valencia13k_dcst_depth2_merged: Valencia 13k merged depth-2 dCST assignments

In linf: L-Infinity Normalization and Dominant Community State Types

Valencia 13k merged depth-2 dCST assignments

Description

A lightweight bundled assignment asset containing merged depth-2 Dominant community state type (dCST) labels for the full Valencia 13k vaginal microbiome training set.

Usage

valencia13k_dcst_depth2_merged

Format

A list with five components:

assignments

Data frame with one row per source sample and columns sample_id (anonymized bundled-data identifier), source_row (row number in the filtered Valencia 13k source), Val_CST, Val_subCST, dcst_depth1, and dcst_depth2.

summaries

Named list of per-depth summary tables. Each table contains depth, dcst_label, n, prop, and path_length.

feature_labels

Character vector of source taxon labels.

params

List recording the construction parameters.

source

Character string documenting provenance.

Details

The asset is computed from the Valencia 13k compositional matrix after L-infinity normalization. dCSTs use n0 = 50 and the merged low.freq.policy = "absorb" view, so samples from low-support provisional states are reassigned to retained states rather than stored as explicit rare buckets.

Source

Generated from the VALENCIA training data at https://github.com/ravel-lab/VALENCIA. See data-raw/build_valencia13k_merged_dcst_depths.R and the installed DATA_PROVENANCE.md file.

Examples

data(valencia13k_dcst_depth2_merged)
nrow(valencia13k_dcst_depth2_merged$assignments)
head(valencia13k_dcst_depth2_merged$summaries$depth2)

linf documentation built on Aug. 5, 2026, 9:08 a.m.