create.phylo: Generating a phylogeny of selected Western Ghats trees

In frmunoz/TreeGhats: Taxonomic name resolution and phylogeny generator for Western Ghats trees

Generating a phylogeny of selected Western Ghats trees

Description

Creates a phylogeny of tree taxa based on species, genus and APGIII family information.

Usage

create.phylo(names = NULL, scenarios = "S3")
create.phylo.all(scenarios = "S3")

Arguments

names	a data frame including taxonomic information for each taxon on row. The columns must be named "Binome", "Genus" and "Family_APGIII", and include latine genus species combination, genus name and APGIII family name, respectively. Genus and species names in "Binome" must be separated with a space. Default value is NULL, the phylogeny is generated for all taxa in the TreeGhatsData database.
scenarios	one of the scenarios of Jin and Qian (2019) proposed for including taxa that are not already present in the megaphylogeny. See phylo.maker for more information on the available options.

Details

create.phylo establishes a baseline phylogeny with the taxa in names that are already present in a reference megaphylogeny, and further includes the missing taxa by branching them to the corresponding genus node or, if the genus is absent from the megaphylogeny, to the corresponding family node.

create.phylo.all is used to generate the phylogeny of all the taxa of the database.

Value

The function returns an object of class link[ape]{phylo}, which can be analyzed and plotted with tools available in ape package.

Author(s)

F. Munoz

References

Jin, Y., Qian, H., 2019. V.PhyloMaker: an R package that can generate very large phylogenies for vascular plants. Ecography 42, 1353–1359. https://doi.org/10.1111/ecog.04434

See Also

phylo.maker

Examples

example <- data.frame(Binome = c("Dipterocarpus indicus", "Michelia champaca", 
"Drypetes roxburghii", "Corypha umbraculifera"), Genus = c("Dipterocarpus", "Michelia", 
"Drypetes", "Corypha"), Family_APGIII = c("Dipterocarpaceae", "Magnoliaceae", 
"Euphorbiaceae", "Aceraceae"), stringsAsFactors = FALSE)

phylo <- create.phylo(example)
plot(phylo$scenario.3)

frmunoz/TreeGhats documentation built on July 29, 2022, 5:21 a.m.