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Last data update: 2014.03.03

R: Get MRCA nodes of taxonomic groups from 'AssessMonophyly'...

GetAncNodes

R Documentation

Get MRCA nodes of taxonomic groups from 'AssessMonophyly' output

Description

Print MRCA node numbers of taxonomic groups from the output of 'AssessMonophyly', either the whole list or for specific groups.

Usage

GetAncNodes(solution, taxa = NULL, taxlevels='ALL')

Arguments

`solution`	Object with saved output of the 'AssessMonophyly' function.
`taxa`	Vector containing taxon names (genera or whichever taxonomic unit was used). Default is 'NULL'
`taxlevels`	Either an integer corresponding to the desired taxonomic level (i.e. the number of its column in the taxonimy table, not counting the tip names), the column name in the header of the taxonomy file, or 'ALL' (which is the default).

Details

Can be used after 'AssessMonophyly' is run to extract MRCA nodes of taxa from it. The argument 'taxa' allows to limit the output to one or several taxa of interest. The argument 'taxlevels' allows to limit the output if several taxonomic levels were used; 'ALL' is default, a specific level can be selected by entering its number or name instead.

Value

List of data frames.

Author(s)

Orlando Schwery

Examples

data(Ericactree)
solution <- AssessMonophyly(Ericactree)
GetAncNodes(solution=solution, taxa=c("Phyllodoce", "Vaccinium", "Erica"))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(MonoPhy)
Loading required package: ape
Loading required package: phytools
Loading required package: maps

 # maps v3.1: updated 'world': all lakes moved to separate new #
 # 'lakes' database. Type '?world' or 'news(package="maps")'.  #


Loading required package: phangorn
Loading required package: RColorBrewer
Loading required package: taxize
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MonoPhy/GetAncNodes.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GetAncNodes
> ### Title: Get MRCA nodes of taxonomic groups from 'AssessMonophyly' output
> ### Aliases: GetAncNodes
> 
> ### ** Examples
> 
> data(Ericactree)
> solution <- AssessMonophyly(Ericactree)
> GetAncNodes(solution=solution, taxa=c("Phyllodoce", "Vaccinium", "Erica"))
$Genera
           MRCA
Phyllodoce  140
Vaccinium    93
Erica       128

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>