O for the 'NeXML' Format

Author: Carl Boettiger
Initial version: 2014-03-21

Definitions of the simmap namespace, as defined for the use in RNeXML. The prefix nex: refers to the NeXML schema.

term | definition ------------------- | ------------- simmap:reconstructions | A container of one or more stochastic character map reconstructions, as a meta child of a the nex:edge element to which the contained stochastic character map reconstructions are being assigned. simmap:reconstruction | A single stochastic character map reconstruction for a given nex:edge. Normally nested within a simmap:reconstructions element. simmap:char | The id of a character trait, as defined by the nex:char element with this value as its id. This is a property of a simmap:reconstruction. simmap:stateChange | A character state assignment to the given nex:edge during a specified interval, as a property of a simmap:reconstruction. Must have children simmap:order, simmap:length, and simmap:state. simmap:order | The chronological order (from the root) in which the state is assigned to the edge. An edge that does not change states still has simmap:order 1. This is a property of a simmap:stateChange. simmap:length | The duration for which the edge occupies the assigned state, in the same units as the nex:length attribute defined on the nex:edge being annotated. This is a property of a simmap:stateChange. simmap:state | The id of a nex:state of the nex:char identified by the simmap:char property of the simmap:reconstruction. This is a property of a simmap:stateChange.