V.PhyloMaker
This R package makes phylogenetic hypotheses for a user-specified list of species, by providing multiple ways of binding the species (tips) to a backbone phylogeny, as described in Jin & Qian (2019).
How to install this package? This package can be installed in R either using the install_github function in the ‘devtools’ package, or using the githubinstall function in the ‘githubinstall’ package. For example, the R code for installation of V.PhyloMaker using the ‘devtools’ package is as follows: devtools::install_github("jinyizju/V.PhyloMaker")
Currently, this package includes two major components: (1) the functions, including ‘phylo.maker’, ‘bind.relative’, ‘build.nodes.1’, ‘build.nodes.2’, ‘at.node’, ‘int.node’ and ‘ext.node’; and (2) the data, including 'GBOTB.extended', ‘tips.info’, ‘nodes.info.1’ and ‘nodes.info.2’.
(1) The functions
The main function ‘phylo.maker’ performs the task of binding tips to a backbone phylogeny, which by default is the maga-phylogeny 'GBOTB.extended' of vascular plants embedded in the package.
The function ‘bind.relative’ performs the task of binding tips to the their species- and genus-level closest relative in the backbone phylogeny, when information is provided. ‘bind.relative’ can work alone or with ‘phylo.maker’, for a list of species, as examplified in the function help page and Jin & Qian (2019).
The functions ‘build.nodes.1’ and ‘build.nodes.2’ extract the genus- and family- level node and age information in a phylogeny in different ways. The information extracted are used by ‘phylo.maker’ and ‘bind.relative’ in binding tips to backbone phylogeny.
The functions ‘at.node’, ‘int.node’ and ‘ext.node’ bind a tip to a phylogeny, at different places. These three functions are fast in binding tip to large phylogenies.
(2) The data
The four data sets work with the functions to make phylogenetic hypotheses for a user-specified list of vascular plant species.
‘GBOTB.extended’ is a mega-tree derived from two recently published mega-trees, described in the help page, and includes 74,531 species and all families of extant vascular plants, is the largest dated phylogeny for vascular plants.
‘tips.info’ is a data frame that contains the information of all the tips, as well as as their genus and family assignments, in ‘GBOTB.extended’.
‘nodes.info.1’ and ‘nodes.info.2’ are the genus- and family-level node and age information in ‘GBOTB.extended’ extracted by ‘build.nodes.1’ and ‘build.nodes.2’, respectively.
Citation: Jin Y & Qian H (2019) V.PhyloMaker: an R package that can generate very large phylogenies for vascular plants. Ecography, 42, 1353–1359.