vivarium-public-health 3.0.3__py3-none-any.whl → 3.0.4__py3-none-any.whl
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- vivarium_public_health/_version.py +1 -1
- vivarium_public_health/disease/state.py +24 -19
- vivarium_public_health/mslt/delay.py +13 -5
- vivarium_public_health/mslt/disease.py +35 -14
- vivarium_public_health/mslt/intervention.py +12 -9
- vivarium_public_health/mslt/observer.py +56 -17
- vivarium_public_health/mslt/population.py +7 -10
- vivarium_public_health/plugins/parser.py +29 -80
- vivarium_public_health/population/add_new_birth_cohorts.py +8 -9
- vivarium_public_health/population/base_population.py +0 -5
- vivarium_public_health/population/data_transformations.py +1 -8
- vivarium_public_health/population/mortality.py +3 -3
- vivarium_public_health/results/columns.py +1 -1
- vivarium_public_health/results/disability.py +85 -11
- vivarium_public_health/results/disease.py +125 -2
- vivarium_public_health/results/mortality.py +78 -2
- vivarium_public_health/results/observer.py +141 -6
- vivarium_public_health/results/risk.py +66 -5
- vivarium_public_health/results/simple_cause.py +8 -2
- vivarium_public_health/results/stratification.py +39 -14
- vivarium_public_health/risks/base_risk.py +14 -16
- vivarium_public_health/risks/data_transformations.py +3 -1
- vivarium_public_health/risks/distributions.py +0 -1
- vivarium_public_health/risks/effect.py +31 -29
- vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py +51 -30
- vivarium_public_health/treatment/scale_up.py +6 -10
- vivarium_public_health/treatment/therapeutic_inertia.py +3 -1
- {vivarium_public_health-3.0.3.dist-info → vivarium_public_health-3.0.4.dist-info}/METADATA +1 -1
- vivarium_public_health-3.0.4.dist-info/RECORD +49 -0
- {vivarium_public_health-3.0.3.dist-info → vivarium_public_health-3.0.4.dist-info}/WHEEL +1 -1
- vivarium_public_health-3.0.3.dist-info/RECORD +0 -49
- {vivarium_public_health-3.0.3.dist-info → vivarium_public_health-3.0.4.dist-info}/LICENSE.txt +0 -0
- {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
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def __init__(self, treatment: str):
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"""
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Parameters
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----------
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treatment
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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)
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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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----------
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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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"""
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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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----------
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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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"""
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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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CONFIGURATION_DEFAULTS = {
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"therapeutic_inertia": {
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@@ -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.
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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
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@@ -0,0 +1,49 @@
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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
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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
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vivarium_public_health-3.0.4.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
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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
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vivarium_public_health-3.0.4.dist-info/RECORD,,
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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/intervention.py,sha256=33HZqYo335H9nxILymoDqmBvmqTJDijRBv8i9u05pLY,10336
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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=UUQBVH47-MhtcMX1_IpaGt2xqbCECY-Txx8Og_raCEk,13941
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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/add_new_birth_cohorts.py,sha256=NhrPZBoFrHvYnwmG0Od_VCU_ptNECe7ZfdqUIqvOWrE,9157
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vivarium_public_health/population/base_population.py,sha256=Xn0sjPOT9KJZKILr1NchCwQFarvb3qWtgQ3Uvu999UU,17091
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vivarium_public_health/population/data_transformations.py,sha256=PsvE1-S-Q_K4viBgF2Ss0DaaoH0WyhRX26ZJYwJ0O84,22322
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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/__init__.py,sha256=XKuX9HTXUur1kpHM7zuMSnkJxlg-W7eMAPmh8LP9Xp4,281
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vivarium_public_health/results/columns.py,sha256=YUI43jdJ3KwvTrm2Gmxk7By2CJjNFzocLwYHhO2pnn0,447
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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/results/observer.py,sha256=mzQEmWpY910eRUpdIxsS9S9eDwDMKm6SB_60EeH4Zyo,3079
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vivarium_public_health/results/risk.py,sha256=80kQoWrC4oxAMKAmPGpYLHk2k1GtzH1uzxrm8d619KA,4453
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vivarium_public_health/results/simple_cause.py,sha256=sr8M8zxCqf2mqAGfc46WNXtML5hZV4fqnCMrRbyk1xY,561
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vivarium_public_health/results/stratification.py,sha256=I7YWUjN2WtWshePwJM38XHTn4tp5qy6LHgP_pknJaPI,4692
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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=CTKx3eywW1pi0XL6zoQfPu9tlgAfLqnJvGJ3wQ45SsQ,10494
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vivarium_public_health/risks/data_transformations.py,sha256=xfhi1nbH49c-fO6q7-41ZJcHGWmpfVWFBhS2UQNztv4,9225
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vivarium_public_health/risks/distributions.py,sha256=roQf8sluFGXlbTptl7KclXYyV_uLSkcYvEnBn_ugWQs,18198
|
38
|
-
vivarium_public_health/risks/effect.py,sha256=0B7x0IcoU8Kd6XlhtZbPH3qCMobC78mFEtGK67QsSJs,20410
|
39
|
-
vivarium_public_health/risks/implementations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
|
40
|
-
vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py,sha256=MtxlBioQ_EdJb6a-1eAaOx5IxTfzhBEdHsWG_KGiPqA,17366
|
41
|
-
vivarium_public_health/treatment/__init__.py,sha256=wONElu9aJbBYwpYIovYPYaN_GYfVhPXtTeFWSdQMgA0,222
|
42
|
-
vivarium_public_health/treatment/magic_wand.py,sha256=i9N57-MEuQv5B6dQ5iVMTAdOPghYcgiRRz-dTzigf1s,1980
|
43
|
-
vivarium_public_health/treatment/scale_up.py,sha256=kifn7oKTjCJ2l1XiYm4U3FAH98USZ1gLPvf4z5-3wsU,7079
|
44
|
-
vivarium_public_health/treatment/therapeutic_inertia.py,sha256=uOvMgIj-Bl5qTk4z7ZnTPUwOVH-xGeKs1pw8WYuE1f4,2340
|
45
|
-
vivarium_public_health-3.0.3.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
|
46
|
-
vivarium_public_health-3.0.3.dist-info/METADATA,sha256=gkZN4BNaL61XIp1c3TLatmgAEUWE9myE94R7BpLb1_o,4061
|
47
|
-
vivarium_public_health-3.0.3.dist-info/WHEEL,sha256=Mdi9PDNwEZptOjTlUcAth7XJDFtKrHYaQMPulZeBCiQ,91
|
48
|
-
vivarium_public_health-3.0.3.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
|
49
|
-
vivarium_public_health-3.0.3.dist-info/RECORD,,
|
{vivarium_public_health-3.0.3.dist-info → vivarium_public_health-3.0.4.dist-info}/LICENSE.txt
RENAMED
File without changes
|
{vivarium_public_health-3.0.3.dist-info → vivarium_public_health-3.0.4.dist-info}/top_level.txt
RENAMED
File without changes
|