| class2tree {taxize} | R Documentation |
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.
class2tree(input, varstep = TRUE, check = TRUE, ...) ## S3 method for class 'classtree' plot(x, ...) ## S3 method for class 'classtree' print(x, ...)
input |
List of classification data.frame's from the function
|
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. |
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.
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.
## 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)