dsh-revbayes-forge-pack-dating-clock

Dating and Clocks pack

Development fixture package dsh-revbayes-forge-pack-dating-clock of the RevBayes Forge plugin (dsh-revbayes-forge).

English

• Pack id: dating
• Tool: revbayes_generate_dating
• Maturity: verified (enabled by default)

What it generates. Builds divergence-time scripts: strict or relaxed (lognormal/exponential) clocks over a rooted time tree, relative age constraints from a constraints file, sequential Bayesian dating, and TimeFIG dating that combines clock models with feature-informed groups (requires the biogeo pack). Calibrations map to node densities, and invariant checks enforce a rooted time tree, constraint/root-age compatibility, and positive clock rates.

Analyses.

Analysis	Title	Canonical golden
strict_clock	Strict clock	strict_clock.Rev
relaxed_clock	Relaxed clock	relaxed_clock.Rev
relative_constraints	Relative constraints	relative_constraints.Rev
sequential	Sequential Bayesian	—
timefig_dating	TimeFIG dating	—

Full spec fields, data requirements, and limitations: docs/en/model-packs.md.

Fixtures. Files under fixtures/ are synthetic small datasets shipped with the repository; they back the golden scripts, canonical specs, and runtime checks used by npm test and npm run test:runtime.

Enablement. Enable this pack in the settings page (RevBayes Forge → Packs); no separate installation is needed.

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中文

• Pack id：dating
• 工具：revbayes_generate_dating
• 成熟度：verified（默认启用）

生成内容。 生成分歧时间脚本：在有根时间树上构建 strict 或 relaxed（lognormal/exponential）分子钟、来自约束文件的相对年龄约束、sequential Bayesian 定年，以及将分子钟模型与 feature-informed 类群结合的 TimeFIG 定年（依赖 biogeo 包）。校准映射为节点密度；不变量检查保证树已定根、约束与根年龄兼容、分子钟速率大于 0。

分析列表。

Analysis	Title	Canonical golden
strict_clock	Strict clock	strict_clock.Rev
relaxed_clock	Relaxed clock	relaxed_clock.Rev
relative_constraints	Relative constraints	relative_constraints.Rev
sequential	Sequential Bayesian	—
timefig_dating	TimeFIG dating	—

完整 spec 字段、数据要求与限制：docs/zh/model-packs.md。

夹具数据。 fixtures/ 下的文件均为随仓库分发的合成小数据，支撑 golden 脚本、canonical spec 与运行时检查，供 npm test 与 npm run test:runtime 使用。

启用方式。 在设置页（RevBayes Forge → Packs）勾选启用即可，无需单独安装。