output

The <output> elements are used to specify particular ways of writing the results of MASTER calculations to disk. There are a number of different types of <output> elements, some of which only make sense for certain simulation types.

JsonOutput

The most general type of output element is the JsonOutput type which is specified in the following way:

    <output spec='JsonOutput' fileName='STRING'/>

where the fileName attribute is used to specify the name of the output file. As indicated by the name of the type, this output generates a JSON-formatted output file. The precise contents of the file depend on the type of the simulation, however:

• For Trajectory simulations, the file contains a t element which is a vector of the times at which population sizes were recorded. It contains additional elements (one for each population type) containing the population sizes at those times.

• For Ensemble simulations, the file contains a trajectories element which is a vector containing t elements and population type elements for each of the populations generated.

• For EnsembleSummary simulations, the file contains a t element which is a vector of times at which the moments were estimated, as well as additional elements (one for each moment) containing the moment estimates themselves.

• The InheritanceTrajectory simulation type results in a similar output file to that of the Trajectory type, with the caveat that the population sizes and times elements will contain no entries unless the samplePopulationSizes attribute of that simulation type is "true".

• Likewise, the InheritanceEnsemble simulation type results in a similar output file to that of the Ensemble type, provided samplePopulationSizes is set to "true".

NewickOutput

The NewickOutput output element is applicable only to those simulations that result in inheritance graphs. It is specified in the following way:

    <output spec='NewickOutput' fileName='STRING'
            reverseTime='BOOLEAN'
            collapseSingleChildNodes='BOOLEAN'/>

where the fileName attribute specifies the name of an output file and reverseTime determines whether the graph should be read in forward or reverse time. Once the simulation is complete, the output file contains one (in the case of InheritanceTrajectory simulations) or more (as in the case of InheritanceEnsemble simulations) extended Newick representations of the simulated inheritance graph(s). (In the special case that a graph is tree-like in the time-direction specified, this extended format reduces to the standard Newick representation.) If the collapseSingleChildNodes attribute is set to "true", nodes that represent changes of lineage state (e.g. migration events) rather than multifurcations are removed from the graph prior to constructing the Newick representation. This is sometimes necessary for the Newick string to be parsed by external utilities such as APE.

NexusOutput

The NexusOutput output element is also only applicable to inheritance simulations. It is specified via:

    <output spec='NexusOutput' fileName='STRING'
            reverseTime='BOOLEAN'
            collapseSingleChildNodes='BOOLEAN'/>

where the attributes have the meanings described above. Just as for NewickOutput, this output produces extended Newick representations of the graphs. This output, however, packs these representations into a NEXUS file. Additionally, this output includes annotations that provide information about the specific population carrying each lineage at each node and the name of the reaction which produced that node. (A grammar for the annotated tree/network format used is available here.) When reticulation is absent, these files can be visualized using FigTree and IcyTree.