L-Infinity Normalization and Dominant Community State Types

Documentation for package ‘linf’ version 0.1.0

agp_gut	American Gut Project gut microbiome dataset
asv.to.linf.csts	From counts to filtered, normalized, truncated dCSTs
collapse.rare	Switch a dCST hierarchy to the "absorb" view (collapse rare buckets)
expand.rare	Switch a dCST hierarchy to the "rare" view (explicit rare buckets)
filter.asv	Filter ASV count matrix by library size (samples) and prevalence (features)
latex.linf.csts	Render dCSTs as a LaTeX table
linf.cells	Dominant-feature assignment
linf.csts	Truncated dominant community state types with configurable low-support handling
linf.dcst.landmark.pipeline	Landmark-aware dCST pipeline
linf.feature.labels	Format feature labels for dominant-feature assignments and dCSTs
linf.hypercube.embedding	Extended homogeneous-coordinate hypercube embedding
linf.landmarks	Landmark points for dCST dominance-lineages
normalize.linf	L-infinity normalization (row-wise)
print.linf.csts	Print method for '"linf.csts"'
refine.linf.csts	Refine a dCST hierarchy by one level
refine.linf.csts.iter	Iteratively refine dCSTs by one additional level
summary.linf.csts	Summarize dCST hierarchy statistics
transfer.dcsts	Transfer samples into a frozen dCST hierarchy
valencia13k_dcst_depth2_merged	Valencia 13k merged depth-2 dCST assignments
valencia13k_dcst_depth3_merged	Valencia 13k merged depth-3 dCST assignments
valencia2k	Valencia 2k vaginal microbiome dataset
valencia_linf_hypercube_1k	Valencia 1k four-component hypercube embedding example