summary-nexml-method: Summary method for nexml objects

In RNeXML: Semantically Rich I/O for the 'NeXML' Format

Summary method for nexml objects

Description

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 signature 'nexml'
summary(object)

Arguments

object

the nexml object

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.

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

Examples

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

# each characters block defines 1 character:
s$ncharacters

# 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

# pretty-printed summary:
nex # this is the same as show(nex)

RNeXML documentation built on Feb. 16, 2023, 6:56 p.m.