create.phylo | R Documentation |
Creates a phylogeny of tree taxa based on species, genus and APGIII family information.
create.phylo(names = NULL, scenarios = "S3") create.phylo.all(scenarios = "S3")
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 |
scenarios |
one of the scenarios of Jin and Qian (2019) proposed for including taxa that are not already present in the megaphylogeny. See |
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.
The function returns an object of class link[ape]{phylo}
, which can be analyzed and plotted with tools available in ape
package.
F. Munoz
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
phylo.maker
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)
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