# L-Infinity Normalization and Dominant Community State Types

## Documentation for package ‘linf’ version 0.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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