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Summary method for nexml objects

Source: R/nexml_methods.R
summary-nexml-method.Rd

Generates a list of various counts of the major elements that comprise a nexml object, such as number of different kinds of blocks, characters, states, OTUs (taxa), etc.

Usage

# S4 method for class 'nexml'
summary(object)

Arguments

object

the nexml object

Value

A list with the following elements:

  • nblocks the number of trees, otus, and characters blocks

  • ncharacters the number of characters in each characters block

  • nstates summary statistics of the number of character states per state set defined for each characters block

  • nnonstdstatedefs the number of polymorphic and uncertain states defined for each character block

  • nmatrixrows the number of rows in the matrix for each character block

  • ntrees the number of trees contained in each trees block

  • notus the number of OTUs defined in each OTUs block

  • nmeta a list of the number of the number of metadata annotations at several levels, specifically:

    • nexml at the top (nexml) level

    • otu at the OTU level, for each OTUs block

    • char at the character level, for each characters block

    • state at the character state level, for each characters block

Details

The show method uses this summary for pretty-printing a summary of the NeXML object, but it can be used on its own as well, in particular for quick inspection of key properties of a NeXML file.

Examples

nex <- nexml_read(system.file("examples", "comp_analysis.xml", package = "RNeXML"))
s <- summary(nex)
# number of major blocks:
s$nblocks
#>      trees       otus characters 
#>          1          1          2 

# each characters block defines 1 character:
s$ncharacters
#> block.1 block.2 
#>       1       1 

# summary stats of states per character (for morphological matrices there is
# typically one state set per character)
s$nstates # note that first block is of continuous type, so no stats there
#>         block.1 block.2
#> Min.         NA       2
#> 1st Qu.      NA       2
#> Median       NA       2
#> Mean         NA       2
#> 3rd Qu.      NA       2
#> Max.         NA       2

# pretty-printed summary:
nex # this is the same as show(nex)
#> A nexml object representing:
#>  	 1 phylogenetic tree block(s), where:
#> 	   block 1 contains 1 phylogenetic tree(s) 
#>  	 2 character block(s), where:
#> 	   block 1 defines 1 continuous character(s) 
#> 	   matrix 1 has 10 row(s)
#> 	   block 2 defines 1 standard/discrete character(s), with 2 states each 
#> 	    and  0 polymorphic or uncertain state(s) defined 
#> 	   matrix 2 has 10 row(s) 
#>  	 10 taxonomic units in 1 block(s) 
#>   Taxa:	 taxon_1, taxon_2, taxon_3, taxon_4, taxon_5, taxon_6 ...
#>   Metadata annotations: 
#> 	2 at top level 
#> 	0 in block 1 at otu level 
#> 	0 in block 1 at char level
#> 	0 in block 2 at char level 
#> 	0 in block 1 at state level
#> 	0 in block 2 at state level
#> 
#> Author(s): rvosa
#> 
#> NeXML generated by Bio::Phylo::Project v.0.56 using schema version: 0.9 
#> Size: 289.3 Kb