% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/taxodist-package.R
\docType{package}
\name{taxodist-package}
\alias{taxodist-package}
\alias{taxodist}
\title{taxodist: Taxonomic Distance and Phylogenetic Lineage Computation}
\description{
taxodist computes phylogenetic distances between any two taxa using
hierarchical lineage data retrieved from The Taxonomicon
(taxonomy.nl), a comprehensive curated classification of all life
based on Systema Naturae 2000.
\subsection{Core functions}{
\itemize{
\item \code{\link[=get_lineage]{get_lineage()}} — retrieve the full lineage of any taxon
\item \code{\link[=taxo_distance]{taxo_distance()}} — compute the tree metric distance between two taxa
\item \code{\link[=mrca]{mrca()}} — find the most recent common ancestor
\item \code{\link[=distance_matrix]{distance_matrix()}} — compute all pairwise distances for a set of taxa
\item \code{\link[=closest_relative]{closest_relative()}} — find the closest relative among candidates
\item \code{\link[=compare_lineages]{compare_lineages()}} — print a side-by-side lineage comparison
\item \code{\link[=shared_clades]{shared_clades()}} — list clades shared between two taxa
\item \code{\link[=is_member]{is_member()}} — test clade membership
\item \code{\link[=filter_clade]{filter_clade()}} — filter taxa by clade membership
\item \code{\link[=check_coverage]{check_coverage()}} — check Taxonomicon coverage for a list of taxa
\item \code{\link[=lineage_depth]{lineage_depth()}} — get the lineage depth of a taxon
\item \code{\link[=clear_cache]{clear_cache()}} — clear the session lineage cache
}
}

\subsection{Mathematical background}{

The distance metric is based on the depth of the most recent common
ancestor (MRCA):

\deqn{d(A, B) = \frac{1}{\text{depth}(\text{MRCA}(A,B))}}

The deeper the shared ancestor, the smaller the distance. This metric
ensures that taxa sharing the same MRCA are always equidistant from any
third taxon, regardless of lineage depth below the split — a key
biological correctness property absent from Jaccard-based approaches.
}

\subsection{Data source}{

All lineage data is sourced from The Taxonomicon (taxonomy.nl), based on
Systema Naturae 2000 by S.J. Brands (1989 onwards). Please cite this
resource when using taxodist in published work.
}
}
\references{
Brands, S.J. (1989 onwards). Systema Naturae 2000. Amsterdam,
The Netherlands. Retrieved from The Taxonomicon,
\url{http://taxonomicon.taxonomy.nl}.
}
\seealso{
Useful links:
\itemize{
  \item \url{https://github.com/rodrigosqrt3/taxodist}
  \item Report bugs at \url{https://github.com/rodrigosqrt3/taxodist/issues}
}

}
\author{
\strong{Maintainer}: Rodrigo Fonseca Villa \email{rodrigo03.villa@gmail.com} (\href{https://orcid.org/0009-0005-2938-2270}{ORCID})

}
