studyTaxonList: Study Taxon List

In hannahlowens/BridgeTree: Tools for Building and Managing Data for Comparative Phylogenetics of Ecological Niches

Description

Takes input phylogenies or vectors of taxon names, checks against taxonomic database, returns vector of cleaned taxonomic names (using taxonRectification) for use in spocc queries, as well as warnings if there are invalid names.

Usage

studyTaxonList(x = NULL, datasources = NULL)

Arguments

x	A phylogeny of class 'phylo' or a vector of class 'character' containing the names of taxa of interest
datasources	A vector of taxonomic datasources implemented in gnr_resolve. See http://gni.globalnames.org/ for more information.

Value

An object of class BridgeTreeData containing the type of inquiry the user has made –a phylogeny or a vector of names– and a dataframe containing input taxa names, the closeset match according to gnr_resolve, and a list of taxonomic datasources that contain the matching name.

Examples

## Inputting a phylogeny
studyTaxonList(x = phylogeny, datasources = c('NCBI', 'EOL'));

## Inputting a vector of taxon names
studyTaxonList(x = c("Buteo buteo", "Buteo buteo hartedi", "Buteo japonicus"), datasources = c('NCBI', 'EOL'));

hannahlowens/BridgeTree documentation built on May 3, 2019, 4:33 p.m.