Vignette overhaul and "Get started" vignette

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Valutazione

Difficoltà
4/5
Tempo stimato
Più di una settimana
Idoneità per principianti
15/100
Tipo di issue
Documentazione
Chiarezza
Abbastanza chiara
Stato di attività
Attiva
Stack tecnologico
markdown, r
Ambito
documentation

Direzione di ricerca

This is a multi-part tracking issue, not a single task: it covers a new Get started vignette, errata in basic_cea, psa_analysis, psa_generation, dsa_generation and voi, and removing unused files. Start with the vignettes/ directory and the specific error list under Fix the audit's errors. Done means each listed correction is made and the vignettes build in under two minutes, which requires a reviewer other than the author.

Scritto dal modello di indicizzazione a partire dal testo della issue.

Descrizione

documentation

Suggested owner: Eva Enns (an author and a second reviewer per vignette) · Plan: Phase 4

Goal

Vignettes that teach the methods correctly and build quickly. Fix the errors the audit found.

Scope

  • New vignettes/dampack.Rmd ("Get started"): a 5-minute end-to-end example covering ICERs, the PSA object, CEAC/ELC and EVPI. It becomes the pkgdown "Get started" page.
  • Reading order: Get started → basic_cea → psa_analysis → voi → psa_generation → dsa_generation.
  • Every vignette:
    • Learning objectives.
    • Methods with formulas: dominance, extended dominance, ICER, NMB/NHB, CEAC versus ELC and the frontier, EVPI/EVPPI/EVSI with the metamodel approach.
    • Interpretation.
    • References from a shared vignettes/references.bib.
    • set.seed() and DARTH naming in the example code.
  • Fix the audit's errors:
    • basic_cea: says the class is "icer" (it is icers); says "cdiff_psa" (the data is psa_cdiff); has an icer_diff typo; never shows print.icers or calculate_icers_psa.
    • psa_analysis:
      • The NMB/NHB formula text says "added to" where it should say subtracted.
      • The tornado text describes a median split, but the code uses the range min/max.
    • psa_generation:
      • Points to the wrong vignette.
      • Relies on partial argument matching (n = 100, effect =).
      • Says "Effect" where it should say "QALY".
      • Ends without any analysis.
    • dsa_generation: l_twsa_det$owsa_NMB typo; add the tornado diagram (#185).
    • voi: wrong help links ?make_psa_object and ?calculate_outcomes; says "adjusted r-squared" but lm reports the unadjusted value; cite Strong et al. 2014 in the vignette text.
  • Remove the unreferenced vignettes/icer_cdiff.png (186 KB) and vignettes/cdiff_icers.csv.
  • Speed: cut the 10,000-sample metamodel runs, or move heavy material to pkgdown-only articles (vignettes/articles/, build-ignored).
  • Close #147: dsa_visualization no longer exists. File a v1.2 issue for a "bring your own DSA data" section.

Acceptance

  • All vignettes build from a clean install, without load_all, in under 2 minutes total.
  • Each vignette has been reviewed by someone other than its author.
Lingua principale
R
Stelle
43
Fork
14
Merge medio
4h 44m
PR unite (30g)
15

Preparare l'ambiente

Come iniziare

  1. Leggi tutta la issue e poi la guida ai contributi del progetto.
  2. Commenta sulla issue per dire che te ne occupi tu — evita che due persone facciano lo stesso lavoro.
  3. Fai un fork del repository e lavora su un branch.
  4. Apri una pull request che faccia riferimento al numero della issue.

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