Self-contain vignettes/examples on bundled data; label interaction scale#2
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Removes the last dependency on the Suggests-only NHANES package and makes the
additive-interaction scale explicit in the output. R CMD check --as-cran
--run-donttest remains clean (0 errors, 0 warnings, 1 expected NOTE).
Vignettes (now build without NHANES installed):
- Convert v1, v2, v3, v5 off NHANESraw onto the bundled nhanes_mortality cohort
(hypertension / insulin / caffeine analyses); fix the malformed inline setup
chunks in v1 and v2.
- v4 already used bundled data; guard its mitools (Suggests) use with
eval = requireNamespace("mitools", ...) and qualify mitools::imputationList.
Interaction interpretation safety:
- addintlist() now returns a `Scale` column ("OR (logistic)", "HR (Cox)",
"RR (log-binomial)", "RR (Poisson)", or "ratio") inferred from the model, so
the effect-measure scale of RERI/AP/S is visible in the output itself.
- Document the rare-outcome RR-vs-OR caveat in addint() and addintlist()
@details, citing VanderWeele and Knol (2014).
Self-containment:
- Convert the remaining NHANES examples (addintlist, jointeffects, plotint,
svytable1, svydiag) to bundled data; svytable1/svydiag stay runnable (plain)
examples, verified fast and lonely-PSU-safe.
- Drop NHANES from Suggests (no longer referenced anywhere).
Tests: 69 passing (adds Scale-column and svykmplot se = TRUE coverage).
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Removes the last dependency on the Suggests-only NHANES package and makes the additive-interaction scale explicit in the output. R CMD check --as-cran --run-donttest remains clean (0 errors, 0 warnings, 1 expected NOTE).
Vignettes (now build without NHANES installed):
Interaction interpretation safety:
Scalecolumn ("OR (logistic)", "HR (Cox)", "RR (log-binomial)", "RR (Poisson)", or "ratio") inferred from the model, so the effect-measure scale of RERI/AP/S is visible in the output itself.Self-containment:
Tests: 69 passing (adds Scale-column and svykmplot se = TRUE coverage).