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January 6, 2021 16:30
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Covid 19 Estimate of Infection Fatality Rate
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| "file_extension": ".py", | |
| "mimetype": "text/x-python", | |
| "name": "python", | |
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| "pygments_lexer": "ipython3", | |
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| "language": "python" | |
| } | |
| }, | |
| "nbformat": 4, | |
| "nbformat_minor": 2, | |
| "cells": [ | |
| { | |
| "source": [ | |
| "import plotly.express as px\n", | |
| "import plotly.graph_objects as go\n", | |
| "from pyspark.sql import SparkSession, SQLContext\n", | |
| "from pyspark import SparkFiles\n", | |
| "spark = SparkSession.builder.appName(\"covid-analysis\").getOrCreate()\n", | |
| "sc = spark.sparkContext\n", | |
| "sqlContext = SQLContext(sc)" | |
| ], | |
| "cell_type": "code", | |
| "metadata": {}, | |
| "execution_count": 2, | |
| "outputs": [] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 3, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "def load(filepath):\n", | |
| " spark.read.format(\"csv\")\\\n", | |
| " .option(\"header\", \"true\")\\\n", | |
| " .option(\"inferSchema\", \"true\")\\\n", | |
| " .load(filepath)\\\n", | |
| " .createOrReplaceTempView(filepath.split('/')[-1][:-4].replace('-','_'))" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 4, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "# Data Collected from https://github.com/owid/covid-19-data/tree/master/public/data on 2021/01/05\n", | |
| "load('/Users/sbussard/Desktop/owid-covid-data.csv')" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 8, | |
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| "output_type": "display_data", | |
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| "plotlyServerURL": "https://plot.ly" | |
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| "data": [ | |
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| "mode": "lines", | |
| "name": "Ephemeral Case Fatality Rate (Percent)", | |
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| ], | |
| "source": [ | |
| "query = spark.sql(\"\"\"\n", | |
| "SELECT\n", | |
| " date,\n", | |
| " 100 * total_deaths / total_cases AS mortality_rate,\n", | |
| " 100 * new_deaths / new_cases AS ephemeral_mortality_rate,\n", | |
| " 100 * LEAD(total_deaths, 56) OVER (ORDER BY date ASC) / total_cases AS adjusted_mortality_rate,\n", | |
| " 100 * LEAD(new_deaths, 56) OVER (ORDER BY date ASC) / new_cases AS adjusted_ephemeral_mortality_rate\n", | |
| "FROM owid_covid_data WHERE iso_code = 'USA'\n", | |
| "ORDER BY date ASC\n", | |
| "\"\"\").toPandas()\n", | |
| "\n", | |
| "fig = go.Figure()\n", | |
| "fig.add_trace(go.Scatter(x=query.get('date'), y=query.get('ephemeral_mortality_rate'), mode='lines', name='Ephemeral Case Fatality Rate (Percent)'))\n", | |
| "fig.add_trace(go.Scatter(x=query.get('date'), y=query.get('mortality_rate'), mode='lines', name='Case Fatality Rate (Percent)'))\n", | |
| "fig.add_trace(go.Scatter(x=query.get('date'), y=query.get('adjusted_mortality_rate'), mode='lines', name='Adjusted Case Fatality Rate (Percent)'))\n", | |
| "fig.add_trace(go.Scatter(x=query.get('date'), y=query.get('adjusted_ephemeral_mortality_rate'), mode='lines', name='Adjusted Ephemeral Case Fatality Rate (Percent)'))\n", | |
| "fig.update_layout(annotations=[\n", | |
| " {\n", | |
| " \"xref\": \"paper\",\n", | |
| " \"yref\": \"paper\",\n", | |
| " \"x\": 0.0,\n", | |
| " \"y\": 1.05,\n", | |
| " \"xanchor\": \"left\",\n", | |
| " \"yanchor\": \"bottom\",\n", | |
| " \"text\": \"Covid Case Fatality Rate\",\n", | |
| " \"font\": { \"family\": \"Arial\", \"size\": 30, \"color\": \"rgb(37,37,37)\" },\n", | |
| " \"showarrow\": False,\n", | |
| " },\n", | |
| " {\n", | |
| " \"xref\": \"paper\",\n", | |
| " \"yref\": \"paper\",\n", | |
| " \"x\": 0.5,\n", | |
| " \"y\": -0.1,\n", | |
| " \"xanchor\": \"center\",\n", | |
| " \"yanchor\": \"top\",\n", | |
| " \"text\": \"Source: Our World in Data\",\n", | |
| " \"font\": { \"family\": \"Arial\", \"size\": 12, \"color\": \"rgb(150,150,150)\" },\n", | |
| " \"showarrow\": False,\n", | |
| " },\n", | |
| "])\n", | |
| "fig.update_layout(yaxis=dict(range=[-5,20]))\n", | |
| "fig.show()" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": null, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [] | |
| } | |
| ] | |
| } |
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Just uploaded the more-complete version I made in February
https://github.com/sbussard/data-playground