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
}