From d4900f49126cd48cf682bca2a1fc96a6bd10aa8f Mon Sep 17 00:00:00 2001 From: TJohnsonAZ <72234106+TJohnsonAZ@users.noreply.github.com> Date: Thu, 15 Aug 2024 11:32:23 -0700 Subject: [PATCH] Adrio2 cdc devlog (#143) Update cdc devlog for adrio2 refactor. --- doc/devlog/2024-07-03-cdc-adrio-demo.ipynb | 1214 ++++++++++++----- epymorph/geo/adrio/__init__.py | 2 +- .../geo/adrio/{cdc => disease}/adrio_cdc.py | 0 3 files changed, 878 insertions(+), 338 deletions(-) rename epymorph/geo/adrio/{cdc => disease}/adrio_cdc.py (100%) diff --git a/doc/devlog/2024-07-03-cdc-adrio-demo.ipynb b/doc/devlog/2024-07-03-cdc-adrio-demo.ipynb index 2577b736..95b5d73f 100644 --- a/doc/devlog/2024-07-03-cdc-adrio-demo.ipynb +++ b/doc/devlog/2024-07-03-cdc-adrio-demo.ipynb @@ -45,16 +45,24 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 33, "metadata": {}, "outputs": [], "source": [ - "from epymorph.geo.adrio.cdc.adrio_cdc import ADRIOMakerCDC\n", + "from unittest.mock import Mock\n", + "\n", + "import numpy as np\n", + "\n", + "from epymorph.data_shape import SimDimensions\n", "from epymorph.geography.us_census import CountyScope, StateScope\n", + "from epymorph.simulation import NamespacedAttributeResolver\n", "\n", - "maker = ADRIOMakerCDC()\n", "county_scope = CountyScope.in_states(['04', '08'])\n", - "state_scope = StateScope.in_states(['04', '08'])" + "state_scope = StateScope.in_states(['04', '08'])\n", + "\n", + "data = Mock(spec=NamespacedAttributeResolver)\n", + "dim = Mock(spec=SimDimensions)\n", + "rng = Mock(spec=np.random.Generator)" ] }, { @@ -79,16 +87,14 @@ "source": [ "from datetime import date\n", "\n", - "from epymorph.data_shape import Shapes\n", + "from epymorph.geo.adrio.cdc import (CovidCasesPer100k,\n", + " CovidHospitalizationsPer100k)\n", "from epymorph.geo.spec import DateRange\n", - "from epymorph.simulation import AttributeDef\n", "\n", "time_period = DateRange(date(2022, 2, 24), date(2023, 5, 4))\n", "\n", - "cases = maker.make_adrio(AttributeDef(\"covid_cases_per_100k\", float,\n", - " Shapes.TxN), state_scope, time_period)\n", - "hospitalizations = maker.make_adrio(AttributeDef(\n", - " \"covid_hospitalizations_per_100k\", float, Shapes.TxN), state_scope, time_period)" + "cases = CovidCasesPer100k(time_period)\n", + "hospitalizations = CovidHospitalizationsPer100k(time_period)" ] }, { @@ -100,11 +106,15 @@ "name": "stdout", "output_type": "stream", "text": [ + "Evaluating CovidCasesPer100k ADRIO...\n", + "Completed CovidCasesPer100k ADRIO (2.425s).\n", "COVID cases per 100k:\n", " [[('2022-02-24', 3217.93) ('2022-02-24', 12475.51)]\n", " [('2022-03-03', 1018.81) ('2022-03-03', 8795.74)]\n", " [('2022-03-10', 1912.86) ('2022-03-10', 12280.08)]]\n", "\n", + "Evaluating CovidHospitalizationsPer100k ADRIO...\n", + "Completed CovidHospitalizationsPer100k ADRIO (1.142s).\n", "COVID hospitalizations per 100k:\n", " [[('2022-02-24', 334.7) ('2022-02-24', 822.5)]\n", " [('2022-03-03', 232.6) ('2022-03-03', 445.5)]\n", @@ -113,8 +123,10 @@ } ], "source": [ - "print(f\"COVID cases per 100k:\\n {cases.get_value()[:3]}\\n\")\n", - "print(f\"COVID hospitalizations per 100k:\\n {hospitalizations.get_value()[:3]}\")" + "print(\n", + " f\"COVID cases per 100k:\\n {cases.evaluate_in_context(data, dim, state_scope, rng)[:3]}\\n\")\n", + "print(\n", + " f\"COVID hospitalizations per 100k:\\n {hospitalizations.evaluate_in_context(data, dim, state_scope, rng)[:3]}\")" ] }, { @@ -133,58 +145,431 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 34, "metadata": {}, "outputs": [], "source": [ + "from epymorph.geo.adrio.cdc import (CovidHospitalizationAvgFacility,\n", + " CovidHospitalizationSumFacility,\n", + " InfluenzaHospitalizationSumFacility,\n", + " InfluenzaHosptializationAvgFacility)\n", + "\n", "time_period = DateRange(date(2020, 12, 13), date(2023, 5, 10))\n", "\n", - "covid_avg = maker.make_adrio(AttributeDef(\n", - " \"covid_hospitalization_avg_facility\", float, Shapes.TxN), state_scope, time_period)\n", - "covid_sum = maker.make_adrio(AttributeDef(\n", - " \"covid_hospitalization_sum_facility\", float, Shapes.TxN), state_scope, time_period)\n", - "flu_avg = maker.make_adrio(AttributeDef(\n", - " \"influenza_hospitalization_avg_facility\", float, Shapes.TxN), state_scope, time_period)\n", - "flu_sum = maker.make_adrio(AttributeDef(\n", - " \"influenza_hospitalization_sum_facility\", float, Shapes.TxN), state_scope, time_period)" + "covid_avg = CovidHospitalizationAvgFacility(time_period)\n", + "covid_sum = CovidHospitalizationSumFacility(time_period)\n", + "flu_avg = InfluenzaHosptializationAvgFacility(time_period)\n", + "flu_sum = InfluenzaHospitalizationSumFacility(time_period)" ] }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 35, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ + "Evaluating CovidHospitalizationAvgFacility ADRIO...\n", + "Completed CovidHospitalizationAvgFacility ADRIO (4.947s).\n", "COVID hospitalization average:\n", - " [[('2020-12-13', -999999.) ('2020-12-13', -999999.)]\n", - " [('2020-12-20', -999999.) ('2020-12-20', -999999.)]\n", - " [('2020-12-27', -999999.) ('2020-12-27', -999999.)]]\n", + " [[('2020-12-13', 6.40000e+00) ('2020-12-13', -9.99999e+05)\n", + " ('2020-12-13', -9.99999e+05) ('2020-12-13', 2.88000e+01)\n", + " ('2020-12-13', 2.48000e+01) ('2020-12-13', 1.96000e+01)\n", + " ('2020-12-13', -9.99999e+05) ('2020-12-13', -9.99999e+05)\n", + " ('2020-12-13', 7.29000e+01) ('2020-12-13', -9.99999e+05)\n", + " ('2020-12-13', 1.65600e+02) ('2020-12-13', 8.80000e+00)\n", + " ('2020-12-13', 2.21000e+02) ('2020-12-13', 3.23200e+02)\n", + " ('2020-12-13', 1.60600e+02) ('2020-12-13', 8.90000e+00)\n", + " ('2020-12-13', 1.44300e+02) ('2020-12-13', -9.99999e+05)\n", + " ('2020-12-13', -9.99999e+05) ('2020-12-13', 7.07000e+01)\n", + " ('2020-12-13', -9.99999e+05) ('2020-12-13', nan)\n", + " ('2020-12-13', nan) ('2020-12-13', nan)\n", + " ('2020-12-13', nan) ('2020-12-13', 7.89000e+01)\n", + " ('2020-12-13', 2.74000e+01) ('2020-12-13', -9.99999e+05)\n", + " ('2020-12-13', -9.99999e+05) ('2020-12-13', 8.10000e+00)\n", + " ('2020-12-13', nan) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', -9.99999e+05) ('2020-12-13', nan)\n", + " ('2020-12-13', 3.33000e+01) ('2020-12-13', -9.99999e+05)\n", + " ('2020-12-13', nan) ('2020-12-13', nan)\n", + " ('2020-12-13', 1.60000e+01) ('2020-12-13', -9.99999e+05)\n", + " ('2020-12-13', nan) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', 6.30000e+00) ('2020-12-13', 5.26000e+01)\n", + " ('2020-12-13', -9.99999e+05) ('2020-12-13', nan)\n", + " ('2020-12-13', 1.04000e+01) ('2020-12-13', 4.90000e+00)\n", + " ('2020-12-13', 8.40000e+00) ('2020-12-13', 6.10000e+00)\n", + " ('2020-12-13', nan) ('2020-12-13', -9.99999e+05)\n", + " ('2020-12-13', 1.14000e+01) ('2020-12-13', -9.99999e+05)\n", + " ('2020-12-13', 0.00000e+00) ('2020-12-13', nan)\n", + " ('2020-12-13', 0.00000e+00) ('2020-12-13', -9.99999e+05)\n", + " ('2020-12-13', nan) ('2020-12-13', 4.27000e+01)\n", + " ('2020-12-13', nan)]\n", + " [('2020-12-20', 1.28000e+01) ('2020-12-20', -9.99999e+05)\n", + " ('2020-12-20', 1.03300e+02) ('2020-12-20', 1.17000e+01)\n", + " ('2020-12-20', 1.11000e+01) ('2020-12-20', 6.70000e+00)\n", + " ('2020-12-20', -9.99999e+05) ('2020-12-20', 1.54200e+02)\n", + " ('2020-12-20', 6.50000e+01) ('2020-12-20', -9.99999e+05)\n", + " ('2020-12-20', 1.66000e+02) ('2020-12-20', 8.00000e+00)\n", + " ('2020-12-20', 2.48400e+02) ('2020-12-20', 3.08000e+02)\n", + " ('2020-12-20', 1.31800e+02) ('2020-12-20', nan)\n", + " ('2020-12-20', 4.74000e+01) ('2020-12-20', nan)\n", + " ('2020-12-20', -9.99999e+05) ('2020-12-20', 5.50000e+01)\n", + " ('2020-12-20', nan) ('2020-12-20', -9.99999e+05)\n", + " ('2020-12-20', 0.00000e+00) ('2020-12-20', nan)\n", + " ('2020-12-20', 1.19000e+01) ('2020-12-20', 6.20000e+01)\n", + " ('2020-12-20', 3.66000e+01) ('2020-12-20', nan)\n", + " ('2020-12-20', 1.01100e+02) ('2020-12-20', 4.40000e+00)\n", + " ('2020-12-20', -9.99999e+05) ('2020-12-20', 0.00000e+00)\n", + " ('2020-12-20', -9.99999e+05) ('2020-12-20', nan)\n", + " ('2020-12-20', 3.23000e+01) ('2020-12-20', nan)\n", + " ('2020-12-20', nan) ('2020-12-20', -9.99999e+05)\n", + " ('2020-12-20', 1.27000e+01) ('2020-12-20', -9.99999e+05)\n", + " ('2020-12-20', nan) ('2020-12-20', nan)\n", + " ('2020-12-20', nan) ('2020-12-20', 1.18000e+01)\n", + " ('2020-12-20', -9.99999e+05) ('2020-12-20', nan)\n", + " ('2020-12-20', nan) ('2020-12-20', -9.99999e+05)\n", + " ('2020-12-20', nan) ('2020-12-20', -9.99999e+05)\n", + " ('2020-12-20', nan) ('2020-12-20', nan)\n", + " ('2020-12-20', 1.13000e+01) ('2020-12-20', -9.99999e+05)\n", + " ('2020-12-20', 0.00000e+00) ('2020-12-20', 0.00000e+00)\n", + " ('2020-12-20', nan) ('2020-12-20', nan)\n", + " ('2020-12-20', nan) ('2020-12-20', 5.72000e+01)\n", + " ('2020-12-20', -9.99999e+05)]\n", + " [('2020-12-27', 1.14000e+01) ('2020-12-27', -9.99999e+05)\n", + " ('2020-12-27', -9.99999e+05) ('2020-12-27', 3.48000e+01)\n", + " ('2020-12-27', 3.26000e+01) ('2020-12-27', 5.80000e+00)\n", + " ('2020-12-27', -9.99999e+05) ('2020-12-27', 2.31700e+02)\n", + " ('2020-12-27', 6.18000e+01) ('2020-12-27', -9.99999e+05)\n", + " ('2020-12-27', 1.64900e+02) ('2020-12-27', 9.20000e+00)\n", + " ('2020-12-27', 1.39300e+02) ('2020-12-27', 2.70600e+02)\n", + " ('2020-12-27', -9.99999e+05) ('2020-12-27', 6.70000e+00)\n", + " ('2020-12-27', 1.02500e+02) ('2020-12-27', -9.99999e+05)\n", + " ('2020-12-27', -9.99999e+05) ('2020-12-27', 4.29000e+01)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', -9.99999e+05)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', nan)\n", + " ('2020-12-27', nan) ('2020-12-27', 7.56000e+01)\n", + " ('2020-12-27', 5.39000e+01) ('2020-12-27', -9.99999e+05)\n", + " ('2020-12-27', nan) ('2020-12-27', nan)\n", + " ('2020-12-27', -9.99999e+05) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', nan) ('2020-12-27', -9.99999e+05)\n", + " ('2020-12-27', 2.56000e+01) ('2020-12-27', nan)\n", + " ('2020-12-27', -9.99999e+05) ('2020-12-27', nan)\n", + " ('2020-12-27', 1.36000e+01) ('2020-12-27', -9.99999e+05)\n", + " ('2020-12-27', -9.99999e+05) ('2020-12-27', -9.99999e+05)\n", + " ('2020-12-27', 6.30000e+00) ('2020-12-27', 3.31000e+01)\n", + " ('2020-12-27', -9.99999e+05) ('2020-12-27', 4.60000e+00)\n", + " ('2020-12-27', nan) ('2020-12-27', nan)\n", + " ('2020-12-27', 5.40000e+00) ('2020-12-27', -9.99999e+05)\n", + " ('2020-12-27', nan) ('2020-12-27', nan)\n", + " ('2020-12-27', 6.30000e+00) ('2020-12-27', -9.99999e+05)\n", + " ('2020-12-27', nan) ('2020-12-27', nan)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', -9.99999e+05)\n", + " ('2020-12-27', -9.99999e+05) ('2020-12-27', 3.72000e+01)\n", + " ('2020-12-27', -9.99999e+05)]]\n", "\n", + "Evaluating CovidHospitalizationSumFacility ADRIO...\n", + "Completed CovidHospitalizationSumFacility ADRIO (5.931s).\n", "COVID hospitalization sum:\n", - " [[('2020-12-13', -999999.) ('2020-12-13', -999999.)]\n", - " [('2020-12-20', 24524.) ('2020-12-20', -999999.)]\n", - " [('2020-12-27', 26680.) ('2020-12-27', -999999.)]]\n", + " [[('2020-12-13', 4.50000e+01) ('2020-12-13', 4.48000e+02)\n", + " ('2020-12-13', 6.78000e+02) ('2020-12-13', 2.01000e+02)\n", + " ('2020-12-13', 1.74000e+02) ('2020-12-13', 9.80000e+01)\n", + " ('2020-12-13', -9.99999e+05) ('2020-12-13', -9.99999e+05)\n", + " ('2020-12-13', 5.10000e+02) ('2020-12-13', 4.68500e+03)\n", + " ('2020-12-13', 1.15800e+03) ('2020-12-13', 6.20000e+01)\n", + " ('2020-12-13', 1.54600e+03) ('2020-12-13', 2.26200e+03)\n", + " ('2020-12-13', 1.12400e+03) ('2020-12-13', 6.20000e+01)\n", + " ('2020-12-13', 1.01000e+03) ('2020-12-13', 6.00000e+00)\n", + " ('2020-12-13', 6.00000e+00) ('2020-12-13', 4.94000e+02)\n", + " ('2020-12-13', -9.99999e+05) ('2020-12-13', nan)\n", + " ('2020-12-13', nan) ('2020-12-13', nan)\n", + " ('2020-12-13', nan) ('2020-12-13', 5.52000e+02)\n", + " ('2020-12-13', 1.92000e+02) ('2020-12-13', 8.00000e+00)\n", + " ('2020-12-13', 1.47900e+03) ('2020-12-13', 5.70000e+01)\n", + " ('2020-12-13', nan) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', 5.00000e+00) ('2020-12-13', nan)\n", + " ('2020-12-13', 2.33000e+02) ('2020-12-13', -9.99999e+05)\n", + " ('2020-12-13', nan) ('2020-12-13', nan)\n", + " ('2020-12-13', 1.12000e+02) ('2020-12-13', 8.90000e+01)\n", + " ('2020-12-13', nan) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', 4.40000e+01) ('2020-12-13', 3.68000e+02)\n", + " ('2020-12-13', 2.60000e+01) ('2020-12-13', nan)\n", + " ('2020-12-13', 7.30000e+01) ('2020-12-13', 3.40000e+01)\n", + " ('2020-12-13', 5.90000e+01) ('2020-12-13', 4.30000e+01)\n", + " ('2020-12-13', nan) ('2020-12-13', 1.10000e+01)\n", + " ('2020-12-13', 8.00000e+01) ('2020-12-13', -9.99999e+05)\n", + " ('2020-12-13', 0.00000e+00) ('2020-12-13', nan)\n", + " ('2020-12-13', 0.00000e+00) ('2020-12-13', 6.00000e+00)\n", + " ('2020-12-13', nan) ('2020-12-13', 2.99000e+02)\n", + " ('2020-12-13', nan)]\n", + " [('2020-12-20', 9.00000e+01) ('2020-12-20', 4.45000e+02)\n", + " ('2020-12-20', 7.23000e+02) ('2020-12-20', 8.20000e+01)\n", + " ('2020-12-20', 7.80000e+01) ('2020-12-20', 4.00000e+01)\n", + " ('2020-12-20', 2.47390e+04) ('2020-12-20', 1.07900e+03)\n", + " ('2020-12-20', 3.74000e+02) ('2020-12-20', 5.14800e+03)\n", + " ('2020-12-20', 1.16200e+03) ('2020-12-20', 5.60000e+01)\n", + " ('2020-12-20', 1.73800e+03) ('2020-12-20', 2.15600e+03)\n", + " ('2020-12-20', 9.22000e+02) ('2020-12-20', nan)\n", + " ('2020-12-20', 3.32000e+02) ('2020-12-20', nan)\n", + " ('2020-12-20', 5.00000e+00) ('2020-12-20', 3.85000e+02)\n", + " ('2020-12-20', nan) ('2020-12-20', 2.10000e+01)\n", + " ('2020-12-20', 0.00000e+00) ('2020-12-20', nan)\n", + " ('2020-12-20', 8.30000e+01) ('2020-12-20', 4.34000e+02)\n", + " ('2020-12-20', 2.56000e+02) ('2020-12-20', nan)\n", + " ('2020-12-20', 7.08000e+02) ('2020-12-20', 3.10000e+01)\n", + " ('2020-12-20', 9.00000e+00) ('2020-12-20', 0.00000e+00)\n", + " ('2020-12-20', 9.00000e+00) ('2020-12-20', nan)\n", + " ('2020-12-20', 2.26000e+02) ('2020-12-20', nan)\n", + " ('2020-12-20', nan) ('2020-12-20', 4.00000e+00)\n", + " ('2020-12-20', 8.90000e+01) ('2020-12-20', 3.73000e+02)\n", + " ('2020-12-20', nan) ('2020-12-20', nan)\n", + " ('2020-12-20', nan) ('2020-12-20', 8.30000e+01)\n", + " ('2020-12-20', 1.70000e+01) ('2020-12-20', nan)\n", + " ('2020-12-20', nan) ('2020-12-20', -9.99999e+05)\n", + " ('2020-12-20', nan) ('2020-12-20', 1.20000e+01)\n", + " ('2020-12-20', nan) ('2020-12-20', nan)\n", + " ('2020-12-20', 7.90000e+01) ('2020-12-20', 4.00000e+00)\n", + " ('2020-12-20', 0.00000e+00) ('2020-12-20', 0.00000e+00)\n", + " ('2020-12-20', nan) ('2020-12-20', nan)\n", + " ('2020-12-20', nan) ('2020-12-20', 4.00000e+02)\n", + " ('2020-12-20', 1.50000e+01)]\n", + " [('2020-12-27', 8.00000e+01) ('2020-12-27', 2.72000e+02)\n", + " ('2020-12-27', 7.51000e+02) ('2020-12-27', 2.44000e+02)\n", + " ('2020-12-27', 2.28000e+02) ('2020-12-27', 2.30000e+01)\n", + " ('2020-12-27', 3.38780e+04) ('2020-12-27', 1.62200e+03)\n", + " ('2020-12-27', 4.32000e+02) ('2020-12-27', 6.18000e+03)\n", + " ('2020-12-27', 1.15400e+03) ('2020-12-27', 6.40000e+01)\n", + " ('2020-12-27', 9.75000e+02) ('2020-12-27', 1.89400e+03)\n", + " ('2020-12-27', 9.45000e+02) ('2020-12-27', 4.70000e+01)\n", + " ('2020-12-27', 7.18000e+02) ('2020-12-27', 1.40000e+01)\n", + " ('2020-12-27', 1.30000e+01) ('2020-12-27', 3.00000e+02)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', -9.99999e+05)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', nan)\n", + " ('2020-12-27', nan) ('2020-12-27', 5.29000e+02)\n", + " ('2020-12-27', 3.77000e+02) ('2020-12-27', 1.20000e+01)\n", + " ('2020-12-27', nan) ('2020-12-27', nan)\n", + " ('2020-12-27', 5.40000e+01) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', nan) ('2020-12-27', 1.30000e+01)\n", + " ('2020-12-27', 1.79000e+02) ('2020-12-27', nan)\n", + " ('2020-12-27', -9.99999e+05) ('2020-12-27', nan)\n", + " ('2020-12-27', 9.50000e+01) ('2020-12-27', -9.99999e+05)\n", + " ('2020-12-27', 8.00000e+00) ('2020-12-27', -9.99999e+05)\n", + " ('2020-12-27', 4.40000e+01) ('2020-12-27', 2.32000e+02)\n", + " ('2020-12-27', 1.90000e+01) ('2020-12-27', 3.20000e+01)\n", + " ('2020-12-27', nan) ('2020-12-27', nan)\n", + " ('2020-12-27', 3.80000e+01) ('2020-12-27', 5.40000e+01)\n", + " ('2020-12-27', nan) ('2020-12-27', nan)\n", + " ('2020-12-27', 4.40000e+01) ('2020-12-27', -9.99999e+05)\n", + " ('2020-12-27', nan) ('2020-12-27', nan)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', 1.10000e+01)\n", + " ('2020-12-27', 9.00000e+00) ('2020-12-27', 2.60000e+02)\n", + " ('2020-12-27', -9.99999e+05)]]\n", "\n", + "Evaluating InfluenzaHosptializationAvgFacility ADRIO...\n", + "Completed InfluenzaHosptializationAvgFacility ADRIO (2.177s).\n", "Influenza hospitalization average:\n", - " [[('2020-12-13', -999999.) ('2020-12-13', -999999.)]\n", - " [('2020-12-20', -999999.) ('2020-12-20', -999999.)]\n", - " [('2020-12-27', -999999.) ('2020-12-27', -999999.)]]\n", + " [[('2020-12-13', 0.) ('2020-12-13', 0.)\n", + " ('2020-12-13', 0.) ('2020-12-13', 0.)\n", + " ('2020-12-13', -999999.) ('2020-12-13', 0.)\n", + " ('2020-12-13', -999999.) ('2020-12-13', -999999.)\n", + " ('2020-12-13', 0.) ('2020-12-13', -999999.)\n", + " ('2020-12-13', 0.) ('2020-12-13', 0.)\n", + " ('2020-12-13', 0.) ('2020-12-13', 0.)\n", + " ('2020-12-13', 0.) ('2020-12-13', 0.)\n", + " ('2020-12-13', 0.) ('2020-12-13', 0.)\n", + " ('2020-12-13', 0.) ('2020-12-13', 0.)\n", + " ('2020-12-13', -999999.) ('2020-12-13', nan)\n", + " ('2020-12-13', nan) ('2020-12-13', nan)\n", + " ('2020-12-13', nan) ('2020-12-13', 0.)\n", + " ('2020-12-13', 0.) ('2020-12-13', 0.)\n", + " ('2020-12-13', 0.) ('2020-12-13', 0.)\n", + " ('2020-12-13', nan) ('2020-12-13', 0.)\n", + " ('2020-12-13', 0.) ('2020-12-13', nan)\n", + " ('2020-12-13', 0.) ('2020-12-13', 0.)\n", + " ('2020-12-13', nan) ('2020-12-13', nan)\n", + " ('2020-12-13', -999999.) ('2020-12-13', 0.)\n", + " ('2020-12-13', nan) ('2020-12-13', 0.)\n", + " ('2020-12-13', 0.) ('2020-12-13', 0.)\n", + " ('2020-12-13', 0.) ('2020-12-13', nan)\n", + " ('2020-12-13', 0.) ('2020-12-13', 0.)\n", + " ('2020-12-13', 0.) ('2020-12-13', 0.)\n", + " ('2020-12-13', nan) ('2020-12-13', 0.)\n", + " ('2020-12-13', 0.) ('2020-12-13', 0.)\n", + " ('2020-12-13', 0.) ('2020-12-13', nan)\n", + " ('2020-12-13', 0.) ('2020-12-13', 0.)\n", + " ('2020-12-13', nan) ('2020-12-13', -999999.)\n", + " ('2020-12-13', nan)]\n", + " [('2020-12-20', -999999.) ('2020-12-20', 0.)\n", + " ('2020-12-20', 0.) ('2020-12-20', 0.)\n", + " ('2020-12-20', 0.) ('2020-12-20', 0.)\n", + " ('2020-12-20', -999999.) ('2020-12-20', 0.)\n", + " ('2020-12-20', 0.) ('2020-12-20', -999999.)\n", + " ('2020-12-20', 0.) ('2020-12-20', 0.)\n", + " ('2020-12-20', 0.) ('2020-12-20', 0.)\n", + " ('2020-12-20', -999999.) ('2020-12-20', nan)\n", + " ('2020-12-20', 0.) ('2020-12-20', nan)\n", + " ('2020-12-20', 0.) ('2020-12-20', 0.)\n", + " ('2020-12-20', nan) ('2020-12-20', 0.)\n", + " ('2020-12-20', 0.) ('2020-12-20', nan)\n", + " ('2020-12-20', 0.) ('2020-12-20', 0.)\n", + " ('2020-12-20', 0.) ('2020-12-20', nan)\n", + " ('2020-12-20', 0.) ('2020-12-20', 0.)\n", + " ('2020-12-20', 0.) ('2020-12-20', 0.)\n", + " ('2020-12-20', 0.) ('2020-12-20', nan)\n", + " ('2020-12-20', 0.) ('2020-12-20', nan)\n", + " ('2020-12-20', nan) ('2020-12-20', 0.)\n", + " ('2020-12-20', -999999.) ('2020-12-20', 0.)\n", + " ('2020-12-20', nan) ('2020-12-20', nan)\n", + " ('2020-12-20', nan) ('2020-12-20', 0.)\n", + " ('2020-12-20', 0.) ('2020-12-20', nan)\n", + " ('2020-12-20', nan) ('2020-12-20', 0.)\n", + " ('2020-12-20', nan) ('2020-12-20', 0.)\n", + " ('2020-12-20', nan) ('2020-12-20', nan)\n", + " ('2020-12-20', 0.) ('2020-12-20', 0.)\n", + " ('2020-12-20', 0.) ('2020-12-20', 0.)\n", + " ('2020-12-20', nan) ('2020-12-20', nan)\n", + " ('2020-12-20', nan) ('2020-12-20', -999999.)\n", + " ('2020-12-20', 0.)]\n", + " [('2020-12-27', -999999.) ('2020-12-27', 0.)\n", + " ('2020-12-27', 0.) ('2020-12-27', 0.)\n", + " ('2020-12-27', 0.) ('2020-12-27', 0.)\n", + " ('2020-12-27', -999999.) ('2020-12-27', 0.)\n", + " ('2020-12-27', 0.) ('2020-12-27', -999999.)\n", + " ('2020-12-27', -999999.) ('2020-12-27', 0.)\n", + " ('2020-12-27', 0.) ('2020-12-27', 0.)\n", + " ('2020-12-27', 0.) ('2020-12-27', 0.)\n", + " ('2020-12-27', 0.) ('2020-12-27', 0.)\n", + " ('2020-12-27', 0.) ('2020-12-27', 0.)\n", + " ('2020-12-27', 0.) ('2020-12-27', 0.)\n", + " ('2020-12-27', 0.) ('2020-12-27', nan)\n", + " ('2020-12-27', nan) ('2020-12-27', 0.)\n", + " ('2020-12-27', 0.) ('2020-12-27', 0.)\n", + " ('2020-12-27', nan) ('2020-12-27', nan)\n", + " ('2020-12-27', 0.) ('2020-12-27', 0.)\n", + " ('2020-12-27', nan) ('2020-12-27', 0.)\n", + " ('2020-12-27', 0.) ('2020-12-27', nan)\n", + " ('2020-12-27', 0.) ('2020-12-27', nan)\n", + " ('2020-12-27', -999999.) ('2020-12-27', 0.)\n", + " ('2020-12-27', 0.) ('2020-12-27', 0.)\n", + " ('2020-12-27', 0.) ('2020-12-27', 0.)\n", + " ('2020-12-27', 0.) ('2020-12-27', 0.)\n", + " ('2020-12-27', nan) ('2020-12-27', nan)\n", + " ('2020-12-27', 0.) ('2020-12-27', 0.)\n", + " ('2020-12-27', nan) ('2020-12-27', nan)\n", + " ('2020-12-27', 0.) ('2020-12-27', 0.)\n", + " ('2020-12-27', nan) ('2020-12-27', nan)\n", + " ('2020-12-27', 0.) ('2020-12-27', 0.)\n", + " ('2020-12-27', 0.) ('2020-12-27', -999999.)\n", + " ('2020-12-27', 0.)]]\n", "\n", + "Evaluating InfluenzaHospitalizationSumFacility ADRIO...\n", + "Completed InfluenzaHospitalizationSumFacility ADRIO (2.313s).\n", "Influenza hospitalization sum:\n", - " [[('2020-12-13', -9.99999e+05) ('2020-12-13', -9.99999e+05)]\n", - " [('2020-12-20', -9.99999e+05) ('2020-12-20', -9.99999e+05)]\n", - " [('2020-12-27', -9.99999e+05) ('2020-12-27', 2.50000e+01)]]\n" + " [[('2020-12-13', 0.00000e+00) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', 0.00000e+00) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', -9.99999e+05) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', -9.99999e+05) ('2020-12-13', -9.99999e+05)\n", + " ('2020-12-13', 0.00000e+00) ('2020-12-13', -9.99999e+05)\n", + " ('2020-12-13', 0.00000e+00) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', 0.00000e+00) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', 0.00000e+00) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', 0.00000e+00) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', 0.00000e+00) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', 6.00000e+00) ('2020-12-13', nan)\n", + " ('2020-12-13', nan) ('2020-12-13', nan)\n", + " ('2020-12-13', nan) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', 0.00000e+00) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', 0.00000e+00) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', nan) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', 0.00000e+00) ('2020-12-13', nan)\n", + " ('2020-12-13', 0.00000e+00) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', nan) ('2020-12-13', nan)\n", + " ('2020-12-13', 7.00000e+00) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', nan) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', 0.00000e+00) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', 0.00000e+00) ('2020-12-13', nan)\n", + " ('2020-12-13', 0.00000e+00) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', 0.00000e+00) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', nan) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', 0.00000e+00) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', 0.00000e+00) ('2020-12-13', nan)\n", + " ('2020-12-13', 0.00000e+00) ('2020-12-13', 0.00000e+00)\n", + " ('2020-12-13', nan) ('2020-12-13', 1.40000e+01)\n", + " ('2020-12-13', nan)]\n", + " [('2020-12-20', -9.99999e+05) ('2020-12-20', 0.00000e+00)\n", + " ('2020-12-20', 0.00000e+00) ('2020-12-20', 0.00000e+00)\n", + " ('2020-12-20', 0.00000e+00) ('2020-12-20', 0.00000e+00)\n", + " ('2020-12-20', -9.99999e+05) ('2020-12-20', 0.00000e+00)\n", + " ('2020-12-20', 0.00000e+00) ('2020-12-20', 1.00000e+01)\n", + " ('2020-12-20', 0.00000e+00) ('2020-12-20', 0.00000e+00)\n", + " ('2020-12-20', 0.00000e+00) ('2020-12-20', 0.00000e+00)\n", + " ('2020-12-20', -9.99999e+05) ('2020-12-20', nan)\n", + " ('2020-12-20', 0.00000e+00) ('2020-12-20', nan)\n", + " ('2020-12-20', 0.00000e+00) ('2020-12-20', 0.00000e+00)\n", + " ('2020-12-20', nan) ('2020-12-20', 0.00000e+00)\n", + " ('2020-12-20', 0.00000e+00) ('2020-12-20', nan)\n", + " ('2020-12-20', 0.00000e+00) ('2020-12-20', 0.00000e+00)\n", + " ('2020-12-20', 0.00000e+00) ('2020-12-20', nan)\n", + " ('2020-12-20', 0.00000e+00) ('2020-12-20', 0.00000e+00)\n", + " ('2020-12-20', 0.00000e+00) ('2020-12-20', 0.00000e+00)\n", + " ('2020-12-20', 0.00000e+00) ('2020-12-20', nan)\n", + " ('2020-12-20', 0.00000e+00) ('2020-12-20', nan)\n", + " ('2020-12-20', nan) ('2020-12-20', 0.00000e+00)\n", + " ('2020-12-20', 7.00000e+00) ('2020-12-20', 0.00000e+00)\n", + " ('2020-12-20', nan) ('2020-12-20', nan)\n", + " ('2020-12-20', nan) ('2020-12-20', 0.00000e+00)\n", + " ('2020-12-20', 0.00000e+00) ('2020-12-20', nan)\n", + " ('2020-12-20', nan) ('2020-12-20', 0.00000e+00)\n", + " ('2020-12-20', nan) ('2020-12-20', 0.00000e+00)\n", + " ('2020-12-20', nan) ('2020-12-20', nan)\n", + " ('2020-12-20', 0.00000e+00) ('2020-12-20', 0.00000e+00)\n", + " ('2020-12-20', 0.00000e+00) ('2020-12-20', 0.00000e+00)\n", + " ('2020-12-20', nan) ('2020-12-20', nan)\n", + " ('2020-12-20', nan) ('2020-12-20', 1.40000e+01)\n", + " ('2020-12-20', 0.00000e+00)]\n", + " [('2020-12-27', -9.99999e+05) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', -9.99999e+05) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', -9.99999e+05)\n", + " ('2020-12-27', -9.99999e+05) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', nan)\n", + " ('2020-12-27', nan) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', nan) ('2020-12-27', nan)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', nan) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', nan)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', nan)\n", + " ('2020-12-27', 7.00000e+00) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', nan) ('2020-12-27', nan)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', nan) ('2020-12-27', nan)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', nan) ('2020-12-27', nan)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', 0.00000e+00)\n", + " ('2020-12-27', 0.00000e+00) ('2020-12-27', 1.40000e+01)\n", + " ('2020-12-27', 0.00000e+00)]]\n" ] } ], "source": [ - "print(f\"COVID hospitalization average:\\n {covid_avg.get_value()[:3]}\\n\")\n", - "print(f\"COVID hospitalization sum:\\n {covid_sum.get_value()[:3]}\\n\")\n", - "print(f\"Influenza hospitalization average:\\n {flu_avg.get_value()[:3]}\\n\")\n", - "print(f\"Influenza hospitalization sum:\\n {flu_sum.get_value()[:3]}\")" + "print(\n", + " f\"COVID hospitalization average:\\n {covid_avg.evaluate_in_context(data, dim, county_scope, rng)[:3]}\\n\")\n", + "print(\n", + " f\"COVID hospitalization sum:\\n {covid_sum.evaluate_in_context(data, dim, county_scope, rng)[:3]}\\n\")\n", + "print(\n", + " f\"Influenza hospitalization average:\\n {flu_avg.evaluate_in_context(data, dim, county_scope, rng)[:3]}\\n\")\n", + "print(\n", + " f\"Influenza hospitalization sum:\\n {flu_sum.evaluate_in_context(data, dim, county_scope, rng)[:3]}\")" ] }, { @@ -203,32 +588,40 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 7, "metadata": {}, "outputs": [], "source": [ + "from epymorph.geo.adrio.cdc import (CovidHospitalizationAvgState,\n", + " CovidHospitalizationSumState,\n", + " InfluenzaHospitalizationAvgState,\n", + " InfluenzaHospitalizationSumState)\n", + "\n", "time_period = DateRange(date(2020, 12, 13), date(2024, 6, 28))\n", "\n", - "covid_avg = maker.make_adrio(AttributeDef(\n", - " \"covid_hospitalization_avg_state\", float, Shapes.TxN), state_scope, time_period)\n", - "covid_sum = maker.make_adrio(AttributeDef(\n", - " \"covid_hospitalization_sum_state\", float, Shapes.TxN), state_scope, time_period)\n", - "flu_avg = maker.make_adrio(AttributeDef(\n", - " \"influenza_hospitalization_avg_state\", float, Shapes.TxN), state_scope, time_period)\n", - "flu_sum = maker.make_adrio(AttributeDef(\n", - " \"influenza_hospitalization_sum_state\", float, Shapes.TxN), state_scope, time_period)" + "covid_avg = CovidHospitalizationAvgState(time_period)\n", + "covid_sum = CovidHospitalizationSumState(time_period)\n", + "flu_avg = InfluenzaHospitalizationAvgState(time_period)\n", + "flu_sum = InfluenzaHospitalizationSumState(time_period)" ] }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 8, "metadata": {}, "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Evaluating CovidHospitalizationAvgState ADRIO...\n" + ] + }, { "name": "stderr", "output_type": "stream", "text": [ - "/home/waff/Desktop/CCL/Epymorph/epymorph/geo/adrio/cdc/adrio_cdc.py:213: UserWarning: State level hospitalization data is voluntary past 5/1/2024.\n", + "/home/waff/Desktop/CCL/Epymorph/epymorph/geo/adrio/cdc.py:115: UserWarning: State level hospitalization data is voluntary past 5/1/2024.\n", " warn(\"State level hospitalization data is voluntary past 5/1/2024.\")\n" ] }, @@ -236,19 +629,21 @@ "name": "stdout", "output_type": "stream", "text": [ + "Completed CovidHospitalizationAvgState ADRIO (2.310s).\n", "COVID hospitalization average:\n", " [[('2020-12-19', 452.) ('2020-12-19', 199.)]\n", " [('2020-12-26', 472.) ('2020-12-26', 164.)]\n", " [('2021-01-02', 495.) ('2021-01-02', 150.)]]\n", "...\n", - "\n" + "\n", + "Evaluating CovidHospitalizationSumState ADRIO...\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "/home/waff/Desktop/CCL/Epymorph/epymorph/geo/adrio/cdc/adrio_cdc.py:213: UserWarning: State level hospitalization data is voluntary past 5/1/2024.\n", + "/home/waff/Desktop/CCL/Epymorph/epymorph/geo/adrio/cdc.py:115: UserWarning: State level hospitalization data is voluntary past 5/1/2024.\n", " warn(\"State level hospitalization data is voluntary past 5/1/2024.\")\n" ] }, @@ -256,19 +651,21 @@ "name": "stdout", "output_type": "stream", "text": [ + "Completed CovidHospitalizationSumState ADRIO (0.403s).\n", "COVID hospitalization sum:\n", " [[('2020-12-19', 3164.) ('2020-12-19', 1396.)]\n", " [('2020-12-26', 3307.) ('2020-12-26', 1148.)]\n", " [('2021-01-02', 3465.) ('2021-01-02', 1051.)]]\n", "...\n", - "\n" + "\n", + "Evaluating InfluenzaHospitalizationAvgState ADRIO...\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "/home/waff/Desktop/CCL/Epymorph/epymorph/geo/adrio/cdc/adrio_cdc.py:213: UserWarning: State level hospitalization data is voluntary past 5/1/2024.\n", + "/home/waff/Desktop/CCL/Epymorph/epymorph/geo/adrio/cdc.py:115: UserWarning: State level hospitalization data is voluntary past 5/1/2024.\n", " warn(\"State level hospitalization data is voluntary past 5/1/2024.\")\n" ] }, @@ -276,19 +673,21 @@ "name": "stdout", "output_type": "stream", "text": [ + "Completed InfluenzaHospitalizationAvgState ADRIO (0.618s).\n", "Influenza hospitalization average:\n", " [[('2020-12-19', 2.) ('2020-12-19', 1.)]\n", " [('2020-12-26', 1.) ('2020-12-26', 1.)]\n", " [('2021-01-02', 6.) ('2021-01-02', 0.)]]\n", "...\n", - "\n" + "\n", + "Evaluating InfluenzaHospitalizationSumState ADRIO...\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "/home/waff/Desktop/CCL/Epymorph/epymorph/geo/adrio/cdc/adrio_cdc.py:213: UserWarning: State level hospitalization data is voluntary past 5/1/2024.\n", + "/home/waff/Desktop/CCL/Epymorph/epymorph/geo/adrio/cdc.py:115: UserWarning: State level hospitalization data is voluntary past 5/1/2024.\n", " warn(\"State level hospitalization data is voluntary past 5/1/2024.\")\n" ] }, @@ -296,6 +695,7 @@ "name": "stdout", "output_type": "stream", "text": [ + "Completed InfluenzaHospitalizationSumState ADRIO (0.389s).\n", "Influenza hospitalization sum:\n", " [[('2020-12-19', 11.) ('2020-12-19', 5.)]\n", " [('2020-12-26', 8.) ('2020-12-26', 5.)]\n", @@ -305,10 +705,14 @@ } ], "source": [ - "print(f\"COVID hospitalization average:\\n {covid_avg.get_value()[:3]}\\n...\\n\")\n", - "print(f\"COVID hospitalization sum:\\n {covid_sum.get_value()[:3]}\\n...\\n\")\n", - "print(f\"Influenza hospitalization average:\\n {flu_avg.get_value()[:3]}\\n...\\n\")\n", - "print(f\"Influenza hospitalization sum:\\n {flu_sum.get_value()[:3]}\\n...\")" + "print(\n", + " f\"COVID hospitalization average:\\n {covid_avg.evaluate_in_context(data, dim, state_scope, rng)[:3]}\\n...\\n\")\n", + "print(\n", + " f\"COVID hospitalization sum:\\n {covid_sum.evaluate_in_context(data, dim, state_scope, rng)[:3]}\\n...\\n\")\n", + "print(\n", + " f\"Influenza hospitalization average:\\n {flu_avg.evaluate_in_context(data, dim, state_scope, rng)[:3]}\\n...\\n\")\n", + "print(\n", + " f\"Influenza hospitalization sum:\\n {flu_sum.evaluate_in_context(data, dim, state_scope, rng)[:3]}\\n...\")" ] }, { @@ -327,284 +731,410 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 23, "metadata": {}, "outputs": [], "source": [ - "time_period = DateRange(date(2020, 12, 13), date(2024, 5, 10))\n", + "from epymorph.geo.adrio.cdc import (CovidBoosterDoses, FullCovidVaccinations,\n", + " OneDoseCovidVaccinations)\n", "\n", - "full = maker.make_adrio(AttributeDef(\"full_covid_vaccinations\",\n", - " float, Shapes.TxN), state_scope, time_period)\n", - "one = maker.make_adrio(AttributeDef(\"one_dose_covid_vaccinations\",\n", - " float, Shapes.TxN), state_scope, time_period)\n", - "booster = maker.make_adrio(AttributeDef(\"covid_booster_doses\",\n", - " float, Shapes.TxN), state_scope, time_period)" + "time_period = DateRange(date(2021, 12, 13), date(2024, 5, 10))\n", + "\n", + "full = FullCovidVaccinations(time_period)\n", + "one = OneDoseCovidVaccinations(time_period)\n", + "booster = CovidBoosterDoses(time_period)" ] }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 24, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ + "Evaluating FullCovidVaccinations ADRIO...\n", + "Completed FullCovidVaccinations ADRIO (2.306s).\n", "Full COVID vaccinations:\n", - " [[('2020-12-13', 0.) 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ADRIO...\n", + "Completed OneDoseCovidVaccinations ADRIO (2.892s).\n", "One dose COVID vaccinations:\n", - " [[('2020-12-13', 0.) 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2.515030e+05) ('2021-12-15', 9.106000e+03)\n", + " ('2021-12-15', 2.014000e+03) ('2021-12-15', 8.609000e+03)\n", + " ('2021-12-15', 7.939200e+04) ('2021-12-15', 6.500000e+02)\n", + " ('2021-12-15', 6.066000e+03) ('2021-12-15', 1.849500e+04)\n", + " ('2021-12-15', 2.194000e+04) ('2021-12-15', 1.437300e+04)\n", + " ('2021-12-15', 9.068000e+03) ('2021-12-15', 3.433000e+03)\n", + " ('2021-12-15', 9.209000e+03) ('2021-12-15', 2.320000e+03)\n", + " ('2021-12-15', 1.718700e+04) ('2021-12-15', 5.404000e+03)\n", + " ('2021-12-15', 9.811600e+04) ('2021-12-15', 2.645000e+03)\n", + " ('2021-12-15', 7.357000e+03) ('2021-12-15', 2.053900e+04)\n", + " ('2021-12-15', 2.471000e+03) ('2021-12-15', 7.180000e+02)\n", + " ('2021-12-15', 7.386000e+03) ('2021-12-15', 1.200000e+03)\n", + " ('2021-12-15', 2.818600e+04) ('2021-12-15', 1.374700e+04)\n", + " ('2021-12-15', 1.593000e+03) ('2021-12-15', 1.980310e+05)\n", + " ('2021-12-15', 4.574000e+03)]]\n", "\n", + "Evaluating CovidBoosterDoses ADRIO...\n", + "Completed CovidBoosterDoses ADRIO (2.241s).\n", "COVID booster doses:\n", - " [[('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan) ('2020-12-13', nan) ('2020-12-13', nan)\n", - " ('2020-12-13', nan)]\n", - " [('2020-12-14', nan) ('2020-12-14', nan) ('2020-12-14', nan)\n", - " ('2020-12-14', nan) ('2020-12-14', nan) ('2020-12-14', nan)\n", - " ('2020-12-14', nan) ('2020-12-14', nan) ('2020-12-14', nan)\n", - " ('2020-12-14', nan) ('2020-12-14', nan) ('2020-12-14', nan)\n", - " ('2020-12-14', nan) ('2020-12-14', nan) ('2020-12-14', nan)\n", - " ('2020-12-14', nan) ('2020-12-14', nan) ('2020-12-14', nan)\n", - " ('2020-12-14', nan) ('2020-12-14', nan) ('2020-12-14', nan)\n", - " ('2020-12-14', nan) ('2020-12-14', nan) ('2020-12-14', nan)\n", - " ('2020-12-14', nan) ('2020-12-14', nan) ('2020-12-14', nan)\n", - " ('2020-12-14', nan) ('2020-12-14', nan) ('2020-12-14', nan)\n", - " ('2020-12-14', nan) ('2020-12-14', nan) ('2020-12-14', nan)\n", - " ('2020-12-14', nan) ('2020-12-14', nan) ('2020-12-14', nan)\n", - " ('2020-12-14', nan) ('2020-12-14', nan) ('2020-12-14', nan)\n", - " ('2020-12-14', nan) ('2020-12-14', nan) ('2020-12-14', nan)\n", - " ('2020-12-14', nan) ('2020-12-14', nan) ('2020-12-14', nan)\n", - " ('2020-12-14', nan) ('2020-12-14', nan) ('2020-12-14', nan)\n", - " ('2020-12-14', nan) 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nan) ('2020-12-15', nan)\n", - " ('2020-12-15', nan) ('2020-12-15', nan) ('2020-12-15', nan)\n", - " ('2020-12-15', nan) ('2020-12-15', nan) ('2020-12-15', nan)\n", - " ('2020-12-15', nan) ('2020-12-15', nan) ('2020-12-15', nan)\n", - " ('2020-12-15', nan) ('2020-12-15', nan) ('2020-12-15', nan)\n", - " ('2020-12-15', nan) ('2020-12-15', nan) ('2020-12-15', nan)\n", - " ('2020-12-15', nan) ('2020-12-15', nan) ('2020-12-15', nan)\n", - " ('2020-12-15', nan) ('2020-12-15', nan) ('2020-12-15', nan)\n", - " ('2020-12-15', nan) ('2020-12-15', nan) ('2020-12-15', nan)\n", - " ('2020-12-15', nan) ('2020-12-15', nan) ('2020-12-15', nan)\n", - " ('2020-12-15', nan) ('2020-12-15', nan) ('2020-12-15', nan)\n", - " ('2020-12-15', nan) ('2020-12-15', nan) ('2020-12-15', nan)\n", - " ('2020-12-15', nan) ('2020-12-15', nan) ('2020-12-15', nan)\n", - " ('2020-12-15', nan) ('2020-12-15', nan) ('2020-12-15', nan)\n", - " ('2020-12-15', nan) ('2020-12-15', nan) ('2020-12-15', nan)\n", - " ('2020-12-15', 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nan)\n", + " ('2021-12-14', nan) ('2021-12-14', nan)\n", + " ('2021-12-14', nan) ('2021-12-14', nan)\n", + " ('2021-12-14', nan) ('2021-12-14', nan)\n", + " ('2021-12-14', nan) ('2021-12-14', nan)\n", + " ('2021-12-14', nan) ('2021-12-14', nan)\n", + " ('2021-12-14', nan) ('2021-12-14', nan)\n", + " ('2021-12-14', nan)]\n", + " [('2021-12-15', 2.00940e+04) ('2021-12-15', 1.80370e+04)\n", + " ('2021-12-15', 3.03170e+04) ('2021-12-15', 9.47000e+03)\n", + " ('2021-12-15', 5.44100e+03) ('2021-12-15', 1.11300e+03)\n", + " ('2021-12-15', 1.77000e+03) ('2021-12-15', 5.76163e+05)\n", + " ('2021-12-15', 2.07320e+04) ('2021-12-15', 2.11070e+04)\n", + " ('2021-12-15', 1.83761e+05) ('2021-12-15', 5.08790e+04)\n", + " ('2021-12-15', 1.00320e+04) ('2021-12-15', 3.02740e+04)\n", + " ('2021-12-15', 2.82930e+04) ('2021-12-15', 9.19710e+04)\n", + " ('2021-12-15', 3.09400e+03) ('2021-12-15', 1.41957e+05)\n", + " ('2021-12-15', 3.60300e+03) ('2021-12-15', 5.06000e+02)\n", + " ('2021-12-15', 6.18000e+02) ('2021-12-15', 9.96980e+04)\n", + " ('2021-12-15', 2.17360e+04) ('2021-12-15', 5.97900e+03)\n", + " ('2021-12-15', 1.79000e+02) ('2021-12-15', 1.78800e+03)\n", + " ('2021-12-15', 1.32100e+03) ('2021-12-15', 1.00600e+03)\n", + " ('2021-12-15', 4.41000e+02) ('2021-12-15', 1.00500e+03)\n", + " ('2021-12-15', 5.43200e+03) ('2021-12-15', 1.85086e+05)\n", + " ('2021-12-15', 3.21000e+02) ('2021-12-15', 9.04910e+04)\n", + " ('2021-12-15', 1.28900e+04) ('2021-12-15', 3.17700e+03)\n", + " ('2021-12-15', 1.21638e+05) ('2021-12-15', 6.09700e+03)\n", + " ('2021-12-15', 1.22030e+04) ('2021-12-15', 1.44300e+03)\n", + " ('2021-12-15', 3.68900e+03) ('2021-12-15', 4.98000e+03)\n", + " ('2021-12-15', 2.33000e+02) ('2021-12-15', 1.37900e+03)\n", + " ('2021-12-15', 2.62000e+02) ('2021-12-15', 1.65523e+05)\n", + " ('2021-12-15', 2.39000e+02) ('2021-12-15', 7.66000e+02)\n", + " ('2021-12-15', 1.44800e+03) ('2021-12-15', 1.67160e+04)\n", + " ('2021-12-15', 8.90960e+04) ('2021-12-15', 2.97500e+03)\n", + " ('2021-12-15', 7.40000e+02) ('2021-12-15', 2.67300e+03)\n", + " ('2021-12-15', 2.73840e+04) ('2021-12-15', 3.52000e+02)\n", + " ('2021-12-15', 1.59900e+03) ('2021-12-15', 6.07400e+03)\n", + " ('2021-12-15', 7.83700e+03) ('2021-12-15', 3.51400e+03)\n", + " ('2021-12-15', 3.21800e+03) ('2021-12-15', 1.57300e+03)\n", + " ('2021-12-15', 3.31300e+03) ('2021-12-15', 5.49000e+02)\n", + " ('2021-12-15', 4.55200e+03) ('2021-12-15', 1.51500e+03)\n", + " ('2021-12-15', 3.29190e+04) ('2021-12-15', 7.46000e+02)\n", + " ('2021-12-15', 2.38500e+03) ('2021-12-15', 8.38500e+03)\n", + " ('2021-12-15', 9.05000e+02) ('2021-12-15', 2.47000e+02)\n", + " ('2021-12-15', 2.61600e+03) ('2021-12-15', 5.05000e+02)\n", + " ('2021-12-15', 7.57000e+03) ('2021-12-15', 5.43800e+03)\n", + " ('2021-12-15', 5.07000e+02) ('2021-12-15', 5.51140e+04)\n", + " ('2021-12-15', 1.30600e+03)]]\n" ] } ], "source": [ - "print(f\"Full COVID vaccinations:\\n {full.get_value()[:3]}\\n\")\n", - "print(f\"One dose COVID vaccinations:\\n {one.get_value()[:3]}\\n\")\n", - "print(f\"COVID booster doses:\\n {booster.get_value()[:3]}\")" + "print(\n", + " f\"Full COVID vaccinations:\\n {full.evaluate_in_context(data, dim, state_scope, rng)[:3]}\\n\")\n", + "print(\n", + " f\"One dose COVID vaccinations:\\n {one.evaluate_in_context(data, dim, state_scope, rng)[:3]}\\n\")\n", + "print(\n", + " f\"COVID booster doses:\\n {booster.evaluate_in_context(data, dim, state_scope, rng)[:3]}\")" ] }, { @@ -623,33 +1153,37 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 11, "metadata": {}, "outputs": [], "source": [ - "deaths = maker.make_adrio(AttributeDef(\"covid_deaths_county\", float, Shapes.TxN),\n", - " state_scope, DateRange(date(2020, 1, 4), date(2024, 4, 5)))" + "from epymorph.geo.adrio.cdc import CovidDeathsCounty\n", + "\n", + "deaths = CovidDeathsCounty(DateRange(date(2021, 1, 4), date(2024, 4, 5)))" ] }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 12, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ + "Evaluating CovidDeathsCounty ADRIO...\n", + "Completed CovidDeathsCounty ADRIO (2.583s).\n", "COVID deaths:\n", - " [[('2020-01-04', 0.) ('2020-01-04', 0.)]\n", - " [('2020-01-11', 0.) ('2020-01-11', 0.)]\n", - " [('2020-01-18', 0.) ('2020-01-18', 0.)]]\n", + " [[('2021-01-09', 921.) ('2021-01-09', 180.)]\n", + " [('2021-01-16', 960.) ('2021-01-16', 125.)]\n", + " [('2021-01-23', 926.) ('2021-01-23', 97.)]]\n", "\n" ] } ], "source": [ - "print(f\"COVID deaths:\\n {deaths.get_value()[:3]}\\n\")" + "print(\n", + " f\"COVID deaths:\\n {deaths.evaluate_in_context(data, dim, state_scope, rng)[:3]}\\n\")" ] }, { @@ -668,44 +1202,50 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 19, "metadata": {}, "outputs": [], "source": [ - "time_period = DateRange(date(2020, 1, 4), date(2024, 4, 5))\n", + "from epymorph.geo.adrio.cdc import CovidDeathsState, InfluenzaDeathsState\n", + "\n", + "time_period = DateRange(date(2021, 1, 4), date(2024, 4, 5))\n", "\n", - "covid_deaths = maker.make_adrio(AttributeDef(\n", - " \"covid_deaths_state\", float, Shapes.TxN), state_scope, time_period)\n", - "flu_deaths = maker.make_adrio(AttributeDef(\n", - " \"influenza_deaths\", float, Shapes.TxN), state_scope, time_period)" + "covid_deaths = CovidDeathsState(time_period)\n", + "flu_deaths = InfluenzaDeathsState(time_period)" ] }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 20, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ + "Evaluating CovidDeathsState ADRIO...\n", + "Completed CovidDeathsState ADRIO (0.488s).\n", "COVID deaths:\n", - " [[('2020-01-04', 0.) ('2020-01-04', 0.)]\n", - " [('2020-01-11', 0.) ('2020-01-11', 0.)]\n", - " [('2020-01-18', 0.) ('2020-01-18', 0.)]]\n", + " [[('2021-01-09', 942.) ('2021-01-09', 211.)]\n", + " [('2021-01-16', 996.) ('2021-01-16', 165.)]\n", + " [('2021-01-23', 959.) ('2021-01-23', 158.)]]\n", "...\n", "\n", + "Evaluating InfluenzaDeathsState ADRIO...\n", + "Completed InfluenzaDeathsState ADRIO (0.483s).\n", "Influenza deaths:\n", - " [[('2020-01-04', 0.) ('2020-01-04', 0.)]\n", - " [('2020-01-11', 0.) ('2020-01-11', 0.)]\n", - " [('2020-01-18', 11.) ('2020-01-18', 0.)]]\n", + " [[('2021-01-09', 0.) ('2021-01-09', 0.)]\n", + " [('2021-01-16', 0.) ('2021-01-16', 0.)]\n", + " [('2021-01-23', 0.) ('2021-01-23', 0.)]]\n", "...\n" ] } ], "source": [ - "print(f\"COVID deaths:\\n {covid_deaths.get_value()[:3]}\\n...\\n\")\n", - "print(f\"Influenza deaths:\\n {flu_deaths.get_value()[:3]}\\n...\")" + "print(\n", + " f\"COVID deaths:\\n {covid_deaths.evaluate_in_context(data, dim, state_scope, rng)[:3]}\\n...\\n\")\n", + "print(\n", + " f\"Influenza deaths:\\n {flu_deaths.evaluate_in_context(data, dim, state_scope, rng)[:3]}\\n...\")" ] } ], diff --git a/epymorph/geo/adrio/__init__.py b/epymorph/geo/adrio/__init__.py index 6c010271..f4dec120 100644 --- a/epymorph/geo/adrio/__init__.py +++ b/epymorph/geo/adrio/__init__.py @@ -1,7 +1,7 @@ """AdrioMaker library.""" -from epymorph.geo.adrio.cdc.adrio_cdc import ADRIOMakerCDC from epymorph.geo.adrio.census.adrio_census import ADRIOMakerCensus from epymorph.geo.adrio.census.lodes import ADRIOMakerLODES +from epymorph.geo.adrio.disease.adrio_cdc import ADRIOMakerCDC from epymorph.geo.adrio.file.adrio_csv import ADRIOMakerCSV from epymorph.geo.dynamic import ADRIOMaker diff --git a/epymorph/geo/adrio/cdc/adrio_cdc.py b/epymorph/geo/adrio/disease/adrio_cdc.py similarity index 100% rename from epymorph/geo/adrio/cdc/adrio_cdc.py rename to epymorph/geo/adrio/disease/adrio_cdc.py