Extract the character matrix
Arguments
- nexml
nexml object (e.g. from read.nexml)
- rownames_as_col
option to return character matrix rownames (with taxon ids) as it's own column in the data.frame. Default is FALSE for compatibility with geiger and similar packages.
Examples
comp_analysis <- system.file("examples", "comp_analysis.xml", package="RNeXML")
nex <- nexml_read(comp_analysis)
get_characters_list(nex)
#> $cs15
#> NA log snout-vent length
#> taxon_8 ou10 -3.2777799
#> taxon_9 ou11 2.0959433
#> taxon_10 ou12 3.1373971
#> taxon_1 ou3 4.7532824
#> taxon_2 ou4 -2.7624146
#> taxon_3 ou5 2.1049413
#> taxon_4 ou6 -4.9504770
#> taxon_5 ou7 1.2714718
#> taxon_6 ou8 6.2593966
#> taxon_7 ou9 0.9099634
#>
#> $cs31
#> reef-dwelling
#> taxon_8 0
#> taxon_9 1
#> taxon_10 0
#> taxon_1 1
#> taxon_2 0
#> taxon_3 0
#> taxon_4 0
#> taxon_5 1
#> taxon_6 1
#> taxon_7 1
#>