Generates phylogenetic trees and distance matrices from a list
of taxon names, or from a higher taxon expanded down to a chosen lower
rank. Trees are obtained as induced subtrees of the Open Tree of Life
synthetic tree using the 'rotl' package (Michonneau, Brown and Winter,
2016,
aptg builds phylogenetic trees and distance matrices from a list of taxon
names, or from a higher taxon expanded down to a lower rank.
Version 0.2.x is a rewrite: the original Phylomatic/brranching backend was
archived from CRAN and its web service shut down, so trees now come from the
Open Tree of Life synthetic tree (via
rotl) or, for ray-finned fishes, the
dated Fish Tree of Life (via fishtree).
See NEWS.md and MIGRATION.md for details.
# install.packages("remotes")
remotes::install_github("christophebenjamin/aptg")
# For the dated fish backend (optional):
install.packages("fishtree")
library(aptg)
# A mixed list is split by phylum: no tree ever spans above phylum.
res <- taxa.tree(c("Canis lupus", "Alces alces", "Rangifer tarandus",
"Acer saccharum", "Acer rubrum", "Betula alleghaniensis"))
names(res$trees) # "Chordata" "Streptophyta"
plot(res$trees[["Chordata"]]$tree)
res$trees[["Chordata"]]$dist # distance matrix
# Expand a higher taxon down to a rank, then build the tree(s).
downto.tree("Cervidae", downto = "species")
# A dated fish chronogram (needs the fishtree package).
taxa.tree(c("Thunnus thynnus", "Gadus morhua", "Salmo salar", "Danio rerio"),
source = "fish")
# Trees for a clade within a geographic area (needs rgbif; radius needs
# geosphere). Species come from GBIF occurrence records.
region.tree("Aves", lat = 45.50, lon = -73.57, radius_km = 50) # radius
region.tree("Mammalia", province = "Nunavut") # Canadian territory
region.tree("Reptilia", gadm = "USA.5_1") # any GADM area
region.tree() supports all 13 Canadian provinces and territories by name or
postal code (AB, BC, MB, NB, NL, NT, NS, NU, ON, PE, QC, SK, YT). Note that
GBIF returns occurrence records, not a curated checklist, so the species list
is sampling-biased — see ?region.tree.
downto.tree() uses NCBI via taxize. To raise the rate limit (3 to 10
req/s), pass an Entrez key as key = "..." (it is exported as ENTREZ_KEY
for the call) or set ENTREZ_KEY in your .Renviron and leave key = NULL.
Both functions return, invisibly, list(trees, unmatched), where trees is
named by phylum and each element is list(tree, dist). The Open Tree backend
is topology-only (distances are edge counts); the fish backend returns a dated
chronogram (patristic/time distances).
MIT (c) Christophe Benjamin. See LICENSE.