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<?xml version="1.0" encoding="ISO-8859-1"?>
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This file is an example of a simple taxa block.
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The nexml root element below is structured as follows:
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* there is a required version attribute. Additions where
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the 'core' remains backward compatible are identified
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by decimal increases (1.1, 1.2, etc.). Changes to the
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core standard are identified by integer increases (2.0,
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3.0, etc.). The former is somewhat likely to happen in
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practice, the latter hopefully isn't.
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* In some places in instance documents, snippets of schema
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language code are necessary, for example to specify
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concrete subclasses. Such snippets are bound to the
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http://www.w3.org/2001/XMLSchema-instance namespace, and
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by convention identified by the 'xsi' prefix.
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http://en.wikipedia.org/wiki/Xsd
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* to facilitate validation, the location of the schema is
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specified in the root element. Such a specification is
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done using the schema language snippet xsi:schemaLocation
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* by convention, root elements of nexml fragments are
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pre-fixed with 'nex', which is bound to the namespace
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http://www.nexml.org/1.0
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* the optional 'generator' attribute can be used to specify
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which program wrote out the file.
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* other xml namespaces (i.e. attributes with the 'xmlns'
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prefix) can be specified here, in case they're used
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in child elements. For example, the xlink namespace
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is used for links ('href' attributes, as in html), so
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that child elements may contain links to other resources.
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http://en.wikipedia.org/wiki/XLink
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xmlns:xlink="http://www.w3.org/1999/xlink"
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xmlns:nex="http://www.nexml.org/2009"
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xmlns="http://www.nexml.org/2009"
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xsi:schemaLocation="http://www.nexml.org/2009 ../xsd/nexml.xsd">
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The taxa element is analogous to the taxa block in nexus
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files. Like all elements that capture things that might
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need to be referred to elsewhere, it requires an 'id'
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attribute, whose value must consist of a string of alpha-
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numeric characters, starting with a letter. In addition,
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it may (optionally) have the following attributes:
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* 'label', a free form string, only meant for humans
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* 'xml:base', indicating the base url of the resource
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* 'xml:lang', indicating a two-letter language code
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* 'xml:id', a file-scope unique ID
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* 'xlink:href', a link to somewhere else
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* 'class', a vector of nexml id references pointing
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to classes the element belongs to (this is analogous
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to 'sets' in nexus, but using the xml idiom to do
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xml:base="http://example.org/"
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The taxon element is analogous to a single label in
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a nexus taxa block. It may have the same additional
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attributes (label, xml:base, xml:lang, xml:id, xlink:href
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and class) as the taxa element.
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removed
inst/examples/taxa.xml
