R: Convert list of classifications to a tree.

class2tree {taxize} | R Documentation

## 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 (columns). You will get a warning if species are not coded, but you can ignore this if that was your intention.
`...` | Further arguments passed on to hclust.
`x` | Input object to print or plot - output from class2tree function.

### 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.

### 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

- 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.

### Examples

    ## Not run:
    spnames <- c('Quercus robur', 'Iris oratoria', 'Arachis paraguariensis',
     'Helianthus annuus','Madia elegans','Lupinus albicaulis',
     'Pinus lambertiana')
    out <- classification(spnames, db='itis')
    tr <- class2tree(out)
    plot(tr)

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

    ## End(Not run)

[Package taxize version 0.9.0 Index]