3 new generators

src/main/resources/physiology/generators/circadian_clock.yml

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+
+# Name of the model file
+
+model: Hong2009_CircadianClock.xml
+
+# Which differential equation solver to use.
+# Options are: adams_bashforth, adams_moulton, dormand_prince_54, dormand_prince_853, euler, gragg_bulirsch_stoer, higham_hall_54, rosenbrock, runge_kutta
+solver: runge_kutta
+
+# Simulation step size in seconds. Note that this can have significant effects on the results and may impact the ability of the solver to complete successfully.
+stepSize: 0.01
+
+# Simulation duration in seconds
+simDuration: 4.0
+
+# Simulation lead time in seconds before output data is captured
+leadTime: 2.0
+
+## Whether the simulation should use other generators before any input thresholds
+## are reached.
+## Very useful for preventing simulation execution when the inputs (and results)
+## are within normal ranges. If this is true, preGenerator attributes must be
+## defined for each output
+#usePreGenerators: true
+#
+## Initializes person attributes. Necessary if input parameters depend on attributes
+## which otherwise may not exist when the generator first executes
+#personAttributeDefaults:
+#  blood_pressure_controlled: false
+#
+## List of input definitions for the model
+## Field descriptions:
+##   "from"              -   attribute or vital sign value to use directly from a Person.
+##                           The "type" field must also be provided to specify which one.
+##   "fromExp"           -   A mathematical expression. Both attributes and vital signs
+##                           can be used within #{} blocks. The result will be assigned to
+##                           the model input parameter indicated by "to".
+##   "to"                -   Target model input parameter to assign
+##   "varianceThreshold" -   Amount of variance to allow in the input parameter
+##                           without performing a re-run of the simulation.
+##                           This can significantly effect overall Synthea runtime.
+##                           Defaults to 0.
+##   "type"              -   Type of the input value "from", if applicable. Must be one of
+##                           "ATTRIBUTE" or "VITAL_SIGN".
+
+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/)
+#  # More research is needed to determine appropriate age / BMI effects on all model parameters.
+ - fromExp: "1.1889 + 0.025 * (#{BMI} - 21.7) + (if #b{blood_pressure_controlled} then 0 else (0.0112 * #{age}))"
+   to: R_sys
+   variance: 0.25 # Allowable variance in input to avoid running simulation
+#  - fromExp: "0.8413 + (if #{age} > 20.0 then 0.0175 * (#{age} - 20.0) else 0)"
+#    to: E_es_ao
+#    variance: 0.2 # Allowable variance in input to avoid running simulation
+
+## List of output definitions for the model
+## Field descriptions:
+##   "from"              -   Model parameter to pull from directly.
+##   "fromExp"           -   A mathematical expression. Any model parameter can be used
+##                           within #{} blocks and will be a List of values for that
+##                           parameter at each time step. The result will be assigned to
+##                           the model input parameter indicated by "to".
+##   "to"                -   Target Person attribute or vital sign to assign. Note that
+##                           attributes are assigned as a side-effect of simulation
+##                           execution, so the model must provide at least one vital sign
+##                           output for the simulation to actually execute.
+##   "varianceThreshold" -   Amount of variance to allow in the input parameter
+##                           without performing a re-run of the simulation.
+##                           This can significantly effect overall Synthea runtime.
+##                           Defaults to 0.
+##   "type"              -   Type of the output value "to". Must be "ATTRIBUTE" or "VITAL_SIGN".
+
+outputs:
+ - fromExp: "((Max(#{V_lv}) - Min(#{V_lv})) / Max(#{V_lv}))*100"
+   to: Left ventricular Ejection fraction
+  #  type: VITAL_SIGN
+   variance: 3.0
+   preGenerator:
+     className: org.mitre.synthea.helpers.RandomValueGenerator
+     args: # Args 2+ for the constructor
+       # From https://my.clevelandclinic.org/health/diseases/17069-heart-failure-understanding-heart-failure
+       - {"value": 55.0, "type": "java.lang.Double", "primitive": true}
+       - {"value": 70.0, "type": "java.lang.Double", "primitive": true}
+#  - fromExp: "Max(#{P_ao})"
+#    to: Systolic Blood Pressure
+#    type: VITAL_SIGN
+#    variance: 10.0
+#    preGenerator:
+#      className: org.mitre.synthea.modules.BloodPressureValueGenerator
+#      args: # Args 2+ for the constructor
+#        - {"value": SYSTOLIC, "type": "org.mitre.synthea.modules.BloodPressureValueGenerator$SysDias"}
+#  - fromExp: "Min(#{P_ao})"
+#    to: Diastolic Blood Pressure
+#    type: VITAL_SIGN
+#    variance: 5.0
+#    preGenerator:
+#      className: org.mitre.synthea.modules.BloodPressureValueGenerator
+#      args: # Args 2+ for the constructor
+#        - {"value": DIASTOLIC, type: "org.mitre.synthea.modules.BloodPressureValueGenerator$SysDias"}
+#

src/main/resources/physiology/generators/menstrual_cycle.yml

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+
+# Name of the model file
+model: Roblitz2013_Menstrual_Cycle.xml
+
+# Which differential equation solver to use.
+# Options are: adams_bashforth, adams_moulton, dormand_prince_54, dormand_prince_853, euler, gragg_bulirsh_stoer, higham_hall_54, rosenbrock, runge_kutta
+solver: adams_bashforth
+
+# Simulation step size in seconds. Note that this can have significant effects on the results and may impact the ability of the solver to complete successfully.
+stepSize: 0.1
+
+# Simulation duration in seconds
+# duration: 2419200
+# duration: 86400
+# duration: 28
+
+# simDuration: 2419200
+simDuration: 28
+
+leadTime: 0.0
+
+usePreGenerators: false
+
+
+
+# List of input definitions for the model
+# Field descriptions:
+#   "from"              -   attribute or vital sign value to use directly from a Person.
+#                           The "type" field must also be provided to specify which one.
+#   "fromExp"           -   A mathematical expression. Both attributes and vital signs
+#                           can be used within #{} blocks. The result will be assigned to
+#                           the model input parameter indicated by "to".
+#   "to"                -   Target model input parameter to assign
+#   "varianceThreshold" -   Amount of variance to allow in the input parameter
+#                           without performing a re-run of the simulation.
+#                           This can significantly effect overall Synthea runtime.
+#                           Defaults to 0.
+#   "type"              -   Type of the input value "from", if applicable. Must be one of
+#                           "ATTRIBUTE" or "VITAL_SIGN".
+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/)
+      # More research is needed to determine appropriate age / BMI effects on all model parameters.
+    - fromExp: "#{BMI} * 0.497 + 56.15"
+      to: mass
+      variance: 0.25 # Allowable variance in input to avoid running simulation
+
+
+
+# List of output definitions for the model
+# Field descriptions:
+#   "from"              -   Model parameter to pull from directly.
+#   "fromExp"           -   A mathematical expression. Any model parameter can be used
+#                           within #{} blocks and will be a List of values for that
+#                           parameter at each time step. The result will be assigned to
+#                           the model input parameter indicated by "to".
+#   "to"                -   Target Person attribute or vital sign to assign. Note that
+#                           attributes are assigned as a side-effect of simulation
+#                           execution, so the model must provide at least one vital sign
+#                           output for the simulation to actually execute.
+#   "varianceThreshold" -   Amount of variance to allow in the input parameter
+#                           without performing a re-run of the simulation.
+#                           This can significantly effect overall Synthea runtime.
+#                           Defaults to 0.
+#   "type"              -   Type of the output value "to". Must be "ATTRIBUTE" or "VITAL_SIGN".
+outputs:
+    - from: "#{E2}"
+      # to: e2
+      # type: ATTRIBUTE
+      variance: 3.0
+      preGenerator:
+         className: org.mitre.synthea.helpers.RandomValueGenerator
+         args: # Args 2+ for the constructoxr
+            # From https://my.clevelandclinic.org/health/diseases/17069-heart-failure-understanding-heart-failure
+            - {"value": 0, "type": "java.lang.Double", "primitive": true}
+            - {"value": 500, "type": "java.lang.Double", "primitive": true}

src/main/resources/physiology/generators/pulmonary_oxygen_intake.yml

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+
+# Name of the model file
+model: Guyton1972_PulmonaryOxygenIntake.xml
+
+# Which differential equation solver to use.
+# Options are: adams_bashforth, adams_moulton, dormand_prince_54, dormand_prince_853, euler, gragg_bulirsch_stoer, higham_hall_54, rosenbrock, runge_kutta
+solver: euler
+
+# Simulation step size in seconds. Note that this can have significant effects on the results and may impact the ability of the solver to complete successfully.
+stepSize: 1
+
+# Simulation duration in seconds
+simDuration: 600
+
+# Simulation lead time in seconds before output data is captured
+leadTime: 2.0
+
+## Whether the simulation should use other generators before any input thresholds
+## are reached.
+## Very useful for preventing simulation execution when the inputs (and results)
+## are within normal ranges. If this is true, preGenerator attributes must be
+## defined for each output
+usePreGenerators: true
+
+#
+## Initializes person attributes. Necessary if input parameters depend on attributes
+## which otherwise may not exist when the generator first executes
+#personAttributeDefaults:
+#  blood_pressure_controlled: false
+#
+## List of input definitions for the model
+## Field descriptions:
+##   "from"              -   attribute or vital sign value to use directly from a Person.
+##                           The "type" field must also be provided to specify which one.
+##   "fromExp"           -   A mathematical expression. Both attributes and vital signs
+##                           can be used within #{} blocks. The result will be assigned to
+##                           the model input parameter indicated by "to".
+##   "to"                -   Target model input parameter to assign
+##   "varianceThreshold" -   Amount of variance to allow in the input parameter
+##                           without performing a re-run of the simulation.
+##                           This can significantly effect overall Synthea runtime.
+##                           Defaults to 0.
+##   "type"              -   Type of the input value "from", if applicable. Must be one of
+##                           "ATTRIBUTE" or "VITAL_SIGN".
+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/)
+ # More research is needed to determine appropriate age / BMI effects on all model parameters.
+ - fromExp: "#{BMI} * 0.497 + 56.15"
+   to: OVA
+   variance: 0.25 # Allowable variance in input to avoid running simulation
+
+#  - fromExp: "0.8413 + (if #{age} > 20.0 then 0.0175 * (#{age} - 20.0) else 0)"
+#    to: E_es_ao
+#    variance: 0.2 # Allowable variance in input to avoid running simulation
+
+## List of output definitions for the model
+## Field descriptions:
+##   "from"              -   Model parameter to pull from directly.
+##   "fromExp"           -   A mathematical expression. Any model parameter can be used
+##                           within #{} blocks and will be a List of values for that
+##                           parameter at each time step. The result will be assigned to
+##                           the model input parameter indicated by "to".
+##   "to"                -   Target Person attribute or vital sign to assign. Note that
+##                           attributes are assigned as a side-effect of simulation
+##                           execution, so the model must provide at least one vital sign
+##                           output for the simulation to actually execute.
+##   "varianceThreshold" -   Amount of variance to allow in the input parameter
+##                           without performing a re-run of the simulation.
+##                           This can significantly effect overall Synthea runtime.
+##                           Defaults to 0.
+##   "type"              -   Type of the output value "to". Must be "ATTRIBUTE" or "VITAL_SIGN".
+
+
+outputs:
+ - fromExp: "(#{PO2ART})"
+   to: Arterial O2 Pressure
+  #  type: VITAL_SIGN
+   variance: 3.0
+   preGenerator:
+     className: org.mitre.synthea.helpers.RandomValueGenerator
+     args: # Args 2+ for the constructor
+       # From https://my.clevelandclinic.org/health/diseases/17069-heart-failure-understanding-heart-failure
+       - {"value": 85.0, "type": "java.lang.Double", "primitive": true}
+       - {"value": 98.0, "type": "java.lang.Double", "primitive": true}
+
+#  - fromExp: "Max(#{P_ao})"
+#    to: Systolic Blood Pressure
+#    type: VITAL_SIGN
+#    variance: 10.0
+#    preGenerator:
+#      className: org.mitre.synthea.modules.BloodPressureValueGenerator
+#      args: # Args 2+ for the constructor
+#        - {"value": SYSTOLIC, "type": "org.mitre.synthea.modules.BloodPressureValueGenerator$SysDias"}
+
+#  - fromExp: "Min(#{P_ao})"
+#    to: Diastolic Blood Pressure
+#    type: VITAL_SIGN
+#    variance: 5.0
+#    preGenerator:
+#      className: org.mitre.synthea.modules.BloodPressureValueGenerator
+#      args: # Args 2+ for the constructor
+#        - {"value": DIASTOLIC, type: "org.mitre.synthea.modules.BloodPressureValueGenerator$SysDias"}
+