menobis filter

TL;DR

Use menobis filter to classify observed edges as upper-significant, lower-significant, or compatible with an independent MENoBiS null model.

Commands

Command	Null model	Input
strength-poisson	fit strength Poisson	edge table
strength-cost-poisson	fit strength-cost Poisson	edge table + coordinates CSV
strength-edges-poisson	fit strength-edges Poisson (zero-inflated)	edge table
strength-degree-poisson	fit strength-degree Poisson (zero-inflated)	edge table
degree-events-poisson	fit degree-events Poisson (zero-inflated)	edge table
custom-poisson	user-supplied Poisson rates	edge table + rates CSV

Examples

menobis filter strength-poisson edges.csv --output-prefix filtered/
menobis filter strength-edges-poisson edges.csv --target-edges 500 --output-prefix filtered/
menobis filter strength-cost-poisson edges.csv --coordinates xy.csv --target-cost 1.5 --output-prefix filtered/
menobis filter strength-degree-poisson edges.csv --output-prefix filtered/
menobis filter degree-events-poisson edges.csv --output-prefix filtered/
menobis filter custom-poisson edges.csv --rates rates.csv --output-prefix filtered/

Outputs

--output-prefix DIR writes:

File	Meaning
upper.csv	observed edges heavier than expected
lower.csv	observed positive edges lighter than expected
compatible.csv	observed edges compatible with the null
absent_lower.csv	absent pairs that should exist under the null

Each file contains p-values, expected occupation, and occupation probability.

Options

Option	Meaning
--alpha	significance level
--tail	upper, lower, or two-sided
--correction	none, bonferroni, or fdr
--detect-absent	stream absent-pair candidates
--min-occupation	absent-edge occupation threshold
--min-expected	absent expected-weight threshold
--max-absent	cap absent output size
--self-loops/--no-self-loops	diagonal handling
--target-edges	target edge count (strength-edges-poisson)
--target-cost	target total cost \(\sum t_{ij}d_{ij}\) (strength-cost-poisson)
--coordinates	Projected XY coordinate CSV path (strength-cost-poisson)
--rates	rates CSV path (custom-poisson)