Output

By default, trajectories.csv will be created in the output directory, with the realization index appended to each observable name in the file. If you prefer, you have the option of creating JSON or MATLAB files that contain the output of a simulation.

Parameter	Data type	Default	Description
channeltitles	bool	false	Specifies whether or not to populate the ChannelTitles array in JSON output files. If set to true, the entries of the ChannelTitles pair with the channel data in the ChannelData array. Each entry in ChannelTitles consists of an observable name followed by the realization number in curly braces, for example susceptible{0}.
compress	bool	false	Specifies whether or not CSV and JSON output files should be compressed using gzip or MATLAB .MAT files with internal compression. This can be useful for large data files.
newmatformat	bool	false	Specifies whether to use the original MATLAB schema or the new MATLAB schema. The original schema included four elements in the .MAT file: version A string. sampletimes A matrix of sample times, with one row and columns equal to the number of samples. observables A matrix of the names of observable quantities, with one column and rows equal to the number of observables. data A matrix with rows equal to the number of observables times the number of realizations and columns equal to the number of samples. The new schema has the same version and sampletimes elements, but combines the observables and data elements into observable1 through observableN (each entry is a matrix with rows equal to the umber of realizations and columns equal to the number of samples).
prefix	string	trajectories	Specifies the main name of the output files to be written, minus the file extension.
writecsv	bool	true	Specifies whether or not to write realization data in CSV format.
writejson	bool	false	Specifies whether or not to write realization data in JSON format. See any example of this type of output format Example.
writematfile	bool	false	Specifies whether or not to write realization data in MATLAB .mat format.
writerealizationindex	bool	true	Specifies whether or not to add a suffix with the realization index to each observable name in a CSV file.

Example

The example configuration file below shows one way you can configure CMS to create JSON output files.

{
    "runs": 1,
    "duration": 365,
    "samples": 100,
    "solver": "SSA",
    "output": {
        "prefix": "test_trajectories",
        "writecsv": false,
        "writejson": true,
        "compress": false,
        "channeltitles": true,
        "writematfile": false,
        "newmatformat": false
    }
}

The test_trajectories.json file below shows the type of output you can expect from the example configuration file above.

{
    "FrameworkVersion": "1.0.176.23",
    "BuildDescription": "clorton (CMS/Main/framework)",
    "Runs": 1,
    "Samples": 100,
    "ObservableNames": [
        "susceptible",
        "exposed",
        "infectious",
        "recovered"
    ],
    "ChannelTitles": [
        "susceptible{0}",
        "exposed{0}",
        "infectious{0}",
        "recovered{0}"
    ],
    "SampleTimes": [
        0.0,
        1.010101,
        2.020202,
        "etc.",
        98.9899,
        100.0
    ],
    "ChannelData": [
        [
            990.0,
            979.0,
            974.0,
            973.0,
            "etc.",
            281.0,
            286.0
        ],
        [
            0.0,
            11.0,
            15.0,
            14.0,
            "etc.",
            5.0,
            3.0
        ],
        [
            10.0,
            9.0,
            8.0,
            6.0,
            "etc.",
            6.0,
            7.0
        ],
        [
            0.0,
            1.0,
            3.0,
            7.0,
            "etc.",
            708.0,
            704.0
        ]
    ],
    "ObservablesCount": 4
}