/// <summary>Writes an organization reports.</summary>
/// <param name="orgId"> The organization.</param>
/// <param name="dir"> The dir.</param>
/// <param name="dateTime"> The period.</param>
/// <param name="deviceData"> Information describing the device.</param>
/// <param name="patientData">Information describing the patient.</param>
/// <param name="testData"> Information describing the test.</param>
/// <param name="workerData"> [out] Information describing the worker.</param>
/// <param name="step"> Amount to increment by.</param>
private static void WriteOrgReportBundle(
string orgId,
string dir,
DateTime dateTime,
OrgDeviceData deviceData,
OrgPatientData patientData,
OrgTestData testData,
OrgWorkerData workerData,
int step)
{
Dictionary <string, FieldValue> fields = OrgUtils.BuildFieldDict(
deviceData,
patientData,
testData,
workerData);
ReportData data = new ReportData(
dateTime,
_orgById[orgId],
_rootLocationByOrgId[orgId],
fields);
string filename = _outputFlat
? Path.Combine(dir, $"{orgId}-{_filenameAdditionForMeasureReports}-{step:0000}{_extension}")
: Path.Combine(dir, $"{orgId}-{_filenameAdditionForMeasureReports}{_extension}");
WriteBundle(
filename,
SanerMeasureReport.GetBundle(data, null));
}
/// <summary>Main entry-point for this application.</summary>
/// <exception cref="ArgumentNullException">Thrown when one or more required arguments are null.</exception>
/// <param name="outputDirectory"> Directory to write files.</param>
/// <param name="dataDirectory"> Allow passing in of data directory.</param>
/// <param name="outputFormat"> The output format, JSON or XML (default: JSON).</param>
/// <param name="state"> State to restrict generation to (default: none).</param>
/// <param name="postalCode"> Postal code to restrict generation to (default: none).</param>
/// <param name="facilityCount"> Number of facilities to generate.</param>
/// <param name="timeSteps"> Number of time-step updates to generate.</param>
/// <param name="timePeriodHours"> Time-step period in hours (default: 24).</param>
/// <param name="seed"> Starting seed to use in generation, 0 for none (default: 0).</param>
/// <param name="recordsToSkip"> Number of records to skip before starting generation (default: 0).</param>
/// <param name="orgSource"> Source for organization records: generate|csv|connectathon (default: connectathon).</param>
/// <param name="prettyPrint"> If output files should be formatted for display.</param>
/// <param name="bedTypes"> Bar separated bed types: ICU|ER... (default: ICU|ER|HU).</param>
/// <param name="operationalStatuses"> Bar separated operational status: U|O|K (default: O|U).</param>
/// <param name="minBedsPerOrg"> The minimum number of beds per hospital (default: 10).</param>
/// <param name="maxBedsPerOrg"> The maximum number of beds per hospital (default: 1000).</param>
/// <param name="changeFactor"> The amount of change in bed state per step (default 0.2).</param>
/// <param name="minIcuPercent"> Minimum percentage of beds for an org which are ICU type.</param>
/// <param name="maxIcuPercent"> Maximum percentage of beds for an org which are ICU type.</param>
/// <param name="ventilatorsPerIcu"> Average number of ventilators per ICU bed.</param>
/// <param name="initialOccupancy"> Initial occupancy of bed percentage.</param>
/// <param name="positiveTestRate"> Rate of people being tested returning positive.</param>
/// <param name="hospitalizationRate"> Rate of people testing positive requiring hospitalization.</param>
/// <param name="patientToIcuRate"> Rate of people hospitalized requiring ICU.</param>
/// <param name="icuToVentilatorRate"> Rate of people in ICU requiring ventilators.</param>
/// <param name="recoveryRate"> Rate of people recovering during hospitalization.</param>
/// <param name="deathRate"> Rate of people dying in hospitalization, when care is available.</param>
/// <param name="outputBundles"> True to output Bundles, false to output raw resources.</param>
/// <param name="outputFlat"> True to output into a single directory, false to nest.</param>
/// <param name="measureMarkdown"> If specified, the filename of the Measure Markdown file.</param>
public static void Main(
string outputDirectory,
string dataDirectory = null,
string outputFormat = "JSON",
string state = null,
string postalCode = null,
int facilityCount = 10,
int timeSteps = 2,
int timePeriodHours = 24,
int seed = 0,
int recordsToSkip = 0,
string orgSource = "connectathon",
bool prettyPrint = true,
string bedTypes = "ICU|ER|HU",
string operationalStatuses = "O|U",
int minBedsPerOrg = 10,
int maxBedsPerOrg = 1000,
double changeFactor = 0.2,
double minIcuPercent = 0.05,
double maxIcuPercent = 0.20,
double ventilatorsPerIcu = 0.20,
double initialOccupancy = 0.20,
double positiveTestRate = 0.5,
double hospitalizationRate = 0.30,
double patientToIcuRate = 0.30,
double icuToVentilatorRate = 0.70,
double recoveryRate = 0.1,
double deathRate = 0.05,
bool outputBundles = true,
bool outputFlat = false,
string measureMarkdown = "")
{
// sanity checks
if (string.IsNullOrEmpty(outputDirectory))
{
throw new ArgumentNullException(nameof(outputDirectory));
}
if (string.IsNullOrEmpty(outputFormat))
{
throw new ArgumentNullException(nameof(outputFormat));
}
if (!Directory.Exists(outputDirectory))
{
Directory.CreateDirectory(outputDirectory);
}
_changeFactor = changeFactor;
_minIcuPercent = minIcuPercent;
_maxIcuPercent = maxIcuPercent;
_ventilatorsPerIcu = ventilatorsPerIcu;
_initialOccupancy = initialOccupancy;
_positiveTestRate = positiveTestRate;
_hospitalizationRate = hospitalizationRate;
_patientToIcuRate = patientToIcuRate;
_icuToVentilatorRate = icuToVentilatorRate;
_recoveryRate = recoveryRate;
_noResourceRecoveryRate = recoveryRate * 0.1;
_deathRate = deathRate;
_noResourceDeathRate = Math.Min(deathRate * 10, 1.0);
_outputBundles = outputBundles;
_outputFlat = outputFlat;
_useJson = outputFormat.ToUpperInvariant().Equals("JSON", StringComparison.Ordinal);
if (_useJson)
{
SerializerSettings settings = new SerializerSettings()
{
Pretty = prettyPrint,
};
_jsonSerializer = new FhirJsonSerializer(settings);
_extension = ".json";
}
else
{
SerializerSettings settings = new SerializerSettings()
{
Pretty = prettyPrint,
};
_xmlSerializer = new FhirXmlSerializer(settings);
_extension = ".xml";
}
_useLookup = (!string.IsNullOrEmpty(orgSource)) || (orgSource.ToUpperInvariant() != "GENERATE");
_connectathon = string.IsNullOrEmpty(orgSource) || (orgSource.ToUpperInvariant() == "CONNECTATHON");
if (seed == 0)
{
_rand = new Random();
}
else
{
_rand = new Random(seed);
}
// always need the geo manager
GeoManager.Init(seed, minBedsPerOrg, maxBedsPerOrg, dataDirectory);
OrgWorkerData.Init(seed);
// only need hospital manager if we are using lookup (avoid loading otherwise)
if (_useLookup || _connectathon)
{
HospitalManager.Init(
seed,
minBedsPerOrg,
maxBedsPerOrg,
dataDirectory,
_connectathon);
}
string dir;
// create our time step directories
if (!_outputFlat)
{
for (int step = 0; step < timeSteps; step++)
{
dir = Path.Combine(outputDirectory, $"t{step}");
if (!Directory.Exists(dir))
{
Directory.CreateDirectory(dir);
}
}
}
// create our organization records
CreateOrgs(facilityCount, state, postalCode, recordsToSkip);
ExportAggregate(outputDirectory, timeSteps, timePeriodHours);
if (!string.IsNullOrEmpty(measureMarkdown))
{
File.WriteAllText(measureMarkdown, SanerMeasure.GetMarkdown());
}
}
/// <summary>Creates aggregate data.</summary>
/// <param name="orgId"> The organization.</param>
/// <param name="deviceData"> [out] Information describing the device.</param>
/// <param name="patientData">[out] Information describing the patient.</param>
/// <param name="testData"> [out] Information describing the test.</param>
/// <param name="workerData"> [out] Information describing the worker.</param>
private static void CreateAggregateData(
string orgId,
out OrgDeviceData deviceData,
out OrgPatientData patientData,
out OrgTestData testData,
out OrgWorkerData workerData)
{
int initialBedCount;
if (_useLookup)
{
initialBedCount = HospitalManager.BedsForHospital(orgId);
}
else
{
initialBedCount = GeoManager.BedsForHospital();
}
double icuRate = (_rand.NextDouble() * (_maxIcuPercent - _minIcuPercent)) + _minIcuPercent;
int icuBeds = (int)(initialBedCount * icuRate);
if (icuBeds < 1)
{
icuBeds = 1;
}
int inpatientBeds = initialBedCount - icuBeds;
int ventilators = (int)(icuBeds * _ventilatorsPerIcu);
if (ventilators < 1)
{
ventilators = 1;
}
// create device data for this org
deviceData = new OrgDeviceData(
initialBedCount,
inpatientBeds,
icuBeds,
ventilators);
// figure out patient numbers based on initial capacity
int patients = (int)(initialBedCount * _initialOccupancy);
int positive = (int)(patients * _positiveTestRate);
int positiveNeedIcu = (int)(positive * _patientToIcuRate);
int positiveNeedVent = (int)(positive * _icuToVentilatorRate);
int negative = patients - positive;
int negativeNeedIcu = 0; // (int)(negative * _patientToIcuRate);
int negativeNeedVent = 0; // (int)(negativeNeedIcu * _icuToVentilatorRate);
int onsetInCare = 0;
int recovered = 0;
int dead = 0;
// create patient data
patientData = new OrgPatientData(
patients,
positive,
positiveNeedIcu,
positiveNeedVent,
negative,
negativeNeedIcu,
negativeNeedVent,
onsetInCare,
recovered,
dead);
// extrapolate test data
int performedTests = (int)(patients / _hospitalizationRate);
int positiveTests = (int)(performedTests * _positiveTestRate);
int negativeTests = performedTests - positive;
int pendingTests = _rand.Next(0, 10);
performedTests += pendingTests;
// create test data record
testData = new OrgTestData(
performedTests,
positiveTests,
negativeTests,
pendingTests);
workerData = new OrgWorkerData();
}
/// <summary>Updates the aggregate data for step.</summary>
/// <param name="deviceData"> [in,out] Information describing the device.</param>
/// <param name="patientData">[in,out] Information describing the patient.</param>
/// <param name="testData"> [in,out] Information describing the test.</param>
/// <param name="workerData"> [out] Information describing the worker.</param>
private static void UpdateAggregateDataForStep(
ref OrgDeviceData deviceData,
ref OrgPatientData patientData,
ref OrgTestData testData,
ref OrgWorkerData workerData)
{
// increase testing
int testDelta = (int)(testData.Performed * _changeFactor);
if (testDelta == 0)
{
testDelta = 1;
}
int testPositiveDelta = (int)(testDelta * _positiveTestRate);
int testNegativeDelta = testDelta - testPositiveDelta;
int testPending = _rand.Next(0, 10);
int patientsShortCare =
Math.Max(0, patientData.PositiveNeedVent - deviceData.Ventilators) +
Math.Max(0, patientData.PositiveNeedIcu - deviceData.ICU) +
Math.Max(0, patientData.PositiveNonIcu - deviceData.Inpatient);
int patientsWithCare = patientData.Positive - patientsShortCare;
double effectiveRecoveryRate = (patientData.Positive == 0)
? 0
: ((_recoveryRate * patientsWithCare) + (_noResourceRecoveryRate * patientsShortCare)) /
((double)patientsWithCare + (double)patientsShortCare);
double effectiveDeathRate = (patientData.Positive == 0)
? 0
: ((_deathRate * patientsWithCare) + (_noResourceDeathRate * patientsShortCare)) /
((double)patientsWithCare + (double)patientsShortCare);
double patientRemovalRate = effectiveDeathRate + effectiveRecoveryRate;
int patientsRemoved = (int)(patientData.Positive * patientRemovalRate);
int patientsDied;
int patientsRecovered;
if (_rand.NextDouble() < 0.5)
{
patientsDied = (int)((double)patientData.Positive * effectiveDeathRate);
patientsRecovered = patientsRemoved - patientsDied;
}
else
{
patientsRecovered = (int)((double)patientData.Positive * effectiveRecoveryRate);
patientsDied = patientsRemoved - patientsRecovered;
}
int positive = patientData.Positive
- patientsRemoved
+ Math.Max((int)(testPositiveDelta * _hospitalizationRate), 1);
int patients = patientData.Total - patientData.Positive + positive;
int positiveNeedIcu = (int)(positive * _patientToIcuRate);
int positiveNeedVent = (int)(positive * _icuToVentilatorRate);
int negative = patients - positive;
int negativeNeedIcu = 0; // (int)(negative * _patientToIcuRate);
int negativeNeedVent = 0; // (int)(negativeNeedIcu * _icuToVentilatorRate);
int dead = patientData.Died + patientsDied;
int recovered = patientData.Recovered + patientsRecovered;
// update records
testData.Update(
testDelta,
testPositiveDelta,
testNegativeDelta,
testPending);
patientData.Update(
patients,
positive,
positiveNeedIcu,
positiveNeedVent,
negative,
negativeNeedIcu,
negativeNeedVent,
0,
recovered,
dead);
workerData.Update();
}
