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Submission

This is an update of mlumr from 0.1.0, which is on CRAN, to 0.2.0. NEWS.md lists the changes. The largest are time-to-event outcomes (parametric and M-spline baselines, fitted to reconstructed Kaplan-Meier data) and prediction of marginal effects in arbitrary target populations.

R CMD check results

Local R CMD check --as-cran --no-manual mlumr_0.2.0.tar.gz on macOS 27.0.1 (aarch64-apple-darwin23), R 4.6.0:

  • 0 errors
  • 1 warning, environmental: the checkbashisms script is not installed on this machine, so the check reports that "a complete check needs the 'checkbashisms' script." CRAN's Linux servers have it.
  • 0 notes. The CRAN incoming feasibility check reports, as information, that cmdstanr is in Suggests and is not in a mainstream repository. It is available from the declared Additional_repositories: https://mc-stan.org/r-packages.

Tests under --as-cran: [ FAIL 0 | WARN 32 | SKIP 93 | PASS 2853 ]. The 93 skips are the Stan-sampling tests, which are marked skip_on_cran() because each one compiles or samples a model. They run in a separate CI job with NOT_CRAN=true (below), where they pass.

Test environments

  • local macOS 27.0.1 (aarch64-apple-darwin23), R 4.6.0
  • GitHub Actions, R CMD check --no-manual --as-cran, R release: macOS, Windows and Ubuntu. Status OK on all three.
  • GitHub Actions, Ubuntu, R release, full test suite with the Stan tests enabled under CmdStan: 4705 passed, 0 failed, 0 skipped.

Reverse dependencies

None. No CRAN package depends on, imports, suggests or links to mlumr.

Notes to CRAN reviewers

  • The package embeds ten Stan models: binomial, normal and Poisson, each with SPFA and relaxed variants, plus parametric and M-spline survival in both variants. They are compiled at install time through the standard rstantools pipeline, so installation takes several minutes of C++ compilation.
  • The installed size is 14.9 Mb: libs 10.2 Mb (the compiled Stan models), R 2.1 Mb and doc 2.0 Mb. As with other Stan-backed packages such as rstanarm and brms, the shared library dominates. The source tarball is 1.9 Mb.
  • cmdstanr is an optional backend. rstan is the default engine and is on CRAN. Examples and tests do not require cmdstanr, and the cmdstanr comparison code is skipped unless cmdstanr and CmdStan are available.
  • Seven of the nine vignettes fit Stan models, so they are pre-rendered and shipped through the R.rsp::asis engine; re-building them runs no Stan. The other two are knitr vignettes: introduction evaluates no code, and data-preparation runs data-setup code only, with no model fitting.