Taxonomic distance and phylogenetic lineage computation for any taxon on Earth.
taxodist retrieves full hierarchical lineages from The Taxonomicon and computes a
tree metric distance between any two taxa: a pair of dinosaurs, a
dinosaur and a fungus, two species of fly, or an oak tree and a
human.
devtools::install_github("rodrigosqrt3/taxodist")library(taxodist)
# Get a full lineage
get_lineage("Tyrannosaurus")
# Distance between two taxa
taxo_distance("Tyrannosaurus", "Velociraptor")
# Most recent common ancestor
mrca("Tyrannosaurus", "Triceratops") # "Dinosauria"
mrca("Tyrannosaurus", "Homo") # "Amniota"
# Pairwise distance matrix
theropods <- c("Tyrannosaurus", "Velociraptor", "Spinosaurus", "Allosaurus")
distance_matrix(theropods)
# Filter taxa by clade
taxa <- c("Tyrannosaurus", "Triceratops", "Homo", "Quercus")
filter_clade(taxa, "Dinosauria")taxodist measures relatedness by asking a single
question: how deep is the most recent common ancestor (MRCA)?
\[d(A, B) = \frac{1}{\text{depth}(\text{MRCA}(A, B))}\]
The deeper the shared ancestor, the smaller the distance and the more related the two taxa are. A shallow MRCA means the two taxa diverged early; a deep MRCA means they share a long common history. The metric returns 0 when one taxon is ancestral to the other, and satisfies the triangle inequality.
The Taxonomicon provides substantially deeper lineage resolution than other programmatic sources, e.g., Tyrannosaurus has over 70 nodes in its lineage, which is what makes the distances meaningful across all of life.
All lineage data is sourced from The Taxonomicon
(taxonomy.nl), based on Systema Naturae 2000 by Sheila J.
Brands (1989 onwards). Please cite this resource in any published work
using taxodist:
Brands, S.J. (1989 onwards). Systema Naturae 2000. Amsterdam, The Netherlands. Retrieved from The Taxonomicon, http://taxonomicon.taxonomy.nl.
Found a taxon with an incorrect lineage? Please open an issue, lineage corrections are the most valuable contribution to this package.