Vignette overhaul and "Get started" vignette

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評価

難易度
4/5
見積もり時間
1週間以上
初心者へのやさしさ
15/100
issue の種類
ドキュメント
明瞭さ
おおむね明確
活発さ
活発
技術スタック
markdown, r
領域
documentation

調査の方向性

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.

索引モデルが issue の本文から書いたものです。

説明

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.
主要言語
R
スター
43
フォーク
14
平均マージ
4時間 44分
マージ済み PR（30日）
15

環境構築

はじめの一歩

  1. issue を最後まで読み、次にプロジェクトのコントリビューションガイドを読みます。
  2. 着手することを issue にコメントします — 二人が同じ作業をするのを防げます。
  3. リポジトリをフォークし、ブランチを切って変更します。
  4. issue 番号を参照したプルリクエストを送ります。

DARTH-git/dampack のほかの issue

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初心者向けの GitHub issue を短くまとめたダイジェスト。