mill: The sawmill Pipeline

In iAM-AMR/sawmill: Process Queries from the CEDAR Database

The sawmill Pipeline

Description

The mill() runs the sawmill pipeline with useful defaults.

Usage

mill(
  timber_path,
  low_cell_threshold = 0,
  low_cell_correction = 0.5,
  log_base = exp(1)
)

Arguments

timber_path	String: a path to a timber file.
low_cell_threshold	Numeric: the two-by-two (contingency) table cell count at which (or lower) the Haldane correction (alt: Woolf-Haldane correction, Haldane-Anscombe correction) should apply.
low_cell_correction	Numeric: the value of the Haldane correction to apply; must be > 0.
log_base	Numeric: the logarithmic base to use when calculating the log(Odds Ratio), and the standard error of the log(Odds Ratio).

iAM-AMR/sawmill documentation built on June 30, 2024, 2:25 a.m.