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Last data update: 2014.03.03 |
Get main result table from 'AssessMonophyly' outputDescriptionExtracts 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'. UsageGetResultMonophyly(solution, taxlevels='ALL') GetSummaryMonophyly(solution, taxlevels='ALL') Arguments
DetailsCan 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. ValueList of data frame(s) containing the main results/summary. NoteCan 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
Examplesdata(Ericactree) solution <- AssessMonophyly(Ericactree, verbosity=5) GetSummaryMonophyly(solution) GetResultMonophyly(solution) Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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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/GetResultMonophyly.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GetResultMonophyly
> ### Title: Get main result table from 'AssessMonophyly' output
> ### Aliases: GetResultMonophyly GetSummaryMonophyly
>
> ### ** Examples
>
> data(Ericactree)
> solution <- AssessMonophyly(Ericactree, verbosity=5)
> GetSummaryMonophyly(solution)
$Genera
Taxa Tips
Total 32 77
Monophyletic 9 25
Non-Monophyletic 6 35
Monotypic 17 17
Intruder 7 11
Outlier 1 2
> GetResultMonophyly(solution)
$Genera
Monophyly MRCA #Tips Delta-Tips #Intruders Intruders
Agapetes Yes 114 3 0 0
Allotropa Monotypic NA 1 NA NA
Andromeda Monotypic NA 1 NA NA
Bruckenthalia Monotypic NA 1 NA NA
Bryanthus Monotypic NA 1 NA NA
Calluna Monotypic NA 1 NA NA
Cassiope Yes 146 5 0 0
Chimaphila Yes 88 2 0 0
Costera Monotypic NA 1 NA NA
Daboecia Yes 126 2 0 0
Dimorphanthera No 96 3 2 1 Paphia
Enkianthus Yes 150 5 0 0
Epigaea Monotypic NA 1 NA NA
Erica No 128 9 1 1 Bruckenthalia
Gaylussacia Monotypic NA 1 NA NA
Gonocalyx Yes 120 2 0 0
Kalmiopsis Yes 142 2 0 0
Ledothamnus Yes 138 2 0 0
Moneses Monotypic NA 1 NA NA
Monotropa Monotypic NA 1 NA NA
Notopora Monotypic NA 1 NA NA
Orthaea Yes 101 2 0 0
Orthilia Monotypic NA 1 NA NA
Oxydendrum Monotypic NA 1 NA NA
Paphia No 97 2 1 1 Dimorphanthera
Phyllodoce No 140 4 2 1 Kalmiopsis
Pyrola No 83 4 1 1 Orthilia
Rhodothamnus Monotypic NA 1 NA NA
Symphysia Monotypic NA 1 NA NA
Utleya Monotypic NA 1 NA NA
Vaccinium No 93 13 17 2 Gaylussacia, Agapetes
Zenobia Monotypic NA 1 NA NA
#Outliers Outliers
Agapetes NA
Allotropa NA
Andromeda NA
Bruckenthalia NA
Bryanthus NA
Calluna NA
Cassiope NA
Chimaphila NA
Costera NA
Daboecia NA
Dimorphanthera 0
Enkianthus NA
Epigaea NA
Erica 0
Gaylussacia NA
Gonocalyx NA
Kalmiopsis NA
Ledothamnus NA
Moneses NA
Monotropa NA
Notopora NA
Orthaea NA
Orthilia NA
Oxydendrum NA
Paphia 0
Phyllodoce 0
Pyrola 0
Rhodothamnus NA
Symphysia NA
Utleya NA
Vaccinium 2 Vaccinium_poasanum, Vaccinium_uliginosum
Zenobia NA
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> dev.off()
null device
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