taxize (version 0.2.2)

class2tree: Convert list of classifications to a tree.

Description

This function converts a list of hierarchies for individual species into a single species by taxonomic level matrix, then calculates a distance matrix based on taxonomy alone, and outputs either a phylo or dist object. See details for more information.

Usage

class2tree(input, varstep = TRUE, check = TRUE, ...)
## S3 method for class 'classtree':
plot(x, ...)
## S3 method for class 'classtree':
print(x, ...)

Arguments

input

List of classification data.frame's from the function classification()

varstep

Vary step lengths between successive levels relative to proportional loss of the number of distinct classes.

check

If TRUE, remove all redundant levels which are different for all rows or constant for all rows and regard each row as a different basal taxon (species). If FALSE all levels are retained and basal taxa (species) also must be coded as variables (col

...

Further arguments passed on to hclust.

x

Input object to print or plot - output from class2tree function.

Value

• An object of class "classtree" with slots:
  • phylo - The resulting object, a phylo object
  • classification - The classification data.frame, with taxa as rows, and different classification levels as columns
  • distmat - Distance matrix from a call totaxa2dist
  • names - The names of the tips of the phylogeny

  Note that when you execute the resulting object, you only get the phylo object. You can get to the other 3 slots by calling them directly, like output$names, etc.

Details

See taxa2dist. Thanks to Jari Oksanen for making the taxa2dist function and pointing it out, and Clarke & Warwick (1998, 2001), which taxa2dist was based on.

Examples

spnames <- c('Klattia flava', 'Trollius sibiricus', 'Arachis paraguariensis',
 'Tanacetum boreale', 'Gentiana yakushimensis','Sesamum schinzianum',
 'Pilea verrucosa','Tibouchina striphnocalyx','Lycium dasystemum',
 'Schoenus centralis','Berkheya echinacea','Androcymbium villosum',
 'Helianthus annuus','Madia elegans','Lupinus albicaulis','Poa annua',
 'Pinus lambertiana')
out <- classification(spnames, db='ncbi')
tr <- class2tree(out)
plot(tr)

# another example using random sets of names with names_list() fxn
spnames <- names_list('species', 50)
out <- classification(spnames, db='ncbi')
out <- out[!is.na(out)]
tr <- class2tree(out)
plot(tr)
plot(tr, no.margin=TRUE)