Reads a Newick or NEXUS tree file using ape. Tries
ape::read.tree first; falls back to ape::read.nexus if that
fails.
Value
An object of class "phylo" when the file contains one tree,
or "multiPhylo" when it contains multiple trees.
Details
For bird phylogenies, BirdTree provides a species-subset download tool for
up to 2,500 species and full-tree distributions for larger sets. Download
and unzip the trees, then read a Newick tree file here. BirdTree documents
its distributions as Newick trees; this function also accepts NEXUS files.
A file with one tree returns a "phylo" object; a file with several
trees returns a "multiPhylo" object.
pigauto does not download BirdTree data automatically. Pass a single-tree
result to impute(traits, tree). A multi-tree result can be passed to
multi_impute_trees(traits, trees) for experimental prediction-
sensitivity checks only; this path has not been validated for downstream
inference.
BirdTree's subset tool defaults to at least 100 draws and recommends a
reasonable sample (more than 100) for analyses using its full-tree
distributions. pigauto's multi_impute_trees() remains experimental:
it supports descriptive checks of prediction sensitivity only, and its
stochastic datasets are not validated for downstream inference. See
vignette("tree-uncertainty").
BirdTree asks researchers using full or partial tree data to cite Jetz et al. (2012). If you use the BirdTree web tool, also credit BirdTree.org.
References
Jetz W, Thomas GH, Joy JB, Hartmann K, Mooers AO (2012). The global diversity of birds in space and time. Nature, 491, 444-448. doi:10.1038/nature11631 . BirdTree.org. Downloads, phylogeny subsets, and FAQ. https://birdtree.org/downloads/ https://birdtree.org/subsets/ https://birdtree.org/faq/.
Examples
# \donttest{
path <- tempfile(fileext = ".tre")
ape::write.tree(ape::rtree(10L), path)
tree <- read_tree(path)
# }