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Extract the character matrix

Source: R/deprecated.R
get_characters_list.Rd

Extract the character matrix

Usage

get_characters_list(nexml, rownames_as_col = FALSE)

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.

Value

the list of taxa

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
#>