Evaluate the population spec against one file's thresholded markers

Usage

score_populations(
  tmat,
  thr,
  parent,
  spec = default_population_spec(),
  hi_thr = NULL,
  quiet = FALSE,
  scoped = NULL
)

tmat: matrix of transformed marker values (cells x markers, named cols)
thr: named numeric vector of thresholds
parent: logical mask (the CD45+ parent)
spec: Population specification mapping population name to marker directions. See default_population_spec(). Default default_population_spec().
hi_thr: named numeric: upper bound for "intermediate" requirements. Derived by derive_intermediate_bounds(); a marker requested as "intermediate" without an upper bound makes its population UNAVAILABLE rather than silently collapsing to "above".
quiet: Suppress the per-population NOTEs about any_of groups losing a member. The gate-uncertainty bootstrap re-scores every population once per replicate, and the note is a property of the SPECIFICATION against the PANEL – identical on every replicate, because neither changes. Emitted from there it produced 2,120 of 2,399 log lines on a 20-sample run, 88% of the log saying one of two things, which buries the NOTEs that do differ between samples. Callers that score once leave it FALSE and see it once per sample; callers that score in a loop pass TRUE.
scoped: Cuts derived within parent populations, from derive_scoped_cuts(), or NULL. Used for every marker the specification's cut_scope attribute (see resolve_population_parents()) places within a parent; without it those markers fall back to the CD45+ cut.

list(masks, labels, unavailable)