vivarium-public-health 3.0.3__py3-none-any.whl → 3.0.4__py3-none-any.whl

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Files changed (33) hide show
  1. vivarium_public_health/_version.py +1 -1
  2. vivarium_public_health/disease/state.py +24 -19
  3. vivarium_public_health/mslt/delay.py +13 -5
  4. vivarium_public_health/mslt/disease.py +35 -14
  5. vivarium_public_health/mslt/intervention.py +12 -9
  6. vivarium_public_health/mslt/observer.py +56 -17
  7. vivarium_public_health/mslt/population.py +7 -10
  8. vivarium_public_health/plugins/parser.py +29 -80
  9. vivarium_public_health/population/add_new_birth_cohorts.py +8 -9
  10. vivarium_public_health/population/base_population.py +0 -5
  11. vivarium_public_health/population/data_transformations.py +1 -8
  12. vivarium_public_health/population/mortality.py +3 -3
  13. vivarium_public_health/results/columns.py +1 -1
  14. vivarium_public_health/results/disability.py +85 -11
  15. vivarium_public_health/results/disease.py +125 -2
  16. vivarium_public_health/results/mortality.py +78 -2
  17. vivarium_public_health/results/observer.py +141 -6
  18. vivarium_public_health/results/risk.py +66 -5
  19. vivarium_public_health/results/simple_cause.py +8 -2
  20. vivarium_public_health/results/stratification.py +39 -14
  21. vivarium_public_health/risks/base_risk.py +14 -16
  22. vivarium_public_health/risks/data_transformations.py +3 -1
  23. vivarium_public_health/risks/distributions.py +0 -1
  24. vivarium_public_health/risks/effect.py +31 -29
  25. vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py +51 -30
  26. vivarium_public_health/treatment/scale_up.py +6 -10
  27. vivarium_public_health/treatment/therapeutic_inertia.py +3 -1
  28. {vivarium_public_health-3.0.3.dist-info → vivarium_public_health-3.0.4.dist-info}/METADATA +1 -1
  29. vivarium_public_health-3.0.4.dist-info/RECORD +49 -0
  30. {vivarium_public_health-3.0.3.dist-info → vivarium_public_health-3.0.4.dist-info}/WHEEL +1 -1
  31. vivarium_public_health-3.0.3.dist-info/RECORD +0 -49
  32. {vivarium_public_health-3.0.3.dist-info → vivarium_public_health-3.0.4.dist-info}/LICENSE.txt +0 -0
  33. {vivarium_public_health-3.0.3.dist-info → vivarium_public_health-3.0.4.dist-info}/top_level.txt +0 -0
@@ -20,8 +20,7 @@ from vivarium_public_health.utilities import EntityString
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  class LinearScaleUp(Component):
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- """
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- A model for applying a linear scale-up to an intervention.
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+ """A model for applying a linear scale-up to an intervention.
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  This component requires input data for beginning and end dates, as well as
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  beginning and end values. Scale-up start and end dates are by default the
@@ -75,10 +74,11 @@ class LinearScaleUp(Component):
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  def __init__(self, treatment: str):
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  """
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+
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  Parameters
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  ----------
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- treatment :
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- the type and name of a treatment, specified as "type.name". Type is singular.
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+ treatment
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+ The type and name of a treatment, specified as "type.name". Type is singular.
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  """
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  super().__init__()
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  self.treatment = EntityString(treatment)
@@ -113,8 +113,7 @@ class LinearScaleUp(Component):
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  return pd.Timestamp(scale_up_config["start"]), pd.Timestamp(scale_up_config["end"])
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  def get_scale_up_values(self, builder: Builder) -> Tuple[LookupTable, LookupTable]:
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- """
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- Get the values at the start and end of the scale-up period.
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+ """Get the values at the start and end of the scale-up period.
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  Parameters
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  ----------
@@ -123,7 +122,6 @@ class LinearScaleUp(Component):
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  Returns
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  -------
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- LookupTable
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  A tuple of lookup tables returning the values at the start and end
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  of the scale-up period.
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  """
@@ -172,8 +170,7 @@ class LinearScaleUp(Component):
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  def get_endpoint_value_from_data(
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  self, builder: Builder, endpoint_type: str
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  ) -> LookupTable:
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- """
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- Get the value at the start or end of the scale-up period from data.
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+ """Get the value at the start or end of the scale-up period from data.
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  Parameters
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  ----------
@@ -185,7 +182,6 @@ class LinearScaleUp(Component):
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  Returns
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  -------
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- LookupTable
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  A lookup table returning the value at the start or end of the
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  scale-up period.
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  """
@@ -17,7 +17,9 @@ from vivarium.framework.engine import Builder
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  class TherapeuticInertia(Component):
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  """Expose a therapeutic inertia pipeline that defines
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  a population-level therapeutic inertia.
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- This is the probability of treatment during a healthcare visit."""
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+
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+ This is the probability of treatment during a healthcare visit.
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+ """
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  CONFIGURATION_DEFAULTS = {
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  "therapeutic_inertia": {
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: vivarium_public_health
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- Version: 3.0.3
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+ Version: 3.0.4
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  Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
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  Home-page: https://github.com/ihmeuw/vivarium_public_health
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  Author: The vivarium developers
@@ -0,0 +1,49 @@
1
+ vivarium_public_health/__about__.py,sha256=RgWycPypKZS80TpSX7o41cREnG8PfguNHDHLuLyl820,487
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+ vivarium_public_health/__init__.py,sha256=tomMOl3PI7O8GdxDWGBiBjT0Bwd31GpyQTYTzwIv108,361
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+ vivarium_public_health/_version.py,sha256=gNoy6uoSQO4ZzowTZAJz3hphzq1F_Y-3X9YrQdb7ppc,22
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+ vivarium_public_health/utilities.py,sha256=5cl9jjVkOQ1UeXT4DjDMAhaBNNjAsDo-SVJwpv6FDw0,3071
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+ vivarium_public_health/disease/__init__.py,sha256=RuuiRcvAJfX9WQGt_WZZjxN7Cu3E5rMTmuaRS-UaFPM,419
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+ vivarium_public_health/disease/model.py,sha256=0WIYDEx-hwlUJp6Zl8m8bUMoWxuVkOWsJvh_YlZiOPs,8234
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+ vivarium_public_health/disease/models.py,sha256=01UK7yB2zGPFzmlIpvhd-XnGe6vSCMDza3QTidgY7Nc,3479
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+ vivarium_public_health/disease/special_disease.py,sha256=3vS1WsO__IwOK0Oe_CUmh3aaKrXIf2CANtmiqlS3pjc,14614
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+ vivarium_public_health/disease/state.py,sha256=PUSDE1UlvoCPT6jPEyCTQO1bXjjYxqzdIa6-Bxpd-7I,22370
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+ vivarium_public_health/disease/transition.py,sha256=ZxYXZBo2EEXzuQCbaj2pHTyj61hYkdqBH1ce2Htdnb4,6412
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+ vivarium_public_health/mslt/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ vivarium_public_health/mslt/delay.py,sha256=aOYjMpMSHEVlJs0FuC2gdq3uj6_vKmkhDjoBtC4i9G0,22812
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+ vivarium_public_health/mslt/disease.py,sha256=TBqa7yj6k1oUbgkAe0rIgLpbdMLMFs4DiZ1Igi2BQBg,16663
14
+ vivarium_public_health/mslt/intervention.py,sha256=m6LT0CdJNwhz9X0FQNap1y9K5N4MhUDcvfDaHVukJZQ,10331
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+ vivarium_public_health/mslt/magic_wand_components.py,sha256=pnl-7MwIJIus6UjtvVmM15pIZOCbSS1mNfP7nS2bAtw,3981
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+ vivarium_public_health/mslt/observer.py,sha256=O4rysQzAGE5oDkdXb0E-qjD9TPFphQHTn7_3Qj7pBL0,15225
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+ vivarium_public_health/mslt/population.py,sha256=v_p5VkjndAVJMuXaJQc3lAdzUWHlWCEQWH4A-c4phPA,7255
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+ vivarium_public_health/plugins/__init__.py,sha256=oBW_zfgG_LbwfgTDjUe0btfy9FaDvAbtXho1zQFnz0Y,76
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+ vivarium_public_health/plugins/parser.py,sha256=v78mj8awpdrB-oqK8udPI_7MZBChoKJOQN_e17fNEj8,31841
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+ vivarium_public_health/population/__init__.py,sha256=17rtbcNVK5LtCCxAex7P7Q_vYpwbeTepyf3nazS90Yc,225
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+ vivarium_public_health/population/add_new_birth_cohorts.py,sha256=k65Li0LYWl-JFHBUvLjJxkRv12EJw_FVxrOYgbd44q8,9078
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+ vivarium_public_health/population/base_population.py,sha256=4lUc8EZwzj5Ba36lSmW9yyxcRuBSMLqi_8Fy69ssq5E,17026
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+ vivarium_public_health/population/data_transformations.py,sha256=QVh_63Wwg9BUkaQm1pMSvBb-wsYrsgyADKIERAiEOVg,22188
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+ vivarium_public_health/population/mortality.py,sha256=w7b_TUssHjRcnULdXu7MXKfZBjCrlYWbB94oO3JWogI,10264
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+ vivarium_public_health/results/__init__.py,sha256=XKuX9HTXUur1kpHM7zuMSnkJxlg-W7eMAPmh8LP9Xp4,281
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+ vivarium_public_health/results/columns.py,sha256=V-L3JgTcsk51Zx9PcUwSgaE1iZjuGyfZ8aShPjynadU,495
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+ vivarium_public_health/results/disability.py,sha256=DqSNI1CEdhNXy-mhTtuTXom22e6XGrvFoaeQwyBdlig,9872
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+ vivarium_public_health/results/disease.py,sha256=q5-g495tPbcs1zfApwoCTfkionAwQbCeXn3JigBUOIk,12526
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+ vivarium_public_health/results/mortality.py,sha256=Bo8l8CYcBmI6BsXl8l_7mPieGLzyUp3XeFBm497mThE,9652
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+ vivarium_public_health/results/observer.py,sha256=-VoOYOaT-vmxVNi0bxm3It0ZFdLIq8D9Ng28xO1JuLw,7143
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+ vivarium_public_health/results/risk.py,sha256=GS4qJVjW3MqsDeRDDac2etFQlqIluxOxIZFMy1Ytmp8,6622
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+ vivarium_public_health/results/simple_cause.py,sha256=jlrllbSiEIOrf69gQvrJww29uMrR8xzK_5TApu1Mxqg,724
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+ vivarium_public_health/results/stratification.py,sha256=4I3YGHVabNAZENE7YboOtWsWU4X-8LUBJ9iwYMbpl6E,5387
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+ vivarium_public_health/risks/__init__.py,sha256=z8DcnZGxqNVAyFZm2WAV-IVNGvrSS4izju_0DNe2Ghw,212
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+ vivarium_public_health/risks/base_risk.py,sha256=WhvB0RRYIsGsPQvJEWckcBlOVSh4Rx-B-VGZDSWWb7s,10416
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+ vivarium_public_health/risks/data_transformations.py,sha256=SgdPKc95BBqgMNUdlAQM8k6iaXcpxnjk5B2ySTES1Yg,9269
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+ vivarium_public_health/risks/distributions.py,sha256=7xCI2zSpnKUEWow4ywRirVbvbpeJaxo6g9us0-Lh0kE,18197
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+ vivarium_public_health/risks/effect.py,sha256=Oc_3A0fbMDUBAJAMJ9aeDRDqdgW_aF75B3SbGv9QELw,20351
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+ vivarium_public_health/risks/implementations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py,sha256=o3Uo6_AQoUHJeGo4HpB0PlouNqKst9NFmm3PRiTr5bg,17924
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+ vivarium_public_health/treatment/__init__.py,sha256=wONElu9aJbBYwpYIovYPYaN_GYfVhPXtTeFWSdQMgA0,222
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+ vivarium_public_health/treatment/magic_wand.py,sha256=i9N57-MEuQv5B6dQ5iVMTAdOPghYcgiRRz-dTzigf1s,1980
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+ vivarium_public_health/treatment/scale_up.py,sha256=aKJmZ2G6N80n7oPkJM8IpqZOhftUBkAMBn4hR4EZzhE,7015
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+ vivarium_public_health/treatment/therapeutic_inertia.py,sha256=8Z97s7GfcpfLu1U1ESJSqeEk4L__a3M0GbBV21MFg2s,2346
45
+ vivarium_public_health-3.0.4.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
46
+ vivarium_public_health-3.0.4.dist-info/METADATA,sha256=mVOUpc6PRXAW7lnKkJ3BRJPKHT3erLyQuS60qlMFUzU,4061
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+ vivarium_public_health-3.0.4.dist-info/WHEEL,sha256=UvcQYKBHoFqaQd6LKyqHw9fxEolWLQnlzP0h_LgJAfI,91
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+ vivarium_public_health-3.0.4.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
49
+ vivarium_public_health-3.0.4.dist-info/RECORD,,
@@ -1,5 +1,5 @@
1
1
  Wheel-Version: 1.0
2
- Generator: setuptools (73.0.1)
2
+ Generator: setuptools (74.0.0)
3
3
  Root-Is-Purelib: true
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4
  Tag: py3-none-any
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5
 
@@ -1,49 +0,0 @@
1
- vivarium_public_health/__about__.py,sha256=RgWycPypKZS80TpSX7o41cREnG8PfguNHDHLuLyl820,487
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- vivarium_public_health/__init__.py,sha256=tomMOl3PI7O8GdxDWGBiBjT0Bwd31GpyQTYTzwIv108,361
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- vivarium_public_health/_version.py,sha256=3PslnGRHLeT8kAWbhtBM110cQkzH_QzfQO5_B6lHOuU,22
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- vivarium_public_health/utilities.py,sha256=5cl9jjVkOQ1UeXT4DjDMAhaBNNjAsDo-SVJwpv6FDw0,3071
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- vivarium_public_health/disease/__init__.py,sha256=RuuiRcvAJfX9WQGt_WZZjxN7Cu3E5rMTmuaRS-UaFPM,419
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- vivarium_public_health/disease/model.py,sha256=0WIYDEx-hwlUJp6Zl8m8bUMoWxuVkOWsJvh_YlZiOPs,8234
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- vivarium_public_health/disease/models.py,sha256=01UK7yB2zGPFzmlIpvhd-XnGe6vSCMDza3QTidgY7Nc,3479
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- vivarium_public_health/disease/special_disease.py,sha256=3vS1WsO__IwOK0Oe_CUmh3aaKrXIf2CANtmiqlS3pjc,14614
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- vivarium_public_health/disease/state.py,sha256=G9rmbpH-l9OZyM2-glLpV_Zefz800cNx6t-N-irg0t8,22106
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- vivarium_public_health/disease/transition.py,sha256=ZxYXZBo2EEXzuQCbaj2pHTyj61hYkdqBH1ce2Htdnb4,6412
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- vivarium_public_health/mslt/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- vivarium_public_health/mslt/delay.py,sha256=X_MPxcHYkGHORW8RKPNbx5m85yilJK1_6DaCVQQUpiM,22582
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- vivarium_public_health/mslt/disease.py,sha256=FaA9bpKpkaopRCeKNHMh7qWuCtLpGdEyUEo59HuORyM,15684
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- vivarium_public_health/mslt/population.py,sha256=6XedM2ZZzaU7U70GQLXj2VcyAvLp0Yjpq5rini-_g6s,7286
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- vivarium_public_health/plugins/__init__.py,sha256=oBW_zfgG_LbwfgTDjUe0btfy9FaDvAbtXho1zQFnz0Y,76
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- vivarium_public_health/plugins/parser.py,sha256=dlH-tafOGCFvOUZx_QdOkSScMCwH4CbqR8dwPwX7dVw,32851
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- vivarium_public_health/population/__init__.py,sha256=17rtbcNVK5LtCCxAex7P7Q_vYpwbeTepyf3nazS90Yc,225
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- vivarium_public_health/population/base_population.py,sha256=Xn0sjPOT9KJZKILr1NchCwQFarvb3qWtgQ3Uvu999UU,17091
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- vivarium_public_health/population/mortality.py,sha256=8T5W4D3oxx-4wjHT-0P1jCLiQI6_zznGLuJ-wobF1BY,10272
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- vivarium_public_health/results/disability.py,sha256=ryb5SiTQ3MCTf5WPWk_1TPN6IC9Z_fY3Wd6XBv3Q9AY,7818
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- vivarium_public_health/results/disease.py,sha256=7xUcyxx_d2T3DQD-WFRHaRxb0qKIOCCpIGWNpEXzixg,8209
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- vivarium_public_health/results/mortality.py,sha256=4KUEPzzo1-kD4TdG0PeRMWW69aJcMQJtho9ED0cpErs,6865
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- vivarium_public_health/treatment/__init__.py,sha256=wONElu9aJbBYwpYIovYPYaN_GYfVhPXtTeFWSdQMgA0,222
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- vivarium_public_health/treatment/magic_wand.py,sha256=i9N57-MEuQv5B6dQ5iVMTAdOPghYcgiRRz-dTzigf1s,1980
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- vivarium_public_health/treatment/scale_up.py,sha256=kifn7oKTjCJ2l1XiYm4U3FAH98USZ1gLPvf4z5-3wsU,7079
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- vivarium_public_health-3.0.3.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
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- vivarium_public_health-3.0.3.dist-info/METADATA,sha256=gkZN4BNaL61XIp1c3TLatmgAEUWE9myE94R7BpLb1_o,4061
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- vivarium_public_health-3.0.3.dist-info/RECORD,,