Analysis code for a transport diagnostic of a calibrated intra-host variant detection filter in Mycobacterium tuberculosis

R pipeline that tests whether a replicate-anchored intra-host single nucleotide variant (iSNV) detection filter, calibrated on a higher-depth Ghana Mycobacterium tuberculosis cohort, transfers to a lower-depth Florida TB surveillance archive. Two transport tests: a per-specimen prevalence-band test (T1) and a within-cluster Jaccard-versus-depth slope test (T2), plus a post-hoc hurdle decomposition separating the extensive and intensive margins of depth-detection coupling. Companion code to: Séraphin MN et al. Can a calibrated intra-host variant detection filter transfer across sequencing depth regimes? A transport diagnostic for Mycobacterium tuberculosis genomic epidemiology. (in preparation, 2026).