% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R
\docType{data}
\name{sarscov2_variants}
\alias{sarscov2_variants}
\title{SARS-CoV-2 VOC/VOI Curated Variant Metadata}
\format{
A named list of 13 elements (12 metadata fields plus a structured
References object). See Details for per-element descriptions.
}
\source{
Compiled from 21 peer-reviewed and surveillance sources; see
\code{sarscov2_variants$References$data} for the full reference table
with DOIs and URLs. Built from \code{SARS_CoV_2_VOC_VOI.xlsx} via
\code{\link{get_variants}}.
}
\usage{
data(sarscov2_variants)
}
\description{
A pre-built named list containing curated biological and epidemiological
metadata for 12 SARS-CoV-2 Variants of Concern (VOC) and Variants of
Interest (VOI): Alpha, Beta, Delta, Epsilon, Eta, Gamma, Iota, Kappa, Lambda,
Omicron, Theta, Zeta. Includes mutation profiles, nomenclature,
temporal detection records, defining SNPs, and a fully citable reference
table with 21 verified references.
}
\details{
The object is available automatically after \code{library(ViralEntropR)}
via lazy loading. It is produced by \code{\link{get_variants}} from the
curated Excel workbook \code{SARS_CoV_2_VOC_VOI.xlsx} (not bundled with
the package; see \code{data-raw/sarscov2_variants.R} for the reproducible
build script).

\strong{List elements:}
\describe{
\item{\code{WHO_Label}}{List of 12. WHO variant label strings
(e.g. \code{"Alpha"}, \code{"Omicron"}).}
\item{\code{Pango_Lineage}}{List of 12. Pango lineage designations
(e.g. \code{"B.1.1.7"}).}
\item{\code{GISAID_Clade}}{Character(12). GISAID clade strings
(e.g. \code{"GRY"}, \code{"GR/484A"}).}
\item{\code{Nextstrain_Clade}}{Character(12). Nextstrain clade strings
(e.g. \code{"20I/501Y.V1"}).}
\item{\code{Country_First_Detected}}{List of 12. Country of first
documented detection per variant.}
\item{\code{Date_Earliest_Sample}}{Character(12). Month-Year of earliest
documented sample (e.g. \code{"Sep-2020"}).}
\item{\code{Date_First_Detected}}{Character(12). Month-Year of
world-level first detection.}
\item{\code{Date_First_Detected_US}}{Character(12). Month-Year of first
US detection.}
\item{\code{Spike_Mutations}}{List of 12. Character vectors of Spike
protein mutations per variant, read from the Excel workbook.}
\item{\code{Mutation_Sites}}{List of 12. Integer vectors of amino acid
positions extracted from \code{Spike_Mutations}.}
\item{\code{Defining_SNPs}}{List of 12. Canonical defining SNP strings
(\code{NA} for variants not characterised in the reference set).}
\item{\code{Defining_SNP_Sites}}{List of 12. Integer positions extracted
from \code{Defining_SNPs}.}
\item{\code{References}}{Named list with three elements:
\code{$data} -- data frame of 21 verified references (columns: ID,
Authors, Year, Title, Journal_Source, Volume_Issue_Pages, DOI, URL,
Type, Variants_Covered, Data_Field, Citation);
\code{$display(variant = NULL)} -- renders an interactive
\code{\link[DT]{datatable}}, optionally filtered by WHO label
(requires the \pkg{DT} package);
\code{$cite(variant)} -- returns formatted citation strings for a
given WHO label, suitable for manuscript use.}
}
}
\section{References}{

The 21 curated references cover peer-reviewed articles, CDC MMWR government
reports, and outbreak.info surveillance database records. Full provenance
is available via \code{sarscov2_variants$References$data} or the
interactive display.
}

\examples{
# Object is available immediately after library(ViralEntropR)

# --- Basic access ---------------------------------------------------------

# All 12 WHO labels
unlist(sarscov2_variants$WHO_Label)

# Pango lineage for Alpha
sarscov2_variants$Pango_Lineage[[
  which(unlist(sarscov2_variants$WHO_Label) == "Alpha")
]]

# World detection dates for all variants
data.frame(
  Variant  = unlist(sarscov2_variants$WHO_Label),
  Detected = sarscov2_variants$Date_First_Detected,
  Country  = unlist(sarscov2_variants$Country_First_Detected)
)

# --- Mutation sites -------------------------------------------------------

# Defining SNPs and sites for Delta
idx <- which(unlist(sarscov2_variants$WHO_Label) == "Delta")
sarscov2_variants$Defining_SNPs[[idx]]
sarscov2_variants$Defining_SNP_Sites[[idx]]

# All Spike mutation sites for Omicron
sarscov2_variants$Mutation_Sites[[
  which(unlist(sarscov2_variants$WHO_Label) == "Omicron")
]]

# --- Nomenclature ---------------------------------------------------------

data.frame(
  WHO        = unlist(sarscov2_variants$WHO_Label),
  PANGO      = unlist(sarscov2_variants$Pango_Lineage),
  GISAID     = sarscov2_variants$GISAID_Clade,
  Nextstrain = sarscov2_variants$Nextstrain_Clade
)

# --- References -----------------------------------------------------------

# Full reference data frame (21 rows)
sarscov2_variants$References$data[,
  c("ID", "Authors", "Year", "Journal_Source")
]

# Formatted citation strings for Gamma
sarscov2_variants$References$cite("Gamma")

if (interactive() && requireNamespace("DT", quietly = TRUE)) {
  # Interactive DT table of all references
  sarscov2_variants$References$display()

  # Filtered to Omicron references only
  sarscov2_variants$References$display(variant = "Omicron")
}
}
\keyword{datasets}
