GetResultMonophyly: Get main result table from 'AssessMonophyly' output

In MonoPhy: Explore Monophyly of Taxonomic Groups in a Phylogeny

Description

Extracts data frame with main result table or containing summary information such as number of tips, number of monophyletic taxa, etc. from the output of 'AssessMonophyly'.

Usage

GetResultMonophyly(solution, taxlevels='ALL')
GetSummaryMonophyly(solution, taxlevels='ALL')

Arguments

solution	Object with saved output of the 'AssessMonophyly' function.
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'.

Details

Can be used after 'AssessMonophyly' is run to extract the results or summary table from it. In the results table, rows are the taxonomic groups used, columns are 'Monophyly' ('Yes', 'No' or 'Monotypic'), 'MRCA' (node number of inferred ancestor), '#Tips' (number of tips assigned to this taxon),'Delta-Tips' (number of tips which share this ancestral node but do not belong to the same taxon), '#Intruders'(how many other taxa interfere with the monophyly of the taxon in quesiton) and 'Intruders' (names of interfering taxa, how many of these are written out is determined by the argument 'verbosity'). If the argument outliercheck was set to TRUE when running 'AssessMonophyly', the table will additionally include '#Outliers' (number of tips which are placed outside the core clade for that group) and 'Outliers' (names of outlier taxa, the number of which also depending on the argument 'verbosity'). The summary table contains two rows with the number of taxa (e.g. genera) and tips (e.g. species) for the total tree, and which were inferred to be monophyletic, non-monophyletic, monotypic, intruders and (if applicable) outliers. 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 corresponding number instead.

Value

List of data frame(s) containing the main results/summary.

Note

Can also be accessed by simply typing 'solution$Taxlevel_i$result' or 'solution$Taxlevel_i$summary' (or whichever name the Taxlevels might have been given, e.g. based on the header) respectively.

Author(s)

Orlando Schwery

See Also

AssessMonophyly, MonoPhy-package

Examples

data(Ericactree)
solution <- AssessMonophyly(Ericactree, verbosity=5)
GetSummaryMonophyly(solution)
GetResultMonophyly(solution)

MonoPhy documentation built on Feb. 18, 2021, 1:06 a.m.