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().lineage.id,
lineage.label, lineage.ids, and
lineage.labels. Depth-1 feature assignments use
depth1.feature.index.retained.feature.* and provisional.feature.*
fields..pure and
.absorb, respectively.cells.to.refine is replaced by
lineages.to.refine.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")."rare" low-frequency policy and view
alias has been removed; use "pure".