Follow mlumr main at 965dfc5 and correct four stale statements - #117
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The lesson loaded mlumr's R code, and described its behavior, at commit 4cfd366 (September 12). Four things it taught changed on main since then: * check_identification() no longer reports target_in_span, target_in_declared_span or target_span_gap (#101). Chapter 11's narration and the package notes described that target check. * predict(), marginal_effects() and the conditional summaries no longer carry n_draws and n_draws_used; they warn once when they leave out NA or NaN draws (#104). Chapter 12's narration, the Incomplete summary card, the report checklist and the capstone asked for those counts. * The checks on tied reconstructed event times that refused or warned before sampling are gone (#100). The survival distributions panel and the notes still named them. * For a normal outcome with an identity link, autoscale = TRUE and the default priors carry the IPD outcome SD (#115). The priors panel and the notes said only that autoscale divides by the covariate SD. What changes: * lesson.sh pins mlumr 965dfc5; README, sources.html and the package notes link that commit. The binomial Stan programs are identical, so the WebAssembly models stay. * Two narration sentences (chapters 11 and 12) and the panel, card, checklist and capstone text above are corrected. The survival panel and the notes now say that any at_time other than 0 is refused under a shared baseline, as the package does. * sources.html adds the published ISPOR Europe 2025 abstract next to the preprint, as the package README does. * workflow.R passes prior_beta_comparator to the relaxed model only; the SPFA refits used to receive it and print the package's warning twice. * scenes/native-record.json is rerun at 965dfc5. Every fitted number is unchanged to the last recorded digit; only the commit, the compiled code's hash, the script hash and the run time differ. * dist/ rebuilt: narration 1686.81 s, only the three changed caption lines differ. Checks: lesson.sh test (74 unit tests), the adapter against a native checkout at 965dfc5 (22 checks, Stan data equal to the package's), dist-manifest verify, and browser-qa.mjs with the R and Stan runtimes (0 errors, both browser fits). Every function and named argument the lesson uses exists at 965dfc5. QA.md and package-notes.md record the runs.
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Inline comments:
In `@QA.md`:
- Line 17: Update the example commands in QA.md to use a shell-safe source-path
placeholder instead of the angle-bracket placeholder, which the shell interprets
as redirection. Show how to set a quoted path variable and use it in both
commands.
In `@scenes/content.ts`:
- Line 86: Update the no-screening statement in `survivalChoices` to limit it
specifically to tied event times; preserve the surrounding guidance and do not
imply that reconstructed survival times receive no pre-fit validation.
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dist/audio.m4ais excluded by!**/dist/**,!**/*.m4adist/audio.webmis excluded by!**/dist/**,!**/*.webmdist/build-manifest.jsonis excluded by!**/dist/**dist/captions.vttis excluded by!**/dist/**dist/player.jsis excluded by!**/dist/**dist/r/DESCRIPTIONis excluded by!**/dist/**dist/r/NAMESPACEis excluded by!**/dist/**dist/r/R/mlumr.Ris excluded by!**/dist/**dist/r/inst/stan/include/survival_functions.stanis excluded by!**/dist/**dist/r/inst/stan/include/survival_mspline_functions.stanis excluded by!**/dist/**dist/sources.htmlis excluded by!**/dist/**dist/tracks.jsonis excluded by!**/dist/**dist/transcript.htmlis excluded by!**/dist/**dist/workflow.Ris excluded by!**/dist/**
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QA.mdREADME.mdlesson.shpackage-notes.mdscenes/content.tsscenes/native-record.jsonscenes/scene.tsscript.mdsources.htmlworkflow.R
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…ll-safe set_agd_surv() still validates the reconstructed survival times, so the survival distributions panel and the package notes now say that mlumr checks the times but no longer screens them for ties before sampling. The QA record's commands use a quoted path variable instead of angle brackets, which the shell reads as redirection. dist/ rebuilt: only player.js and the manifest changed.
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The lesson loaded mlumr's R code, and described its behavior, at commit
4cfd366 (September 12). Four things it taught changed on main since then:
target_in_declared_span or target_span_gap (Trim the identification screen, the engine setter and the repository CI #101). Chapter 11's
narration and the package notes described that target check.
carry n_draws and n_draws_used; they warn once when they leave out NA
or NaN draws (Drop the source fingerprints, draw tallies and the copula import #104). Chapter 12's narration, the Incomplete summary
card, the report checklist and the capstone asked for those counts.
before sampling are gone (Let the sampler decide instead of the pre-sampling propriety guards #100). The survival distributions panel and
the notes still named them.
default priors carry the IPD outcome SD (Put the normal family's default priors on the outcome scale #115). The priors panel and
the notes said only that autoscale divides by the covariate SD.
What changes:
notes link that commit. The binomial Stan programs are identical, so
the WebAssembly models stay.
checklist and capstone text above are corrected. The survival panel
and the notes now say that any at_time other than 0 is refused under
a shared baseline, as the package does.
the preprint, as the package README does.
SPFA refits used to receive it and print the package's warning twice.
unchanged to the last recorded digit; only the commit, the compiled
code's hash, the script hash and the run time differ.
lines differ.
Checks: lesson.sh test (74 unit tests), the adapter against a native
checkout at 965dfc5 (22 checks, Stan data equal to the package's),
dist-manifest verify, and browser-qa.mjs with the R and Stan runtimes
(0 errors, both browser fits). Every function and named argument the
lesson uses exists at 965dfc5. QA.md and package-notes.md record the
runs.
Summary by CodeRabbit