### Run Synthea with Custom Exporter (Basic Setup)

Source: https://github.com/synthetichealth/synthea/wiki/Custom-Exporters

Execute Synthea with your custom exporter JAR added to the classpath. This command assumes a basic Synthea setup.

```sh
java -jar synthea-with-dependencies.jar -cp path/to/custom-exporter-template.jar
```

--------------------------------

### Example Synthea Properties File

Source: https://github.com/synthetichealth/synthea/wiki/Common-Configuration

This is an example of a Synthea properties file, showing comments and export settings. Default settings can be overridden in a local settings file.

```properties
# this is a comment
exporter.ccda.export = false
exporter.fhir.export = true
exporter.fhir_stu3.export = false
exporter.fhir_dstu2.export = false
```

--------------------------------

### Apply Profiles Action Example

Source: https://github.com/synthetichealth/synthea/wiki/Flexporter

Example configuration for the 'Apply Profiles' action to assign specific profiles to Patient and Encounter resources.

```yaml
 - name: Apply Profiles
   profiles:
   - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-patient
     applicability: Patient
   - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-encounter
     applicability: Encounter
```

--------------------------------

### Example Usage of Value Functions

Source: https://github.com/synthetichealth/synthea/wiki/Flexporter

An example demonstrating the use of Synthea value functions within resource definition.

```APIDOC
```yaml
-  create_resource:
     - resourceType: ServiceRequest
       based_on:
         resource: Procedure
       fields:
         - location: ServiceRequest.intent
           value: plan
         - location: ServiceRequest.encounter.reference
           value: $getField([Procedure.encounter.reference])
         - location: ServiceRequest.subject.reference
           value: $findRef([Patient])
         - location: ServiceRequest.code.coding
           value: $randomCode([http://hl7.org/fhir/us/mcode/ValueSet/mcode-laterality-vs])
```
```

--------------------------------

### Install Graphviz and Generate Synthea Rules Diagram

Source: https://github.com/synthetichealth/synthea/wiki/Graphviz-Rules-Diagram

Install Graphviz using Homebrew and then execute the rake task to generate a flowchart diagram of Synthea's rules and attributes. The diagram will be saved in the output/graphviz folder.

```bash
brew install graphviz
bundle exec rake synthea:graphviz
```

--------------------------------

### Example: Display Help Messages

Source: https://github.com/synthetichealth/synthea/wiki/Developer-Setup-and-Running

Display help messages and command-line options without further processing.

```bash
run_synthea -h
```

--------------------------------

### Example: Generate Population of 1000 Patients

Source: https://github.com/synthetichealth/synthea/wiki/Developer-Setup-and-Running

Generate a population consisting of 1000 patients.

```bash
run_synthea -p 1000
```

--------------------------------

### Physiology Generator Input Example

Source: https://github.com/synthetichealth/synthea/wiki/Physiology-Models

Example structure for physiology model inputs.

```yaml
inputs:
#  # Effects of age and BMI loosely estimated from a comprehensive study on adult blood pressure
#  # percentiles (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4553889/)
```

--------------------------------

### Example: Generate Population in Massachusetts

Source: https://github.com/synthetichealth/synthea/wiki/Developer-Setup-and-Running

Generate a population for all cities and towns within Massachusetts.

```bash
run_synthea Massachusetts
```

--------------------------------

### Run Synthea with Dependencies

Source: https://github.com/synthetichealth/synthea/wiki/Basic-Setup-and-Running

Execute the Synthea JAR file to start the data generation process. Ensure you are in the directory where the JAR was downloaded.

```bash
cd /directory/you/downloaded/synthea/to
java -jar synthea-with-dependencies.jar
```

--------------------------------

### Lookup Table CSV Example

Source: https://github.com/synthetichealth/synthea/wiki/Generic-Module-Framework:-Transitions

An example CSV file defining probabilities for 'Lookuptablitis' and 'No_Lookuptablitis' transitions based on age, gender, and state. The last two columns correspond to the transition names defined in the JSON configuration.

```csv
age,gender,state,Lookuptablitis,No_Lookuptablitis
0-17,M,Massachusetts,0,1
18-44,M,Massachusetts,0.25,0.75
45-64,M,Massachusetts,0.5,0.5
64-140,M,Massachusetts,0.75,0.25
0-17,F,Massachusetts,0,1
18-44,F,Massachusetts,0.3,0.7
45-64,F,Massachusetts,0.8,0.2
64-140,F,Massachusetts,0,1
...
```

--------------------------------

### Example: Generate Population in Juneau, Alaska

Source: https://github.com/synthetichealth/synthea/wiki/Developer-Setup-and-Running

Generate a population specifically for Juneau, Alaska.

```bash
run_synthea Alaska Juneau
```

--------------------------------

### Example: Generate Population in Seattle with Seed

Source: https://github.com/synthetichealth/synthea/wiki/Developer-Setup-and-Running

Generate a population in Seattle, Washington, using a specific seed.

```bash
run_synthea -s 987 Washington Seattle
```

--------------------------------

### Module Remarks Example

Source: https://github.com/synthetichealth/synthea/wiki/Generic-Module-Framework:-Basics

Illustrates how to add remarks (comments) to a module. Remarks are lists of strings and are ignored by Synthea.

```json
{
  "remarks": [
    "Remarks describe their parent object or detail important ",
    "aspects of the module. Links to sources may be included here: ",
    "http://www.example.com/source/ ",
    
    "You may write use extra newlines to separate out remarks."
  ]
}
```

--------------------------------

### Programmatically Generate Patient Records

Source: https://github.com/synthetichealth/synthea/wiki/Embedding

Example of initializing the Generator and running it to produce patient records.

```java
package com.example.generator;

import org.mitre.synthea.engine.Generator;
import org.mitre.synthea.helpers.Config;

public class Main {

    public static void main(String[] args) {
        Generator.GeneratorOptions options = new Generator.GeneratorOptions();
        options.population = 10;
        Config.set("exporter.hospital.fhir.export", "false");
        Config.set("exporter.practitioner.fhir.export", "false");
        Generator generator = new Generator(options);
        generator.run();
    }
    
}
```

--------------------------------

### Run Synthea with custom modules

Source: https://github.com/synthetichealth/synthea/wiki/Generic-Module-Framework:-Running-New-Modules

Commands to specify a custom module directory for different Synthea installation types.

```bash
java -jar synthea-with-dependencies.jar -d path/to/modules/directory
```

```bash
./run_synthea -d path/to/modules/directory
```

--------------------------------

### Example: Generate Population Aged 30-40

Source: https://github.com/synthetichealth/synthea/wiki/Developer-Setup-and-Running

Generate a population where all patients are between 30 and 40 years old.

```bash
run_synthea -a 30-40
```

--------------------------------

### View Text-Based Patient Record Sample

Source: https://github.com/synthetichealth/synthea/wiki/Getting-Started

Example of the human-readable text output generated by the Synthea exporter.

```text
Mekhi724 Kemmer911
==================
Race:           White
Ethnicity:      Non-Hispanic
Gender:         F
Age:            33
Birth Date:     1983-11-04
Marital Status: M
--------------------------------------------------------------------------------
ALLERGIES: N/A
--------------------------------------------------------------------------------
MEDICATIONS:
2013-08-22 [CURRENT] : Acetaminophen 160 MG for Acute bronchitis (disorder)
1996-05-12 [CURRENT] : Acetaminophen 160 MG for Acute bronchitis (disorder)
1995-04-13 [CURRENT] : Acetaminophen 160 MG for Acute bronchitis (disorder)
1984-01-14 [CURRENT] : Penicillin V Potassium 250 MG for Streptococcal sore throat (disorder)
--------------------------------------------------------------------------------
CONDITIONS:
2015-10-30 - 2015-11-07 : Fetus with chromosomal abnormality
2015-10-30 - 2015-11-07 : Miscarriage in first trimester
2015-10-30 - 2015-11-07 : Normal pregnancy
2013-08-22 - 2013-09-08 : Acute bronchitis (disorder)
1985-08-07 -            : Food Allergy: Fish
--------------------------------------------------------------------------------
CARE PLANS:
2013-08-22 [STOPPED] : Respiratory therapy
                         Reason: Acute bronchitis (disorder)
                         Activity: Recommendation to avoid exercise
                         Activity: Deep breathing and coughing exercises
--------------------------------------------------------------------------------
OBSERVATIONS:
2014-01-14 : Body Weight                              73.9 kg
2014-01-14 : Body Height                              163.7 cm
2014-01-14 : Body Mass Index                          27.6 kg/m2
2014-01-14 : Systolic Blood Pressure                  133.0 mmHg
2014-01-14 : Diastolic Blood Pressure                 76.0 mmHg
2014-01-14 : Blood Pressure                           2.0 
--------------------------------------------------------------------------------
PROCEDURES:
2015-10-30 : Standard pregnancy test for Normal pregnancy
2014-01-14 : Documentation of current medications
--------------------------------------------------------------------------------
ENCOUNTERS:
2015-11-07 : Encounter for Fetus with chromosomal abnormality
2015-10-30 : Encounter for Normal pregnancy
2014-01-14 : Outpatient Encounter
2013-08-22 : Encounter for Acute bronchitis (disorder)
--------------------------------------------------------------------------------
```

--------------------------------

### Example: Generate Population with Specific Seed

Source: https://github.com/synthetichealth/synthea/wiki/Developer-Setup-and-Running

Generate a population using a specific seed value for reproducible results.

```bash
run_synthea -s 12345
```

--------------------------------

### Migrate MedicationOrder to CallSubmodule

Source: https://github.com/synthetichealth/synthea/wiki/Medication-Diversification-Tool-(MDT)

Example showing the transition from a legacy MedicationOrder state to a CallSubmodule state in an asthma module.

```json
...
    "Prescribe_Maintenance_Inhaler": {
      "type": "MedicationOrder",
      "reason": "asthma_condition",
      "codes": [
        {
          "system": "RxNorm",
          "code": "895994",
          "display": "120 ACTUAT Fluticasone propionate 0.044 MG/ACTUAT Metered Dose Inhaler"
        }
      ],
      "prescription": {
        "as_needed": true
      },
      "direct_transition": "Prescribe_Emergency_Inhaler",
      "chronic": true
    },
...
```

```json
...
    "Prescribe_Maintenance_Inhaler": {
      "type": "CallSubmodule",
      "submodule": "medications/maintenance_inhaler",
      "direct_transition": "Prescribe_Emergency_Inhaler"
    },
...
```

--------------------------------

### Submodule Log Example

Source: https://github.com/synthetichealth/synthea/wiki/Generic-Module-Framework:-Submodules

Shows the state transition log for a medication submodule when processed independently. This log details the sequence of states within the submodule itself.

```text
/===============================================================================
| Medication Submodule Log
|===============================================================================
| Entered                   | Exited                    | State
|---------------------------|---------------------------|-----------------------
| 2017-01-17T09:50:41-05:00 | 2017-01-17T09:50:41-05:00 | Initial
| 2017-01-17T09:50:41-05:00 | 2017-01-17T09:50:41-05:00 | Prescribe_Medication
| 2017-01-17T09:50:41-05:00 | 2017-01-17T09:50:41-05:00 | Med_Terminal
\===============================================================================
```

--------------------------------

### Initial State Configuration

Source: https://github.com/synthetichealth/synthea/wiki/Generic-Module-Framework:-States

The Initial state marks the starting point of a generic module. It requires the type to be set to 'Initial' and can only appear once per module.

```json
"Initial": {
  "type": "Initial"
}
```

--------------------------------

### Example: Export FHIR with US Core IG

Source: https://github.com/synthetichealth/synthea/wiki/Developer-Setup-and-Running

Generate a population that exports FHIR data according to the US Core R4 Implementation Guide profiles.

```bash
run_synthea --exporter.fhir.use_us_core_ig true --exporter.fhir.us_core_version 4.0.0
```

--------------------------------

### Invalid Attribute Name Example

Source: https://github.com/synthetichealth/synthea/wiki/Generic-Module-Framework:-Basics

Shows an example of a bad attribute name, which is not in lower_snake_case and contains spaces.

```json
{
  "assign_to_attribute": "Type of Alzheimer's"
}
```

--------------------------------

### Synthea Snapshot Evolution Example

Source: https://github.com/synthetichealth/synthea/wiki/Evolving-a-Population

This sequence demonstrates creating an initial population, saving a snapshot, and then evolving it over time in multiple steps, saving updated snapshots at each stage. Ensure unique base directories for each step to avoid export failures.

```bash
$ mkdir -p output/1 output/2 output/3
$ ./run_synthea -p 5 -u output/1/snap --exporter.baseDirectory output/1
$ ./run_synthea -i output/1/snap -u output/2/snap -t 100 --exporter.baseDirectory output/2
$ ./run_synthea -i output/2/snap -u output/3/snap -t 100 --exporter.baseDirectory output/3
```

--------------------------------

### Procedure: Appendectomy Example

Source: https://github.com/synthetichealth/synthea/wiki/Generic-Module-Framework:-States

Example of a Procedure state for an appendectomy, including reason and duration. The duration is specified in hours.

```JSON
"Appendectomy": {
  "type": "Procedure",
  "reason": "Appendicitis",
  "codes": [
    {
      "system": "SNOMED-CT",
      "code": "6025007",
      "display": "Laparoscopic appendectomy"
    }
  ],
  "duration": {
    "low": 2,
    "high": 3,
    "unit": "hours"
  }
}
```

--------------------------------

### Run Synthea with Custom Settings (Developer)

Source: https://github.com/synthetichealth/synthea/wiki/Common-Configuration

Use this command to run Synthea with a custom settings file when using the developer setup. The `-c` flag specifies the path to your settings file.

```bash
./run_synthea -c path/to/settings/file
```

--------------------------------

### Build and Run Synthea via Gradle

Source: https://context7.com/synthetichealth/synthea/llms.txt

Use Gradle commands to build the project from source and execute the simulator using convenience scripts.

```bash
# Clone the repository
git clone https://github.com/synthetichealth/synthea.git
cd synthea

# Build and run tests
./gradlew build check test

# Run Synthea using Gradle
./gradlew run

# Run using the convenience script (easier for passing arguments)
./run_synthea -p 100 Massachusetts Boston

# Generate 1000 patients with a specific seed
./run_synthea -s 987 -p 1000 Washington Seattle

# Use a custom configuration file
./run_synthea -c /path/to/custom.properties -p 100

# Use custom disease modules from a directory
./run_synthea -d /path/to/custom/modules -p 100

# Generate GraphViz visualizations of disease modules
./gradlew graphviz

# Generate a list of concepts used in records
./gradlew concepts

# Generate a list of patient attributes
./gradlew attributes

# On Windows, use the .bat equivalents
.\gradlew.bat build
.\run_synthea.bat -p 100
```

--------------------------------

### SNOMED Code Example

Source: https://github.com/synthetichealth/synthea/wiki/Generic-Module-Framework:-Basics

Example of a SNOMED-CT code used for clinical findings, symptoms, or diagnoses within Synthea states.

```json
{
  "system": "SNOMED-CT",
  "code": "44054006",
  "display": "Diabetes"
}
```

--------------------------------

### FHIR query reference example

Source: https://github.com/synthetichealth/synthea/wiki/FHIR-Transaction-Bundles

Example of a query reference used within patient bundles to refer to omitted Practitioner resources.

```text
Practitioner?identifier=http://hl7.org/fhir/sid/us-npi|999999647
```

--------------------------------

### Main Module with Submodule Log Example

Source: https://github.com/synthetichealth/synthea/wiki/Generic-Module-Framework:-Submodules

Demonstrates the combined state transition log when a submodule is called by a main module. The submodule's states are interleaved within the main module's log, showing inline execution.

```text
/===============================================================================
| Main Module Log
|===============================================================================
| Entered                   | Exited                    | State
|---------------------------|---------------------------|-----------------------
| 2017-01-17T09:50:41-05:00 | 2017-01-17T09:50:41-05:00 | Initial
| 2017-01-17T09:50:41-05:00 | 2017-01-17T09:50:41-05:00 | Example_Condition
| 2017-01-17T09:50:41-05:00 | 2017-01-17T09:50:41-05:00 | Encounter
| 2017-01-17T09:50:41-05:00 | 2017-01-17T09:50:41-05:00 | CallSubmodule
| 2017-01-17T09:50:41-05:00 | 2017-01-17T09:50:41-05:00 | Initial
| 2017-01-17T09:50:41-05:00 | 2017-01-17T09:50:41-05:00 | Prescribe_Medication
| 2017-01-17T09:50:41-05:00 | 2017-01-17T09:50:41-05:00 | Med_Terminal
| 2017-01-17T09:50:41-05:00 |                           | Terminal
\===============================================================================
```

--------------------------------

### Abridged Zip Code CSV Example for UK

Source: https://github.com/synthetichealth/synthea/wiki/Zip-or-Postal-Codes

Example format for defining non-US geography data using the required CSV structure.

```csv
,USPS,ST,NAME,ZCTA5,LAT,LON
0,West Midlands,WMS,Shrewsbury,SY1,52.7081,-2.7549
1,West Midlands,WMS,Shrewsbury,SY2,52.7083,-2.7546
2,West Midlands,WMS,Shrewsbury,SY3,52.7089,-2.7543
```

--------------------------------

### Build and Run Synthea with Custom Exporters

Source: https://context7.com/synthetichealth/synthea/llms.txt

Commands for building the custom exporter JAR and executing Synthea with the custom classpath.

```bash
# Build the custom exporter JAR
./gradlew jar

# Run Synthea with custom exporter
# Basic setup:
java -jar synthea-with-dependencies.jar -cp path/to/custom-exporter.jar -p 100

# Developer setup:
# Place JAR in ./lib/custom/ directory
./run_synthea -p 100
```

--------------------------------

### Intersection Function Example

Source: https://github.com/synthetichealth/synthea/wiki/Physiology-Models

This is a placeholder for an intersection function example, intended to represent discrete data generated by medical devices and wearables. The specific implementation is left to the reader.

```yml
...
```

--------------------------------

### Clone and Build Synthea Project

Source: https://github.com/synthetichealth/synthea/wiki/Developer-Setup-and-Running

Clone the Synthea repository and build the project using Gradle. Ensure Java 17 or newer is installed. On Windows, use `.\gradlew.bat`.

```bash
git clone https://github.com/synthetichealth/synthea.git
cd synthea
./gradlew build check test
```

--------------------------------

### List Synthea output files

Source: https://github.com/synthetichealth/synthea/wiki/Docker

Navigates to the mounted directory and lists the generated output files.

```bash
$ cd /mnt/synthea && ls
  CCDA  fhir  html
```

--------------------------------

### Override File Format Example

Source: https://github.com/synthetichealth/synthea/wiki/Module-Overrides

This is an example of a Java properties file used for module overrides. It specifies the module file path, a JSONPath to the value, and the new value.

```properties
congestive_heart_failure.json\:\:$['states']['Age_70-79-Chance\ of\ CHF']['distributed_transition'][0]['distribution'] = 0.024
congestive_heart_failure.json\:\:$['states']['Age_80-Chance\ of\ CHF']['distributed_transition'][0]['distribution'] = 0.045
atopy.json\:\:$['states']['Initial']['complex_transition'][0]['distributions'][0]['distribution'] = 0.917
atopy.json\:\:$['states']['Initial']['complex_transition'][1]['distributions'][0]['distribution'] = 0.033
```

--------------------------------

### Run Synthea with Custom Settings (JAR)

Source: https://github.com/synthetichealth/synthea/wiki/Common-Configuration

Use this command to run Synthea with a custom settings file when using the JAR distribution. The `-c` flag specifies the path to your settings file.

```bash
java -jar synthea-with-dependencies.jar -c path/to/settings/file
```

--------------------------------

### Hospital CSV File Format Example (UK)

Source: https://github.com/synthetichealth/synthea/wiki/Provider-Data

This CSV example demonstrates the expected format for hospital data, including columns for ID, name, address, location (LAT/LON), and other relevant details. The first column is ignored by the program.

```csv
,id,name,address,city,state,zip,county,phone,type,ownership,emergency,quality,LAT,LON
0,010001,Royal Shrewsbury Hospital,Mytton Oak Rd,Shrewsbury,WMS,SY3 8XQ,Shropshire,01743261000,NHS Teaching Hospital,Government - Hospital District or Authority,Yes,5,52.7091,-2.7931
```

--------------------------------

### ImagingStudy: Ankle X-Ray Example

Source: https://github.com/synthetichealth/synthea/wiki/Generic-Module-Framework:-States

Example of an ImagingStudy state for an ankle X-ray. It includes procedure code, series details (body site, modality), and image instances with titles and SOP classes. The modality is 'Digital Radiography' and the SOP class is 'Digital X-Ray Image Storage'.

```JSON
"Ankle_X_Ray": {
  "type": "ImagingStudy",
  "procedure_code": {
    "system": "SNOMED-CT",
    "code": "19490002",
    "display": "Ankle X-ray"
  },
  "series": [
    {
      "body_site": {
        "system": "SNOMED-CT",
        "code": "344001",
        "display": "Ankle"
      },
      "modality": {
        "system": "DICOM-DCM",
        "code": "DX",
        "display": "Digital Radiography"
      },
      "instances": [
        {
          "title": "Image of ankle",
          "sop_class": {
            "system": "DICOM-SOP",
            "code": "1.2.840.10008.5.1.4.1.1.1.1",
            "display": "Digital X-Ray Image Storage"
          }
        }
      ]
    }
  ]
}
```

--------------------------------

### Examplitis Module Definition (JSON)

Source: https://github.com/synthetichealth/synthea/wiki/Generic-Module-Framework:-Complete-Example

This JSON defines a complete medical module for the artificial disease 'Examplitis'. It includes states for initial conditions, age guards, disease onset, treatment, and outcomes like death. Use this structure to define custom medical scenarios in Synthea.

```json
{
  "name": "Examplitis",
  "remarks": [
    "Examplitis is a painful condition that affects only males. Most patients ",
    "can be cured with Examplitol or an Examplotomy but some never recover."
  ],
  "states": {

    "Initial": {
      "type": "Initial",
      "conditional_transition": [
        {
          "condition": {
            "condition_type": "Gender",
            "gender": "M"
          },
          "transition": "Age_Guard"
        },
        {
          "transition": "Terminal"
        }
      ]
    },

    "Age_Guard": {
      "type": "Guard",
      "allow": {
        "condition_type": "Age",
        "operator": ">",
        "quantity": 40,
        "unit": "years"
      },
      "distributed_transition": [
        {
          "distribution": 0.10,
          "transition": "Pre_Examplitis"
        },
        {
          "distribution": 0.90,
          "transition": "Terminal"
        }
      ]
    },

    "Pre_Examplitis": {
      "type": "Delay",
      "range": {
        "low": 0,
        "high": 10,
        "unit": "years"
      },
      "direct_transition": "Examplitis"
    },

    "Examplitis": {
      "type": "ConditionOnset",
      "target_encounter": "Wellness_Encounter",
      "codes": [
        {
          "system": "SNOMED-CT",
          "code": "123",
          "display": "Examplitis"
        }
      ],
      "direct_transition": "Wellness_Encounter"
    },

    "Wellness_Encounter": {
      "type": "Encounter",
      "wellness": true,
      "direct_transition": "Examplitol"
    },

    "Examplitol": {
      "type": "MedicationOrder",
      "reason": "Examplitis",
      "codes": [
        {
          "system": "RxNorm",
          "code": "456",
          "display": "Examplitol"
        }
      ],
      "distributed_transition": [
        {
          "distribution": 0.2,
          "transition": "Pre_Examplotomy"
        },
        {
          "distribution": 0.1,
          "transition": "Last_Days"
        },
        {
          "distribution": 0.7,
          "transition": "Terminal"
        }
      ]
    },

    "Pre_Examplotomy": {
      "type": "Delay",
      "range": {
        "low": 18,
        "high": 36,
        "unit": "months"
      },
      "direct_transition": "Examplotomy_Encounter"
    },

    "Examplotomy_Encounter": {
      "type": "Encounter",
      "encounter_class": "ambulatory",
      "codes": [
        {
          "system": "SNOMED-CT",
          "code": "ABC",
          "display": "Examplotomy Encounter"
        }
      ],
      "direct_transition": "Examplotomy"
    },

    "Examplotomy": {
      "type": "Procedure",
      "duration": {
        "low": 2,
        "high": 3,
        "unit": "hours"
      },
      "codes": [
        {
          "system": "SNOMED-CT",
          "code": "789",
          "display": "Examplotomy"
        }
      ],
      "reason": "Examplitis",
      "direct_transition": "End_Examplotomy_Encounter"
    },

    "End_Examplotomy_Encounter": {
    	"type": "EncounterEnd",
    	"distributed_transition": [
        {
          "distribution": 0.1,
          "transition": "Death"
        },
        {
          "distribution": 0.9,
          "transition": "Terminal"
        }
      ]
    },

    "Last_Days": {
      "type": "Delay",
      "range": {
          "low": 8,
          "high": 20,
          "unit": "years"
      },
      "direct_transition": "Death"
    },

    "Death": {
      "type": "Death"
    },

    "Terminal": {
      "type": "Terminal"
    }
  }
}

```

--------------------------------

### Example: Generate Only Female Patients

Source: https://github.com/synthetichealth/synthea/wiki/Developer-Setup-and-Running

Generate a population consisting solely of female patients.

```bash
run_synthea -g F
```

--------------------------------

### Run Synthea with Script

Source: https://github.com/synthetichealth/synthea/wiki/Developer-Setup-and-Running

Use the `run_synthea` script for easier command-line argument passing. On Windows, use `.\run_synthea.bat`.

```bash
./run_synthea
```

--------------------------------

### Example: Generate Population in Salt Lake City with Seed and Size

Source: https://github.com/synthetichealth/synthea/wiki/Developer-Setup-and-Running

Generate a population of 100 patients in Salt Lake City, Utah, using a specific seed.

```bash
run_synthea -s 21 -p 100 Utah "Salt Lake City"
```

--------------------------------

### Code with ValueSet Example

Source: https://github.com/synthetichealth/synthea/wiki/Generic-Module-Framework:-Basics

Includes a code with system, code, and display, along with an optional ValueSet for terminology services. Requires a configured terminology service URL.

```json
{
  "system": "SNOMED-CT",
  "code": "2501000087107",
  "display": "MRI of right knee with contrast",
  "value_set": "http://snomed.info/sct?fhir_vs=ecl/<<2491000087104"
}
```

--------------------------------

### Define MedicationOrder States

Source: https://github.com/synthetichealth/synthea/wiki/Generic-Module-Framework:-States

Examples of prescribing medications with optional dosage, duration, and as-needed status.

```json
"Prescribe_Metformin": {
  "type": "MedicationOrder",
  "assign_to_attribute": "diabetes_medication",
  "reason": "Diabetes",
  "codes": [
    {
      "system": "RxNorm",
      "code": "860975",
      "display": "24 HR Metformin hydrochloride 500 MG Extended Release Oral Tablet"
    }
  ]
}
```

```json
"Examplitol": {
  "type": "MedicationOrder",
  "reason": "Examplitis",
  "codes": [
    {
      "system": "RxNorm",
      "code": "123456",
      "display": "Examplitol 100mg [Examplitol]"
    }
  ],
  "prescription": {
    "refills": 2,
    "dosage": {
      "amount": 1,
      "frequency": 2,
      "period": 1,
      "unit": "days"
    },
    "duration": {
      "quantity": 2,
      "unit": "weeks"
    },
    "instructions": [
      {
        "system": "SNOMED-CT",
        "code": "311501008",
        "display": "Half to one hour before food"
      }
    ]
  }
}
```

```json
"Examplitol": {
  "type": "MedicationOrder",
  "reason": "Examplitis",
  "codes": [
    {
      "system": "RxNorm",
      "code": "123456",
      "display": "Examplitol 100mg [Examplitol]"
    }
  ],
  "prescription": {
    "as_needed": true
  }
}
```

--------------------------------

### Run Synthea with Overrides

Source: https://github.com/synthetichealth/synthea/wiki/Module-Overrides

Execute the simulation using the custom override properties file.

```bash
run_synthea --module_override=./appendicitis_overrides.properties
```

--------------------------------

### Run One-Off Physiology Simulations

Source: https://github.com/synthetichealth/synthea/wiki/Physiology-Models

Execute individual physiology models using Gradle for debugging and optimization.

```bash
  ./gradlew physiology --args="config/simulations/circadian_clock.yml"
  ./gradlew physiology --args="config/simulations/ecg.yml"
  ./gradlew physiology --args="config/simulations/insulin_signalling_diabetic.yml"
  ./gradlew physiology --args="config/simulations/insulin_signalling_normal.yml"
  ./gradlew physiology --args="config/simulations/liver_metabolism.yml"
  ./gradlew physiology --args="config/simulations/mammalian_circadian_rhythm_non_24hr.yml"
  ./gradlew physiology --args="config/simulations/menstrual_cycle.yml"
  ./gradlew physiology --args="config/simulations/o2_transport_metabolism.yml"
  ./gradlew physiology --args="config/simulations/plasma_melatonin.yml"  
  ./gradlew physiology --args="config/simulations/pulmonary_fluid_dynamics.yml"
  ./gradlew physiology --args="config/simulations/pulmonary_oxygen_intake.yml"
  ./gradlew physiology --args="config/simulations/telomere_associated_dna_damage.yml"
  ./gradlew physiology --args="config/simulations/weight_change.yml"
```

--------------------------------

### Define MedicationEnd States

Source: https://github.com/synthetichealth/synthea/wiki/Generic-Module-Framework:-States

Examples of ending medication prescriptions using codes, attributes, or state references.

```json
"End_Metformin": {
  "type": "MedicationEnd",
  "codes": [
    {
      "system": "RxNorm",
      "code": "860975",
      "display": "24 HR Metformin hydrochloride 500 MG Extended Release Oral Tablet"
    }
  ]
}
```

```json
"End_Insulin_Medicine": {
  "type": "MedicationEnd",
  "referenced_by_attribute": "insulin_medicine"
},
```

```json
"End_Bromocriptine": {
  "type": "MedicationEnd",
  "medication_order": "Bromocriptine_Start"
},
```

--------------------------------

### Clone and Build Synthea Repository

Source: https://github.com/synthetichealth/synthea/wiki/Dev-Days

Clone the Synthea repository from GitHub and build the project using Gradle. This is a prerequisite for running Synthea.

```bash
git clone https://github.com/synthetichealth/synthea.git
cd synthea
./gradlew test
```

--------------------------------

### Synthea Command-Line Options

Source: https://github.com/synthetichealth/synthea/wiki/Developer-Setup-and-Running

Overview of command-line arguments for `run_synthea`, including options for seed, population size, age, gender, configuration, and location.

```bash
run_synthea [-h]
            [-s seed]
            [-cs clinician seed]
            [-p populationSize]
            [-g gender]
            [-a minAge-maxAge]
            [-c localConfigFilePath]
            [-d localModulesDirPath]
            [state [city]]
```

--------------------------------

### False Condition Example

Source: https://github.com/synthetichealth/synthea/wiki/Generic-Module-Framework:-Logic

This condition always evaluates to false and is primarily for testing purposes. It requires no sub-conditions.

```json
{
  "condition_type": "False"
}
```

--------------------------------

### Run Synthea Simulation

Source: https://github.com/synthetichealth/synthea/wiki/Developer-Setup-and-Running

Execute the primary Synthea simulation using the `run` Gradle task. On Windows, use `.\gradlew.bat`.

```bash
./gradlew run
```

--------------------------------

### True Condition Example

Source: https://github.com/synthetichealth/synthea/wiki/Generic-Module-Framework:-Logic

This condition always evaluates to true and is primarily for testing purposes. It requires no sub-conditions.

```json
{
  "condition_type": "True"
}
```

--------------------------------

### Running Synthea Data Generator

Source: https://github.com/synthetichealth/synthea/wiki/Other-Areas

Execute the Synthea generator from the command line with specified population, location, and other options. The output shows the loading of modules and the generation progress.

```bash
./run_synthea -p 1 "West Midlands" Shrewsbury

...abridged...

Loaded 70 modules.
Running with options:
Population: 1
Seed: 0
Location: Shrewsbury, West Midlands
Min Age: 0
Max Age: 140
1 -- Brigitte394 Stark857 (50 y/o F) Shrewsbury, West Midlands DECEASED
1 -- Jeanine128 Gleason633 (57 y/o F) Shrewsbury, West Midlands 
{alive=1, dead=1}
```

--------------------------------

### Or Condition Example

Source: https://github.com/synthetichealth/synthea/wiki/Generic-Module-Framework:-Logic

Use this condition to return true if any of the sub-conditions are met. It requires a list of conditions to evaluate.

```json
{
  "condition_type": "Or",
  "conditions": [
    {
      "condition_type": "Gender",
      "gender": "M" 
    },
    {
      "condition_type": "Age",
      "operator": ">=",
      "quantity": 40,
      "unit": "years"
    }
  ]
}
```

--------------------------------

### Build JAR File with Gradle

Source: https://github.com/synthetichealth/synthea/wiki/Custom-Exporters

Use this Gradle command to compile your custom exporter code and package it into a JAR file for use with Synthea.

```sh
./gradlew jar
```

--------------------------------

### Measurement Unit Example

Source: https://github.com/synthetichealth/synthea/wiki/Generic-Module-Framework:-Basics

Defines a unit of measurement. Any string is valid, but metric units are typically used.

```json
{
  "unit": "cm"
}
```

--------------------------------

### Age Unit Example

Source: https://github.com/synthetichealth/synthea/wiki/Generic-Module-Framework:-Basics

Specifies a quantity with a unit of age. Valid age units are the same as time units.

```json
{
  "quantity": 40,
  "unit": "years"
}
```

--------------------------------

### Synthea Help Option

Source: https://github.com/synthetichealth/synthea/wiki/Basic-Setup-and-Running

Use the -h flag to display help messages and command-line options without running Synthea.

```bash
java -jar synthea-with-dependencies.jar -h
```