% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R
\docType{data}
\name{valencia_linf_hypercube_1k}
\alias{valencia_linf_hypercube_1k}
\title{Valencia 1k four-component hypercube embedding example}
\format{
A list with four components:
\describe{
\item{rel4}{Numeric matrix (1000 x 4). Rows are samples and columns are
\code{Li}, \code{Lc}, \code{Gv}, and \code{Bv}. Each row sums to 1 after
restricting the original Valencia profile to the four mapped taxa.}
\item{meta}{Data frame (1000 rows) with columns:
\code{sample_id} (anonymized bundled-data identifier),
\code{source_row} (row number in the filtered Valencia 13k source),
\code{Val_CST}, \code{Val_subCST}, \code{selected_mass} (original
relative-abundance mass carried by the four selected taxa), and
\code{dominant_component} (largest of \code{Li}, \code{Lc},
\code{Gv}, \code{Bv} after renormalization).}
\item{component_map}{Named character vector mapping \code{Li},
\code{Lc}, \code{Gv}, and \code{Bv} to the original Valencia taxon names:
\code{Lactobacillus_iners}, \code{Lactobacillus_crispatus},
\code{Gardnerella_vaginalis}, and \code{BVAB1}.}
\item{source}{Character string documenting provenance.}
}
}
\source{
Generated from the VALENCIA training data at
\url{https://github.com/ravel-lab/VALENCIA}. See
\code{data-raw/build_valencia_linf_hypercube_1k.R} and the installed
\code{DATA_PROVENANCE.md} file.
}
\usage{
valencia_linf_hypercube_1k
}
\description{
A stratified 1,000-sample subset of the Valencia 13k vaginal microbiome
training set, reduced to four selected phylotype coordinates and
L1-normalized over those coordinates. The object is bundled as a lightweight
example for the zero-aware homogeneous-coordinate hypercube embedding in
\code{\link{linf.hypercube.embedding}}.
}
\details{
Rows with zero total mass in the four selected taxa are removed before
renormalization. Sampling is stratified by the dominant selected component,
using \code{set.seed(20261604)}. The object is not intended to replace the
full Valencia matrix; it is a compact reproducible example for visualizing
compositional projective-space coordinate charts.
}
\examples{
data(valencia_linf_hypercube_1k)
dim(valencia_linf_hypercube_1k$rel4)
table(valencia_linf_hypercube_1k$meta$dominant_component)
emb <- linf.hypercube.embedding(
  valencia_linf_hypercube_1k$rel4,
  reference = "Li"
)
dim(emb)

}
\keyword{datasets}
