getCitations: Get the DOIs and quantify the contribution of published...

In clootl: Fetch and Explore the Cornell Lab of Ornithology Open Tree of Life Avian Phylogeny

Get the DOIs and quantify the contribution of published studies

Description

Standing on the shoulders of giants

Usage

getCitations(tree, version = "1.4", data_path = FALSE)

Arguments

tree	A phylogeny obtained from extractTree (see details).
version	The desired version of the tree. Default to the most recent version of the tree. Other versions available are '0.1','1.0','1.2','1.3','1.4' and can be passed as a character string or as numeric.
data_path	Default to FALSE, it will look for a path containing the bird tree. If the tree has not been downloaded yet using get_avesdata_repo(), it will load the default tree using utils::data() and version and taxonomy_year will be ignored?? If the tree has been downloaded using get_avesdata_repo(), it will read the tree file corresponding to the version and taxonomy_year provided and load it as a phylo object.

Details

Importantly: an internet connection is required for this function to work, as it relies on Open Tree of Life APIs. The function will determine what proportion of nodes in your phylogeny (possibly but not necessarily pruned to a set of study taxa) are supported by each study that goes into creating the final clootl tree. In any resulting publication, you should always cite the clootl tree, and you should also "always" cite all the trees/DOIs that contributed to your phylogeny. That said, we are well aware of citation and word count limits that plague modern publishing, and for this reason we quantify the contribution of each study; depending on your phylogeny, it is very possible that one or two studies contributed the majority of information. Currently, this function assumes your output tree matches the taxonomy of the corresponding tree on the OpenTree server. Since the function is actually using the named internal nodes for the API query, and these should not be lost between tree versions and taxonomies, this should not matter, but this has not yet been tested.

Value

A dataframe of the percent of internal nodes supported by a given study, as well as the DOI of that study. The proportion of taxa in the tree supported by taxonomic addition only is included in the dataframe.

Author(s)

Eliot Miller, Emily Jane McTavish

Examples

#pull the taxonomy file out
data(clootl_data)
tax <- clootl_data$taxonomy.files$Year2021
ls(tax)
#subset to species only
# TODO: this step seems no longer necessary, is it??
# tax <- tax[tax$CATEGORY=="species",]

#simulate extracting a tree for a particular family
temp <- tax[tax$FAMILY=="Rhinocryptidae (Tapaculos)",]
spp <- temp$SCI_NAME

#get your tree
prunedTree <- extractTree(species=spp, label_type="scientific",
   taxonomy_year=2021, version="1.4")

#get your citation DF
 yourCitations <- getCitations(tree=prunedTree)

clootl documentation built on April 11, 2025, 5:38 p.m.