{ "cells": [ { "cell_type": "markdown", "id": "241ef7f5", "metadata": { "papermill": { "duration": 0.016884, "end_time": "2022-02-21T22:36:44.665247", "exception": false, "start_time": "2022-02-21T22:36:44.648363", "status": "completed" }, "tags": [] }, "source": [ "# timeseries_us_data.ipynb\n", "\n", "Analyze COVID-19 statistics over time for all counties in the United States.\n", "\n", "Inputs:\n", "* `outputs/us_counties_clean.feather`: The contents of `data/us_counties.csv` after data cleaning by [clean_us_data.ipynb](./clean_us_data.ipynb)\n", "* `outputs/dates.feather`: Dates that go with the points in the time series in `outputs/us_counties_clean.feather`, produced by [clean_us_data.ipynb](./clean_us_data.ipynb).\n", "\n", "**Note:** You can redirect these input files by setting the environment variable `COVID_OUTPUTS_DIR` to a replacement for the prefix `outputs` in the above paths." ] }, { "cell_type": "code", "execution_count": 1, "id": "95365a93", "metadata": { "execution": { "iopub.execute_input": "2022-02-21T22:36:44.700173Z", "iopub.status.busy": "2022-02-21T22:36:44.699840Z", "iopub.status.idle": "2022-02-21T22:36:46.087890Z", "shell.execute_reply": "2022-02-21T22:36:46.087209Z" }, "papermill": { "duration": 1.408734, "end_time": "2022-02-21T22:36:46.090489", "exception": false, "start_time": "2022-02-21T22:36:44.681755", "status": "completed" }, "tags": [] }, "outputs": [], "source": [ "# Initialization boilerplate\n", "import os\n", "import pandas as pd\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", "\n", "# Local file of utility functions\n", "import util\n", "\n", "# Allow environment variables to override data file locations.\n", "_OUTPUTS_DIR = os.getenv(\"COVID_OUTPUTS_DIR\", \"outputs\")\n", "util.ensure_dir_exists(_OUTPUTS_DIR) # create if necessary\n", "\n", "# Size of the line charts in this notebook, in inches\n", "_FIGSIZE = (13, 8)\n", "\n", "# Globally adjust the font size for matplotlib.\n", "plt.rcParams.update({'font.size': 16})" ] }, { "cell_type": "code", "execution_count": 2, "id": "34402797", "metadata": { "execution": { "iopub.execute_input": "2022-02-21T22:36:46.124460Z", "iopub.status.busy": "2022-02-21T22:36:46.124118Z", "iopub.status.idle": "2022-02-21T22:36:46.344767Z", "shell.execute_reply": "2022-02-21T22:36:46.343896Z" }, "papermill": { "duration": 0.240362, "end_time": "2022-02-21T22:36:46.347146", "exception": false, "start_time": "2022-02-21T22:36:46.106784", "status": "completed" }, "tags": [] }, "outputs": [ { "data": { "text/html": [ "
\n", " | State | \n", "County | \n", "Population | \n", "Confirmed | \n", "Deaths | \n", "Recovered | \n", "Confirmed_Outlier | \n", "Deaths_Outlier | \n", "Recovered_Outlier | \n", "Confirmed_7_Days | \n", "Deaths_7_Days | \n", "
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FIPS | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
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1003 | \n", "Alabama | \n", "Baldwin | \n", "223234 | \n", "[ 0, 0, 0, 0, 0, 0, ... | \n", "[ 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "319 | \n", "9 | \n", "
1005 | \n", "Alabama | \n", "Barbour | \n", "24686 | \n", "[ 0, 0, 0, 0, 0, 0, ... | \n", "[ 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "20 | \n", "3 | \n", "
1007 | \n", "Alabama | \n", "Bibb | \n", "22394 | \n", "[ 0, 0, 0, 0, 0, 0, ... | \n", "[ 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "40 | \n", "2 | \n", "
1009 | \n", "Alabama | \n", "Blount | \n", "57826 | \n", "[ 0, 0, 0, 0, 0, 0, ... | \n", "[ 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "116 | \n", "3 | \n", "
\n", " | State | \n", "County | \n", "Population | \n", "Confirmed_per_100 | \n", "Deaths_per_100 | \n", "Recovered_per_100 | \n", "Confirmed_per_100_Outlier | \n", "Deaths_per_100_Outlier | \n", "
---|---|---|---|---|---|---|---|---|
FIPS | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
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1003 | \n", "Alabama | \n", "Baldwin | \n", "223234 | \n", "[ 0.0, 0.0,... | \n", "[ 0.0, 0.0,... | \n", "[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "
1005 | \n", "Alabama | \n", "Barbour | \n", "24686 | \n", "[ 0.0, 0.0,... | \n", "[ 0.0, 0.0,... | \n", "[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "
1007 | \n", "Alabama | \n", "Bibb | \n", "22394 | \n", "[ 0.0, 0.0,... | \n", "[ 0.0, 0.0,... | \n", "[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "
1009 | \n", "Alabama | \n", "Blount | \n", "57826 | \n", "[ 0.0, 0.0,... | \n", "[ 0.0, 0.0,... | \n", "[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
56037 | \n", "Wyoming | \n", "Sweetwater | \n", "42343 | \n", "[ 0.0, 0.0,... | \n", "[ 0.0, 0.0,... | \n", "[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "
56039 | \n", "Wyoming | \n", "Teton | \n", "23464 | \n", "[ 0.0, 0.0,... | \n", "[ 0.0, 0.0,... | \n", "[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "
56041 | \n", "Wyoming | \n", "Uinta | \n", "20226 | \n", "[ 0.0, 0.0,... | \n", "[ 0.0, 0.0,... | \n", "[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "
56043 | \n", "Wyoming | \n", "Washakie | \n", "7805 | \n", "[ 0.0, 0.0,... | \n", "[ 0.0, 0.0,... | \n", "[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "
56045 | \n", "Wyoming | \n", "Weston | \n", "6927 | \n", "[ 0.0, 0.0,... | \n", "[ 0.0, 0.0,... | \n", "[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... | \n", "
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