dsh-revbayes-forge-pack-coalescent-demography

Coalescent and Demography pack

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

English

• Pack id: coalescent-demography
• Tool: revbayes_generate_coalescent
• Maturity: verified (enabled by default)

What it generates. Builds coalescent scripts for the multispecies coalescent (alignment plus guide species tree and population size), coalescent skyline plots with piecewise population windows, and StairwayPlot analyses driven by a site-frequency spectrum array. Locus/species mappings, positive population sizes, and non-negative SFS entries are validated before generation.

Analyses.

Analysis	Title	Canonical golden
multispecies_coalescent	Multispecies coalescent	multispecies_coalescent.Rev
skyline	Coalescent skyline	skyline.Rev
stairwayplot	StairwayPlot	stairwayplot.Rev

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：coalescent-demography
• 工具：revbayes_generate_coalescent
• 成熟度：verified（默认启用）

生成内容。 生成溯祖脚本：多物种溯祖（比对数据 + 引导物种树 + 群体大小）、分段群体窗口的 coalescent skyline，以及由位点频谱数组驱动的 StairwayPlot 分析。生成前校验 locus/物种映射完整、群体大小为正、SFS 条目非负。

分析列表。

Analysis	Title	Canonical golden
multispecies_coalescent	Multispecies coalescent	multispecies_coalescent.Rev
skyline	Coalescent skyline	skyline.Rev
stairwayplot	StairwayPlot	stairwayplot.Rev

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。