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

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/create.phylo.R

Description

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

Usage

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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 Qian and Jin (2016) proposed for including taxa that are not already present in the megaphylogeny qian. See S.PhyloMaker for more information on the available options.

Details

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

create.phylo.all is used to generate the phylogeny of all the taxa of the database ($phylo.all in qian).

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

Qian H. & Jin Y. (2016). An updated megaphylogeny of plants, a tool for generating plant phylogenies, and an analysis of phylogenetic community structure. Journal of Plant Ecology. 9(2):233-239.

See Also

qian S.PhyloMaker

Examples

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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 March 24, 2018, 5:24 a.m.