help page). - cran-comments.md: refresh for 0.8.0. Local R CMD check --as-cran: 0 errors | 0 warnings | 0 notes (the only local NOTE is the machine-specific "HTML Tidy not found"). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
gg_state_occupation() was defined identically in two files; R/ggplot-extensions.R
won by source-collation order, leaving R/gg_state_occupation.R as dead code
(and stale: it still carried the removed group_labels/nrow parameters). Delete
the dead file.
Address the "no visible binding for global variable" NOTE at the source by
referencing NSE column names through the .data pronoun / tidyselect strings in
the live gg_state_occupation() (trans_prob_matrix, df_long, time, prob, state),
instead of widening the package-wide utils::globalVariables() allowlist with
generic names. Revert zzz.R to the minimal c(".", "id") set.
Local R CMD check --as-cran: 0 errors | 0 warnings | 0 notes
(only the machine-specific "HTML Tidy not found" NOTE remains).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Pull request overview
Prepares the pammtools 0.8.0 CRAN release by bumping version metadata, consolidating release notes, addressing R CMD check --as-cran NOTE/doc issues, and regenerating Rd files (including removing a stale duplicate implementation of gg_state_occupation()).
Changes:
- Bump package version/date to 0.8.0 and refresh CRAN submission metadata (DESCRIPTION, cran-comments, build ignore patterns).
- Fix/adjust documentation and NSE-related code to satisfy
R CMD check(e.g.,.datapronoun usage,utils::head(), roxygen/Rd updates, donttest examples). - Remove dead/duplicate
gg_state_occupationsource file and keep the exported implementation inR/ggplot-extensions.R.
Reviewed changes
Copilot reviewed 9 out of 20 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| R/sim-ic.R | Switch example from \\dontrun to \\donttest for faster runnable checks. |
| R/ggplot-extensions.R | Adjust gg_state_occupation() internals to use .data/tidyselect-safe column access. |
| R/gg_state_occupation.R | Remove stale duplicate implementation (dead code). |
| R/as-ped.R | Roxygen updates: document forwarded id/combine via ..., adjust CR docs. |
| R/add-functions.R | Qualify head() as utils::head() to avoid namespace ambiguity. |
| NEWS.md | Consolidate release notes into a single categorized 0.8.0 section. |
| man/split_data.Rd | Sync Rd with updated ... forwarding docs (id/combine). |
| man/split_data_multistate.Rd | Sync Rd with updated ... forwarding docs (id/combine). |
| man/pammtools.Rd | Add maintainer entry to package help page. |
| man/interval_censored.Rd | Sync Rd with updated ... forwarding docs (id/combine). |
| man/geom_stepribbon.Rd | Clean up Rd metadata (remove incorrect \\docType{data}/datasets keyword). |
| man/geom_hazard.Rd | Clean up Rd metadata (remove incorrect \\docType{data}/datasets keyword). |
| man/as_ped.Rd | Sync Rd with updated ... forwarding docs; remove mismatched args from usage. |
| man/as_ped_cr.Rd | Re-home/clarify combine docs for competing risks variant. |
| man/add_trans_prob.Rd | Update examples wrapper (simplify withAutoprint usage). |
| man/add_inspections.Rd | Switch example from \\dontrun to \\donttest. |
| man/add_cif.Rd | Minor documentation tweak for nsim argument text. |
| DESCRIPTION | Bump Version/Date for 0.8.0; update roxygen metadata field. |
| cran-comments.md | Refresh CRAN comments for 0.8.0 submission details. |
| .Rbuildignore | Add/adjust ignore rules for dev/check artifacts and generated files. |
Files not reviewed (11)
- man/add_cif.Rd: Generated file
- man/add_inspections.Rd: Generated file
- man/add_trans_prob.Rd: Generated file
- man/as_ped.Rd: Generated file
- man/as_ped_cr.Rd: Generated file
- man/geom_hazard.Rd: Generated file
- man/geom_stepribbon.Rd: Generated file
- man/interval_censored.Rd: Generated file
- man/pammtools.Rd: Generated file
- man/split_data.Rd: Generated file
- man/split_data_multistate.Rd: Generated file
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Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Release preparation for the next CRAN submission. CRAN currently has 0.7.4; this bundles the GitHub-only 0.7.5/0.7.6 dev versions plus the merged backend/xgboost/interval-censored work into 0.8.0.
What's in here
0.8.0section covering make gg_smooth terms interface fully general #284/[codex] Add prediction-grid boundary rows #287/Use type-6 quantiles for simulation-based CIs (fixes #288) #289/Full support for shape-constrained PAMMs via scam (closes #286) #290/Add interval-censored survival support via multiple imputation #291/Consolidated PRs #284, #287, #289, #290, #291 and consistent t=0 boundary rows, shared simulation draws, and S3 dispatch fixes foradd_*functions #292/Simplified & streamlined inference backend + vignette for xgboost backend #293 (scam engine, interval-censored MI workflow, pluggableget_hazard/sim_hazardinference backend + xgboost vignette, type-6 sim-CI quantiles,make_newdatabreaking change, boundary rows,gg_smoothgeneralization). DuplicateEnhancementsheading removed.0.7.6→0.8.0, Date2026-06-17.R CMD check --as-cranNOTE fixes:.Rbuildignore: exclude dev/check artifacts (fixes "non-standard files at top level").R/ggplot-extensions.R: use the.datapronoun / tidyselect strings for NSE column names ingg_state_occupation()(fixes "no visible binding").R/add-functions.R:utils::head()qualification.R/as-ped.R: document forwardedid/combinevia..., re-home@param combineonas_ped_cr(fixes "documented arguments not in usage").R/gg_state_occupation.R, an identical-but-stale duplicate of thegg_state_occupation()inR/ggplot-extensions.R(shadowed by collation order; still carried the removedgroup_labels/nrowargs).R/sim-ic.R:add_inspections()example\dontrun→\donttest(runs in ~2s).Checks
Local
R CMD check --as-cran(incl.--run-donttest+ PDF manual): 0 errors | 0 warnings | 0 notes (only a machine-local "HTML Tidy not found" NOTE).Reviewed by an external multi-model panel (Codex/Gemini/Claude).
reverse-dependency check (
revdepcheck) and R-hub/win-builder runs are in progress / to follow.🤖 Generated with Claude Code