linf 0.3.0

This release simplifies the public API and requires the explicit dCST object structure introduced in linf 0.2.0.

• refine.linf.csts() now supports both automatic and explicit dominance-lineage selection through lineages.to.refine; it can be called repeatedly to add successive hierarchy depths.
• refine.linf.csts.iter() has been removed in favor of repeated calls to refine.linf.csts().
• The narrow convenience wrapper asv.to.linf.csts() has been removed. Use filter.asv(), normalize.linf(), and linf.csts() explicitly so that each stage and its dCST parameters remain visible.
• The standalone formatter latex.linf.csts() has been removed; dCST summary tables can be formatted with general reporting tools such as knitr::kable().
• Pre-0.2 flat dCST objects are no longer accepted. Functions consuming fitted dCSTs now require the explicit active, pure-policy, and absorb-policy hierarchies produced by linf.csts().

linf 0.2.0

This release adopts the dominance-sample-set and dominance-lineage terminology used in the methods paper. It is intentionally a breaking release: obsolete cell-based names and compatibility aliases are not retained.

• linf.cells() is replaced by linf.dominant.features().
• dCST assignments now use lineage.id, lineage.label, lineage.ids, and lineage.labels. Depth-1 feature assignments use depth1.feature.index.
• Retained and provisional depth-1 features now use the retained.feature.* and provisional.feature.* fields.
• Pure- and absorb-policy fields now end in .pure and .absorb, respectively.
• cells.to.refine is replaced by lineages.to.refine.
• Landmark summaries are returned in lineages, with lineage.id, lineage.label, and lineage.size columns.
• collapse.rare() and expand.rare() are replaced by dcst.view(csts, view = "absorb") and dcst.view(csts, view = "pure").
• The deprecated "rare" low-frequency policy and view alias has been removed; use "pure".