Evaluates a range of prevalence thresholds for DA analysis

Usage

# S3 method for class 'prev.eval'
basin(
  object,
  y,
  basin.vertices,
  counts,
  prevalences = seq(0.05, 0.5, by = 0.05),
  min.count = 10L,
  plot.pdf = NULL,
  X.rel = object,
  ...
)

Arguments

object: Relative abundance matrix (samples × features)
y: Binary response vector (named and aligned to samples)
basin.vertices: Vector of vertex IDs for subsetting
counts: Raw count matrix (features × samples)
prevalences: Numeric vector of prevalence thresholds (0–1)
min.count: Integer minimal count threshold for inputs
plot.pdf: Path to save diagnostic plots (optional)
X.rel: Backward-compatible alias for object.
...: Additional arguments (currently ignored).

Value

A list with summary metrics and detailed outputs by prevalence