Use input data files¶

The input data files contain the relatively fixed information about the population within each geographic node. For example, the number of individuals, geography, climate, demographics, and migration data. This topic describes how to download and use the input data files. These are in contrast to the demographic, geography, and migration parameters in the configuration file that control simulation-wide qualities, such as enabling air migration across all nodes in the simulation.

Except for the demographics file, you will generally use input data files without modifying them in any way. Only the demographics file is required, though migration files may be required for multi-node simulations. See Input data files for an overview of each of the different input files, including which are required for different simulations. See Input data file structure for reference information about the structure of each of these files.

Download input files¶

The EMOD-InputData repository uses large file storage (LFS) to manage the binaries and large JavaScript Object Notation (JSON) files. A standard Git clone of the repository will only retrieve the metadata for these files managed with LFS. To retrieve the actual data, follow the steps below.

Install the Git LFS plugin, if it is not already installed.
- For Windows users, download the plugin from https://git-lfs.github.com.
- For CentOS on Azure users, the plugin is included with the PrepareLinuxEnvironment.sh script.
Using a Git client or Command Prompt window, clone the input data repository to retrieve the metadata:
```
git clone https://github.com/InstituteforDiseaseModeling/EMOD-InputData.git
```
Navigate to the directory where you downloaded the metadata for the input data files.
Cache the actual data on your local machine:
```
git lfs fetch
```
Replace the metadata in the files with the actual contents:
```
git lfs checkout
```

Specify input files in the configuration file¶

Follow the steps below to specify which input files to use in a simulation. Only the demographics file is required, though additional files are generally needed for a realistic simulation.

Place all input files for a simulation in the same directory. You will specify this directory when you run a simulation. See Run simulations for more information.
In your configuration file, specify the path to each of these files, relative to the directory above, in the appropriate parameter. Generally, these parameters are appended with “_Filename” or “_Filenames”.

For example, the example below shows the relevant portion of a configuration file. See :doc :parameter-configuration for a complete list of the parameters.

{
    "parameters": {
        "Air_Temperature_Filename": "Namawala_single_node_air_temperature_daily.bin",
        "Air_Temperature_Offset": 0,
        "Air_Temperature_Variance": 2,
        "Base_Rainfall": 100,
        "Campaign_Filename": "campaign.json",
        "Climate_Model": "CLIMATE_BY_DATA",
        "Climate_Update_Resolution": "CLIMATE_UPDATE_DAY",
        "Config_Name": "VectorAndMalaria_5_Namawala_Vector_ITNs",
        "Demographics_Filenames": [
            "Namawala_single_node_demographics.json"
        ],
        "Geography": "Namawala",
        "Land_Temperature_Filename": "Namawala_single_node_land_temperature_daily.bin",
        "Land_Temperature_Offset": 0,
        "Land_Temperature_Variance": 2,
        "Load_Balance_Filename": "",
        "Rainfall_Filename": "Namawala_single_node_rainfall_daily.bin",
        "Rainfall_In_mm_To_Fill_Swamp": 1000.0,
        "Rainfall_Scale_Factor": 1,
        "Relative_Humidity_Filename": "Namawala_single_node_relative_humidity_daily.bin",
        "Relative_Humidity_Scale_Factor": 1,
        "Relative_Humidity_Variance": 0.05
    }
}

Modify demographics files¶

The demographics files provided by IDM generally contain information about prevalence, immunity, risk, population size, and more for a geographic region. However, you will almost certainly want to modify the file to provide more detail or to set up groups within a population to more accurately model heterogeneous populations in terms of transmission, group transitions, or targeted interventions.

The demographics file is the only required input data file, with one exception. You have the option to run a simulation without a demographics file if you set Enable_Demographics_Builtin to 1 in the configuration file. However, this option is primarily used for software testing. It will not provide meaningful simulation data as it does not represent the population of a real geographic location.