% 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 Hierarchy Distances and Lineage Analysis}
\description{
taxodist retrieves taxonomic lineages from The Taxonomicon (taxonomy.nl)
and computes distances from the depth of the most recent common ancestor.
The resulting values describe separation within the source classification;
they are not estimates of evolutionary time or phylogenetic branch length.
\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 ultrametric 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,A) = 0}{d(A,A) = 0}
\deqn{d(A,B) = 1 / h(A,B)}{d(A,B) = 1 / h(A,B)}

Here, \code{h(A,B)} denotes the depth of the MRCA. The deeper the shared
ancestor, the smaller the distance. Zero is reserved
for identical hierarchy nodes; distinct ancestor-descendant pairs therefore
have positive distance. The measure is an ultrametric on each connected
taxonomic hierarchy. Its numerical values depend on the resolution of the
classification returned by the data source.
}

\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})

}
