config file error

[kirankumarduddu]

What happened?

after i change generate.only_dead_patients = false to true and run synthia during run process config file changes to false automatically and doesnt create any dead patients

Environment

- OS:windows
- Java:

Relevant log output

No response

[dehall]

Please make sure that you are editing the synthea.properties that exists in src/main/resources, not a version under the bin or build directories. The gradle build process will overwrite the bin and build directories, so if you modify files in those then you'll see this issue of files changing back unexpectedly. Make your changes in the src version instead and they will stick.

Other than that, nothing in Synthea has the ability to write to that config file. If you're 100% sure you're editing the right version there is something else on your system that is reverting it somehow.

[kirankumarduddu]

@dehall Thanks for your response , I am getting below error after changing properties under main

PS C:\Visual Code\synthea> ./run_synthea -p 10 -m "hospice_treatment"
ARG = -p
ARG = 10
ARG = -m
ARG = hospice_treatment
ARG =
syntheaArgs = '-p','10','-m','hospice_treatment',

Task :run
SLF4J: No SLF4J providers were found.
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#noProviders for further details.
Scanned 84 modules and 140 submodules.
Loading submodule modules\allergies\allergy_panel.json
Loading submodule modules\allergies\drug_allergy_incidence.json
Loading submodule modules\allergies\environmental_allergy_incidence.json
Loading submodule modules\allergies\food_allergy_incidence.json
Loading submodule modules\allergies\immunotherapy.json
Loading submodule modules\allergies\outgrow_env_allergies.json
Loading submodule modules\allergies\outgrow_food_allergies.json
Loading submodule modules\allergies\severe_allergic_reaction.json
Loading submodule modules\anemia\anemia_sub.json
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Loading submodule modules\contraceptives\intrauterine_device.json
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Loading submodule modules\dermatitis\mid_severe_eczema_obs.json
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Loading submodule modules\heart\avrr\intraop_meds_blood.json
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Loading submodule modules\heart\cabg\icu_meds_devices.json
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Loading submodule modules\heart\chf_meds_hfmef.json
Loading submodule modules\heart\chf_meds_hfref_nyha2.json
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Loading Lookup Table: or_blood_anemia_check.csv
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Loading submodule modules\medications\ear_infection_antibiotic.json
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Loading submodule modules\medications\hypertension_medication.json
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Loading submodule modules\medications\moderate_opioid_pain_reliever.json
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Loading Lookup Table: statin_ingredient_distribution.csv
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Loading submodule modules\medications\strong_opioid_pain_reliever.json
Loading submodule modules\metabolic_syndrome\amputations.json
Loading submodule modules\metabolic_syndrome\dme_supplies.json
Loading submodule modules\metabolic_syndrome\eye_conditions.json
Loading submodule modules\metabolic_syndrome\kidney_conditions.json
Loading submodule modules\metabolic_syndrome\medications.json
Loading submodule modules\snf\skilled_nursing_facility.json
Loading submodule modules\surgery\general_anesthesia.json
Loading submodule modules\total_joint_replacement\functional_status_assessments.json
Loading submodule modules\veterans\veteran_suicide_probabilities.json
Loading submodule modules\weight_loss\mend_week.json
Loading module modules\hospice_treatment.json
Running with options:
Population: 10
Seed: 1689863202140
Provider Seed:1689863202140
Reference Time: 1689863202140
Location: Massachusetts
Min Age: 0
Max Age: 140
Modules: Hospice Treatment Module
> [1 loaded]
Waiting for threads to finish... java.util.concurrent.ThreadPoolExecutor@7f5b9db[Shutting down, pool size = 10, active threads = 10, queued tasks = 0, completed tasks = 0]
java.lang.RuntimeException: Failed to produce a matching patient after 1000 attempts. Ensure that it is possible for all requested demographics to meet the criteria. (e.g., make sure there is no age restriction that conflicts with a requested condition, such as limiting age to 0-18 and requiring all patients have a condition that only onsets after 55.) If you are confident that the constraints are possible to satisfy but rare, consider increasing the value in config setting generate.max_attempts_to_keep_patient
at org.mitre.synthea.engine.Generator.generatePerson(Generator.java:502)
at org.mitre.synthea.engine.Generator.lambda$run$3(Generator.java:382)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
java.lang.RuntimeException: Failed to produce a matching patient after 1000 attempts. Ensure that it is possible for all requested demographics to meet the criteria. (e.g., make sure there is no age restriction that conflicts with a requested condition, such as limiting age to 0-18 and requiring all patients have a condition that only onsets after 55.) If you are confident that the constraints are possible to satisfy but rare, consider increasing the value in config setting generate.max_attempts_to_keep_patient
at org.mitre.synthea.engine.Generator.generatePerson(Generator.java:502)
at org.mitre.synthea.engine.Generator.lambda$run$3(Generator.java:382)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
java.lang.RuntimeException: Failed to produce a matching patient after 1000 attempts. Ensure that it is possible for all requested demographics to meet the criteria. (e.g., make sure there is no age restriction that conflicts with a requested condition, such as limiting age to 0-18 and requiring all patients have a condition that only onsets after 55.) If you are confident that the constraints are possible to satisfy but rare, consider increasing the value in config setting generate.max_attempts_to_keep_patient
at org.mitre.synthea.engine.Generator.generatePerson(Generator.java:502)
at org.mitre.synthea.engine.Generator.lambda$run$3(Generator.java:382)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
java.lang.RuntimeException: Failed to produce a matching patient after 1000 attempts. Ensure that it is possible for all requested demographics to meet the criteria. (e.g., make sure there is no age restriction that conflicts with a requested condition, such as limiting age to 0-18 and requiring all patients have a condition that only onsets after 55.) If you are confident that the constraints are possible to satisfy but rare, consider increasing the value in config setting generate.max_attempts_to_keep_patient
at org.mitre.synthea.engine.Generator.generatePerson(Generator.java:502)
at org.mitre.synthea.engine.Generator.lambda$run$3(Generator.java:382)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
java.lang.RuntimeException: Failed to produce a matching patient after 1000 attempts. Ensure that it is possible for all requested demographics to meet the criteria. (e.g., make sure there is no age restriction that conflicts with a requested condition, such as limiting age to 0-18 and requiring all patients have a condition that only onsets after 55.) If you are confident that the constraints are possible to satisfy but rare, consider increasing the value in config setting generate.max_attempts_to_keep_patient
at org.mitre.synthea.engine.Generator.generatePerson(Generator.java:502)
at org.mitre.synthea.engine.Generator.lambda$run$3(Generator.java:382)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
java.lang.RuntimeException: Failed to produce a matching patient after 1000 attempts. Ensure that it is possible for all requested demographics to meet the criteria. (e.g., make sure there is no age restriction that conflicts with a requested condition, such as limiting age to 0-18 and requiring all patients have a condition that only onsets after 55.) If you are confident that the constraints are possible to satisfy but rare, consider increasing the value in config setting generate.max_attempts_to_keep_patient
at org.mitre.synthea.engine.Generator.generatePerson(Generator.java:502)
at org.mitre.synthea.engine.Generator.lambda$run$3(Generator.java:382)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
Waiting for threads to finish... java.util.concurrent.ThreadPoolExecutor@7f5b9db[Shutting down, pool size = 4, active threads = 4, queued tasks = 0, completed tasks = 6]
java.lang.RuntimeException: Failed to produce a matching patient after 1000 attempts. Ensure that it is possible for all requested demographics to meet the criteria. (e.g., make sure there is no age restriction that conflicts with a requested condition, such as limiting age to 0-18 and requiring all patients have a condition that only onsets after 55.) If you are confident that the constraints are possible to satisfy but rare, consider increasing the value in config setting generate.max_attempts_to_keep_patient
at org.mitre.synthea.engine.Generator.generatePerson(Generator.java:502)
at org.mitre.synthea.engine.Generator.lambda$run$3(Generator.java:382)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
java.lang.RuntimeException: Failed to produce a matching patient after 1000 attempts. Ensure that it is possible for all requested demographics to meet the criteria. (e.g., make sure there is no age restriction that conflicts with a requested condition, such as limiting age to 0-18 and requiring all patients have a condition that only onsets after 55.) If you are confident that the constraints are possible to satisfy but rare, consider increasing the value in config setting generate.max_attempts_to_keep_patient
at org.mitre.synthea.engine.Generator.generatePerson(Generator.java:502)
at org.mitre.synthea.engine.Generator.lambda$run$3(Generator.java:382)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
java.lang.RuntimeException: Failed to produce a matching patient after 1000 attempts. Ensure that it is possible for all requested demographics to meet the criteria. (e.g., make sure there is no age restriction that conflicts with a requested condition, such as limiting age to 0-18 and requiring all patients have a condition that only onsets after 55.) If you are confident that the constraints are possible to satisfy but rare, consider increasing the value in config setting generate.max_attempts_to_keep_patient
at org.mitre.synthea.engine.Generator.generatePerson(Generator.java:502)
at org.mitre.synthea.engine.Generator.lambda$run$3(Generator.java:382)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
java.lang.RuntimeException: Failed to produce a matching patient after 1000 attempts. Ensure that it is possible for all requested demographics to meet the criteria. (e.g., make sure there is no age restriction that conflicts with a requested condition, such as limiting age to 0-18 and requiring all patients have a condition that only onsets after 55.) If you are confident that the constraints are possible to satisfy but rare, consider increasing the value in config setting generate.max_attempts_to_keep_patient
at org.mitre.synthea.engine.Generator.generatePerson(Generator.java:502)
at org.mitre.synthea.engine.Generator.lambda$run$3(Generator.java:382)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
Records: total=0, alive=0, dead=0
RNG=10
Clinician RNG=5643

BUILD SUCCESSFUL in 1m 37s
4 actionable tasks: 2 executed, 2 up-to-date

[dehall]

It looks like you're trying to get a population of only deceased hospice patients, is that right?

First, do not use the -m flag. It doesn't mean "all patients must go through this module", it means "only load this module and not any others". In the case of the hospice module, nothing happens unless another module sends the patient into hospice, and when you use the -m flag there are no other modules that can do that. ( More on that here: https://github.com/synthetichealth/synthea/wiki/The--M-Feature )

Instead, I would recommend using a "keep" module to only keep patients that have a particular condition or attribute of interest. For example, breast cancer or lung cancer might send a patient to hospice, so you can create a keep module to only keep those patients. Or, if you inspect the hospice module you'll see it uses the attribute hospice which you can filter on. More on keep modules here: https://github.com/synthetichealth/synthea/wiki/Keep-Patients-Module

Here's a simple keep module to keep patients with that attribute hospice: keep_hospice.json.txt

You can use this by putting it in the synthea folder and running with ./run_synthea -p 10 -k keep_hospice.json
You may also want to specify an age range, otherwise it will try generating patients of all ages, and it may not be possible for people under a certain age to enter hospice in Synthea, and you'll see some of those same errors again

[kirankumarduddu]

@dehall Thank you so much for your help and response ( I am looking for FHIR bundles of hospice patients with multiple conditions who are dead, as per recommendation updated keep module to below -
{
"name": "keep_hospice",
"states": {
"Initial": {
"type": "Initial",
"conditional_transition": [
{
"transition": "Keep",
"condition": {
"condition_type": "Attribute",
"attribute": "hospice_treatment",
"operator": "is not nil"
}
},
{
"transition": "Terminal"
}
]
},
"Terminal": {
"type": "Terminal"
},
"Keep": {
"type": "Terminal"
}
},
"gmf_version": 2
}

and added keep module to src/main/resources/module and still getting error below
PS C:\Visual Code\synthea> ./run_synthea -p 10 -k keep_hospice.json
ARG = -p
ARG = 10
ARG = -k
ARG = keep_hospice.json
ARG =
syntheaArgs = '-p','10','-k','keep_hospice.json',

Task :run
java.io.FileNotFoundException: Specified keep-patients file (keep_hospice.json) does not exist
at App.main(App.java:199)
Usage: run_synthea [options] [state [city]]
Options: [-s seed] [-cs clinicianSeed] [-p populationSize]
[-ps singlePersonSeed]
[-r referenceDate as YYYYMMDD]
[-e endDate as YYYYMMDD]
[-g gender] [-a minAge-maxAge]
[-o overflowPopulation]
[-c localConfigFilePath]
[-d localModulesDirPath]
[-i initialPopulationSnapshotPath]
[-u updatedPopulationSnapshotPath]
[-t updateTimePeriodInDays]
[-f fixedRecordPath]
[-k keepMatchingPatientsPath]
[--config*=value]
* any setting from src/main/resources/synthea.properties
Examples:
run_synthea Massachusetts
run_synthea Alaska Juneau
run_synthea -s 12345
run_synthea -p 1000
run_synthea -s 987 Washington Seattle
run_synthea -s 21 -p 100 Utah "Salt Lake City"
run_synthea -g M -a 60-65
run_synthea -p 10 --exporter.fhir.export=true
run_synthea --exporter.baseDirectory="./output_tx/" Texas

BUILD SUCCESSFUL in 5s
4 actionable tasks: 3 executed, 1 up-to-date

[dehall]

The path used with -k is relative to the current directory not the modules directory, so the best place for keep_hospice.json is the base synthea/ directory. (Alternatively you could put it somewhere else and reference it as -k ./path/to/keep_hospice.json)

[kirankumarduddu]

@dehall That worked !! but is this normal ?? I need to genrate 1000's of patients !!!

PS C:\Visual Code\synthea> ./run_synthea -p 10 -k keep_hospice.json
ARG = -p
ARG = 10
ARG = -k
ARG = keep_hospice.json
ARG =
syntheaArgs = '-p','10','-k','keep_hospice.json',

Task :run
SLF4J: No SLF4J providers were found.
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#noProviders for further details.
Scanned 84 modules and 140 submodules.
Loading submodule modules\allergies\allergy_panel.json
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Loading submodule modules\dermatitis\early_moderate_eczema_obs.json
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Loading submodule modules\heart\savrepair\operative_status.json
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Loading submodule modules\heart\stemi_fibrinolytic.json
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Loading submodule modules\hiv\art_sequence.json
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Loading submodule modules\medications\ear_infection_antibiotic.json
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Loading submodule modules\medications\hypertension_medication.json
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Loading submodule modules\medications\moderate_opioid_pain_reliever.json
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Loading submodule modules\medications\strong_opioid_pain_reliever.json
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Loading module modules\home_health_treatment.json
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Loading module modules\wellness_encounters.json
Loading module C:\Visual Code\synthea\keep_hospice.json
Running with options:
Population: 10
Seed: 1689870997699
Provider Seed:1689870997699
Reference Time: 1689870997699
Location: Massachusetts
Min Age: 0
Max Age: 140
3 -- Imogene688 Joetta231 Gerlach374 (77 y/o F) Lynn, Massachusetts DECEASED (109479)
9 -- Denny560 Kuvalis369 (49 y/o M) Bridgewater, Massachusetts DECEASED (85094)
Waiting for threads to finish... java.util.concurrent.ThreadPoolExecutor@1cc8416a[Shutting down, pool size = 8, active threads = 8, queued tasks = 0, completed tasks = 2]
4 -- Regine404 Sauer652 (52 y/o F) Worcester, Massachusetts DECEASED (110533)
10 -- Luciana251 Koch169 (49 y/o F) Stow, Massachusetts DECEASED (73973)
7 -- Lynn917 Greenfelder433 (52 y/o M) South Hadley, Massachusetts DECEASED (108371)
8 -- Coy949 Herzog843 (38 y/o M) Westport, Massachusetts DECEASED (56237)
Waiting for threads to finish... java.util.concurrent.ThreadPoolExecutor@1cc8416a[Shutting down, pool size = 4, active threads = 4, queued tasks = 0, completed tasks = 6]
java.lang.RuntimeException: Failed to produce a matching patient after 1000 attempts. Ensure that it is possible for all requested demographics to meet the criteria. (e.g., make sure there is no age restriction that conflicts with a requested condition, such as limiting age to 0-18 and requiring all patients have a condition that only onsets after 55.) If you are confident that the constraints are possible to satisfy but rare, consider increasing the value in config setting generate.max_attempts_to_keep_patient
at org.mitre.synthea.engine.Generator.generatePerson(Generator.java:502)
at org.mitre.synthea.engine.Generator.lambda$run$3(Generator.java:382)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
Waiting for threads to finish... java.util.concurrent.ThreadPoolExecutor@1cc8416a[Shutting down, pool size = 3, active threads = 3, queued tasks = 0, completed tasks = 7]
6 -- Lahoma872 Maryland870 Waters156 (34 y/o F) Weymouth, Massachusetts DECEASED (49529)
Waiting for threads to finish... java.util.concurrent.ThreadPoolExecutor@1cc8416a[Shutting down, pool size = 2, active threads = 2, queued tasks = 0, completed tasks = 8]
1 -- Ram≤n841 Partida347 (36 y/o M) Upton, Massachusetts DECEASED (50879)
Waiting for threads to finish... java.util.concurrent.ThreadPoolExecutor@1cc8416a[Shutting down, pool size = 1, active threads = 1, queued tasks = 0, completed tasks = 9]
java.lang.RuntimeException: Failed to produce a matching patient after 1000 attempts. Ensure that it is possible for all requested demographics to meet the criteria. (e.g., make sure there is no age restriction that conflicts with a requested condition, such as limiting age to 0-18 and requiring all patients have a condition that only onsets after 55.) If you are confident that the constraints are possible to satisfy but rare, consider increasing the value in config setting generate.max_attempts_to_keep_patient
at org.mitre.synthea.engine.Generator.generatePerson(Generator.java:502)
at org.mitre.synthea.engine.Generator.lambda$run$3(Generator.java:382)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
Records: total=8, alive=0, dead=8
RNG=10
Clinician RNG=5642

BUILD SUCCESSFUL in 2m 59s
4 actionable tasks: 2 executed, 2 up-to-date

[dehall]

Yes, unfortunately the way the keep module works is it tries repeatedly to generate a patient until one meeting the criteria is found, so for uncommon criteria such as hospice then it will take a long time. The other approach would be to modify the modules to make your conditions of interest more common.

I'd suggest adding another command line flag -a 45-70 (or feel free to adjust if you need a wider range) to limit the age range, like I said it's probably especially uncommon if not impossible for people below a certain age to go into hospice in Synthea, so it should speed up this scenario to define a specific age range.