Package: linf 0.3.1

linf: L-Infinity Normalization and Dominant Community State Types

Implements L-infinity normalization for compositional matrices, assigns samples to dominant features, constructs truncated and hierarchically refined dominant community state types, constructs unordered dominance sets with support-based sample filtering, and computes representative landmark profiles. The methods are described by Gajer and Ravel (2025) <doi:10.48550/arXiv.2503.21543>. Bundled vaginal and gut microbiome data support reproducible demonstrations of the package interface; phenotype fields in the stratified gut subset are illustrative and are not suitable for population-level inference.

Authors:Pawel Gajer [aut, cre]

linf_0.3.1.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
linf/json (API)

# Install 'linf' in R:
install.packages('linf', repos = c('https://pgajer.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pgajer/linf/issues

Pkgdown/docs site:https://pgajer.github.io

Datasets:

On CRAN:

Conda:

5.51 score 342 downloads 13 exports 2 dependencies

Last updated from:810a0a8478. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK132
source / vignettesOK198
linux-releaseOK143
macos-releaseOK103
macos-oldrelOK102
windows-develOK89
windows-releaseOK103
windows-oldrelOK102
wasm-releaseOK93

Exports:dcst.viewfilter.asvlinf.cstslinf.dcst.landmark.pipelinelinf.dominant.featureslinf.feature.labelslinf.hypercube.embeddinglinf.landmarkslinf.udcst.graphlinf.udcstsnormalize.linfrefine.linf.cststransfer.dcsts

Dependencies:latticeMatrix

Finding your way around linf
Choose a task | A small workflow, with stopping points | Function catalog | Prepare and assign | Fit and inspect a hierarchy | Reuse and display | Matrix and identity conventions | Unordered dominance sets | Filtering, scaling and grouping answer different questions | Ties and random seeds | What a dCST hierarchy stores | Refinement choices | Landmarks are selected observations | The optional pipeline | Transfer to a frozen reference | Inspect a transfer decision and saved refinement settings | Embeddings and display labels | Resource planning | Finding help and migrating older code | Triple-supported pair-state graphs
Rendered fromfunction-guide.Rmdusingknitr::rmarkdown

Last update: 2026-10-04
Started: 2026-09-15

Example datasets and reproducible workflows
Choose a dataset | Provenance and scope | Gut counts | Valencia abundance data and saved assignments | Four-component data | Align data and metadata | Constructed edge cases | Reference and query | A static chart from the four-component data
Rendered fromexample-datasets.Rmdusingknitr::rmarkdown

Last update: 2026-09-15
Started: 2026-09-15

Dominant Community State Types: From Normalization to a Gut Demonstration
Part 1: Quick Start with Toy Data | L-infinity normalization | Dominance sample sets | Truncated dCSTs | Part 2: Gut Microbiome dCST Demonstration | Background | The data | Step 1: Quality filtering | Step 2: L-infinity normalization | Step 3: Depth-1 dCSTs | How sensitive is depth 1 to the support threshold? | Step 4: Depth-2 refinement | Dominance strength | dCST size distribution | Phenotype metadata | Limitations | Summary
Rendered fromlinf-intro.Rmdusingknitr::rmarkdown

Last update: 2026-09-15
Started: 2025-09-25

dCSTs for Vaginal Microbiome Data
Introduction | The Valencia 2k dataset | Reconstructing counts | $L^\infty$ normalization | Dominance sample sets: dominant species assignment | Depth-1 dCSTs | Concordance with Valencia CSTs | Depth-2 refinement | Concordance with Valencia sub-CSTs | The full pipeline | Landmark points | Summary | References
Rendered fromlinf-vaginal.Rmdusingknitr::rmarkdown

Last update: 2026-09-15
Started: 2026-03-25