GetIntruderTaxa: Get taxa or tips which are intruders or outliers to a taxon...
In MonoPhy: Explore Monophyly of Taxonomic Groups in a Phylogeny

Description Usage Arguments Details Value Note Author(s) See Also Examples

View source: R/GetIntruderTaxa.R

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)

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

`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.

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.

List of character strings

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.

Orlando Schwery

AssessMonophyly, GetAncNodes, MonoPhy-package

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"))