GetIntruderTaxa {MonoPhy}

Get taxa or tips which are intruders or outliers to a taxon from AssessMonophyly

Description

Prints names of taxa (genera or whichever taxonomic unit used) or tip names (species, most likely) interfering with the monophyly of one or several (or all) groups, either as intruders (sharing a clade with said taxon) or outliers (being placed outside of the taxon's core clade)

Usage

GetIntruderTaxa(solution, taxa = NULL, taxlevels='ALL')
GetIntruderTips(solution, taxa = NULL, taxlevels='ALL')
GetOutlierTaxa(solution, taxlevels='ALL')
GetOutlierTips(solution, taxa = NULL, taxlevels='ALL')

Arguments

solution

Object with saved output of the 'AssessMonophyly' function.

taxa

Vector containing taxon names (genus or whichever taxonomic unit was used). Default NULL will return intruders/outliers for all taxa.

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 intruder/outlier taxa or intruder/outlier tips from it. The argument 'taxa' allows to limit the output to one or several taxa of interest. It is not available for GetOutlierTaxa, since this is just one vector with names anyway (a taxon can only be outlier of itself). The argument 'taxlevels' allows to limit the output if several taxonomic levels were used; 'ALL' is default, a single level can be selected by entering its number or name instead. Outliers can of course only be retrieved if the argument outliercheck was set to TRUE when running AssessMonophyly.

Value

List of character strings

Note

Noteworthy difference: intruder tips for e.g. Vaccinium will be tips of OTHER taxa that are placed inside the Vaccinium clade, whereas outlier tips for Vaccinium will be Vaccinium species that are placed outside of the Vaccinium core clade. Can also be accessed by simply typing 'solution$Taxlevel_i$IntruderTaxa' or 'solution$Taxlevel_i$IntruderTaxa$taxonname' and 'solution$Taxlevel_i$IntruderTips' or 'solution$Taxlevel_i$IntruderTips$taxonname' respectively (or whichever name the Taxlevels might have been given, e.g. based on the header); same for outliers.

Author(s)

Orlando Schwery

See Also

AssessMonophyly, GetAncNodes, MonoPhy-package

Examples

data(Ericactree)
solution <- AssessMonophyly(Ericactree)
GetIntruderTaxa(solution=solution)
GetOutlierTaxa(solution=solution)
GetIntruderTips(solution=solution, taxa=c("Phyllodoce", "Vaccinium", "Erica"))
GetOutlierTips(solution=solution, taxa=c("Vaccinium"))