From bc03ef22a0cfc90fe5ccfdb5a52181845aa3e8c7 Mon Sep 17 00:00:00 2001
From: Rok Roskar <rokroskar@gmail.com>
Date: Thu, 9 Apr 2020 17:12:02 +0200
Subject: [PATCH] feat: add nytimes converter and example notebook
---
notebooks/examples/us-nyt-covid-19.ipynb | 144 ++++++++++++++++++
.../covid_19_utils/covid_19_utils/__init__.py | 2 +-
.../covid_19_utils/converters/nyt.py | 62 ++++++++
3 files changed, 207 insertions(+), 1 deletion(-)
create mode 100644 notebooks/examples/us-nyt-covid-19.ipynb
create mode 100644 src/covid-19/covid_19_utils/covid_19_utils/converters/nyt.py
diff --git a/notebooks/examples/us-nyt-covid-19.ipynb b/notebooks/examples/us-nyt-covid-19.ipynb
new file mode 100644
index 000000000..af70e8023
--- /dev/null
+++ b/notebooks/examples/us-nyt-covid-19.ipynb
@@ -0,0 +1,144 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# COVID-19 Case data for U.S. from the New York Times\n",
+ "\n",
+ "Data from the [New York Times Covid-19 case database](https://github.com/nytimes/covid-19-data).\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "%load_ext autoreload\n",
+ "%autoreload 2"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import pandas as pd\n",
+ "import altair as alt\n",
+ "\n",
+ "from IPython.display import display, HTML\n",
+ "\n",
+ "from covid_19_utils import helper, plotting\n",
+ "from covid_19_utils.converters import CaseConverter"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "html_credits=HTML('''\n",
+ "<p style=\"font-size: smaller\">Data Sources: \n",
+ " <a href=\"https://github.com/nytimes/covid-19-data\">New York Times</a>, <a href=\"https://www.census.gov/\">U.S. Census</a>\n",
+ "<br>\n",
+ "Analysis and Visualization:\n",
+ " <a href=\"https://renkulab.io/projects/covid-19/covid-19-public-data\">Covid-19 Public Data Collaboration Project</a>\n",
+ "</p>''')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "data_folder = \"../../data/covid-19-us-nyt/\"\n",
+ "converter = CaseConverter('../../data/atlas')\n",
+ "df = converter.read_convert(data_folder).rename(columns={'region_label':'state', 'admin2_label': 'county'})\n",
+ "df['county_state'] = df.apply(lambda row: f\"{row['county']}, {row['state']}\", axis=1)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# determine the top ten most affected counties\n",
+ "\n",
+ "latest_dt = df.date.iloc[-1]\n",
+ "top10 = df[df.date==latest_dt].sort_values(by='positive',ascending=False).iloc[:10]['county_state'].to_list()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "display_data",
+ "data": {
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\"2020-03-02T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 1, \"deceased\": 0, \"positive_100k\": 0.011994985616212999, \"deceased_100k\": 0.0, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-03T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 2, \"deceased\": 0, \"positive_100k\": 0.023989971232425997, \"deceased_100k\": 0.0, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-04T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 2, \"deceased\": 0, \"positive_100k\": 0.023989971232425997, \"deceased_100k\": 0.0, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-05T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 4, \"deceased\": 0, \"positive_100k\": 0.047979942464851995, \"deceased_100k\": 0.0, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-06T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 5, \"deceased\": 0, \"positive_100k\": 0.05997492808106499, \"deceased_100k\": 0.0, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-07T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 12, \"deceased\": 0, \"positive_100k\": 0.14393982739455596, \"deceased_100k\": 0.0, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-08T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 14, \"deceased\": 0, \"positive_100k\": 0.16792979862698199, \"deceased_100k\": 0.0, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-09T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 20, \"deceased\": 0, \"positive_100k\": 0.23989971232425997, \"deceased_100k\": 0.0, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-10T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 37, \"deceased\": 0, \"positive_100k\": 0.44381446779988093, \"deceased_100k\": 0.0, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-11T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 52, \"deceased\": 0, \"positive_100k\": 0.6237392520430759, \"deceased_100k\": 0.0, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-12T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 96, \"deceased\": 0, \"positive_100k\": 1.1515186191564477, \"deceased_100k\": 0.0, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-13T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 155, \"deceased\": 0, \"positive_100k\": 1.8592227705130147, \"deceased_100k\": 0.0, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-14T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 269, \"deceased\": 1, \"positive_100k\": 3.226651130761297, \"deceased_100k\": 0.011994985616212999, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-15T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 330, \"deceased\": 5, \"positive_100k\": 3.9583452533502896, \"deceased_100k\": 0.05997492808106499, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-16T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 464, \"deceased\": 7, \"positive_100k\": 5.565673325922831, \"deceased_100k\": 0.08396489931349099, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-17T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 645, \"deceased\": 10, \"positive_100k\": 7.736765722457384, \"deceased_100k\": 0.11994985616212998, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-18T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 1339, \"deceased\": 20, \"positive_100k\": 16.061285740109206, \"deceased_100k\": 0.23989971232425997, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-19T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 2468, \"deceased\": 22, \"positive_100k\": 29.603624500813677, \"deceased_100k\": 0.26388968355668596, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-20T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 4408, \"deceased\": 43, \"positive_100k\": 52.873896596266896, \"deceased_100k\": 0.5157843814971589, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-21T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 6211, \"deceased\": 60, \"positive_100k\": 74.50085566229893, \"deceased_100k\": 0.7196991369727799, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-22T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 9045, \"deceased\": 99, \"positive_100k\": 108.49464489864657, \"deceased_100k\": 1.1875035760050867, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-23T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 12305, \"deceased\": 131, \"positive_100k\": 147.59829800750094, \"deceased_100k\": 1.5713431157239028, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-24T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 14905, \"deceased\": 192, \"positive_100k\": 178.78526060965476, \"deceased_100k\": 2.3030372383128954, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-25T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 20011, \"deceased\": 280, \"positive_100k\": 240.03165716603831, \"deceased_100k\": 3.3585959725396393, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-26T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 23112, \"deceased\": 365, \"positive_100k\": 277.22810756191484, \"deceased_100k\": 4.378169749917744, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-27T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 25399, \"deceased\": 450, \"positive_100k\": 304.6606396661939, \"deceased_100k\": 5.397743527295849, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-28T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 30766, \"deceased\": 672, \"positive_100k\": 369.0377274684091, \"deceased_100k\": 8.060630334095135, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-29T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 33768, \"deceased\": 776, \"positive_100k\": 405.04667428828054, \"deceased_100k\": 9.308108838181287, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-30T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 38087, \"deceased\": 914, \"positive_100k\": 456.8530171647045, \"deceased_100k\": 10.96341685321868, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-03-31T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 43139, \"deceased\": 1096, \"positive_100k\": 517.4516844978125, \"deceased_100k\": 13.146504235369447, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-04-01T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 47440, \"deceased\": 1374, \"positive_100k\": 569.0421176331446, \"deceased_100k\": 16.48111023667666, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-04-02T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 51810, \"deceased\": 1562, \"positive_100k\": 621.4602047759954, \"deceased_100k\": 18.736167532524703, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-04-03T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 57160, \"deceased\": 1867, \"positive_100k\": 685.6333778227349, \"deceased_100k\": 22.394638145469667, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-04-04T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 63307, \"deceased\": 2254, \"positive_100k\": 759.3665544055963, \"deceased_100k\": 27.036697578944096, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-04-05T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 67552, \"deceased\": 2472, \"positive_100k\": 810.2852683464205, \"deceased_100k\": 29.651604443278533, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-04-06T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 68776, \"deceased\": 3485, \"positive_100k\": 824.9671307406652, \"deceased_100k\": 41.802524872502296, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}, {\"date\": \"2020-04-07T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"\", \"state\": \"New York\", \"admin2\": \"\", \"county\": \"New York City\", \"tested\": null, \"positive\": 76876, \"deceased\": 4009, \"positive_100k\": 922.1265142319905, \"deceased_100k\": 48.087897335397905, \"tested_100k\": null, \"county_state\": \"New York City, New York\"}]}}, {\"mode\": \"vega-lite\"});\n</script>",
+ "text/plain": "alt.Chart(...)"
+ },
+ "metadata": {}
+ },
+ {
+ "output_type": "display_data",
+ "data": {
+ "text/plain": "<IPython.core.display.HTML object>",
+ "text/html": "\n<p style=\"font-size: smaller\">Data Sources: \n <a href=\"https://github.com/nytimes/covid-19-data\">New York Times</a>, <a href=\"https://www.census.gov/\">U.S. Census</a>\n<br>\nAnalysis and Visualization:\n <a href=\"https://renkulab.io/projects/covid-19/covid-19-public-data\">Covid-19 Public Data Collaboration Project</a>\n</p>"
+ },
+ "metadata": {}
+ }
+ ],
+ "source": [
+ "base = alt.Chart(df[df['county_state'].isin(top10)], title=\"Covid-19 Cases per 100k population in Top 10 U.S. Counties\")\n",
+ "\n",
+ "chart = plotting.generate_region_chart(\n",
+ " base, \n",
+ " 'positive_100k', \n",
+ " 'county_state', \n",
+ " 'Cases per 100k population', \n",
+ " 'Cases/100k', \n",
+ " scale_type='symlog'\n",
+ ")\n",
+ "\n",
+ "display(chart)\n",
+ "display(html_credits)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "metadata": {
+ "hide_input": true,
+ "kernelspec": {
+ "display_name": "Python 3.7.7 64-bit ('.venv': venv)",
+ "language": "python",
+ "name": "python37764bitvenvvenv814492364d964019a25eb1cf3dc3e99c"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.7.7-final"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
\ No newline at end of file
diff --git a/src/covid-19/covid_19_utils/covid_19_utils/__init__.py b/src/covid-19/covid_19_utils/covid_19_utils/__init__.py
index 8c5400c2a..47beb193c 100644
--- a/src/covid-19/covid_19_utils/covid_19_utils/__init__.py
+++ b/src/covid-19/covid_19_utils/covid_19_utils/__init__.py
@@ -4,4 +4,4 @@ __author__ = """Chandrasekhar Ramakrishnan"""
__email__ = "cramakri@ethz.ch"
__version__ = "0.1.0"
-from .converters import covidtracking, italy, jhu, spain, switzerland
+from .converters import covidtracking, italy, jhu, nyt, spain, switzerland
diff --git a/src/covid-19/covid_19_utils/covid_19_utils/converters/nyt.py b/src/covid-19/covid_19_utils/covid_19_utils/converters/nyt.py
new file mode 100644
index 000000000..81709b13f
--- /dev/null
+++ b/src/covid-19/covid_19_utils/covid_19_utils/converters/nyt.py
@@ -0,0 +1,62 @@
+"""
+Covid-19 converters for data from the New York Times.
+
+Data source: https://github.com/nytimes/covid-19-data
+"""
+
+from pathlib import Path
+
+import numpy as np
+import pandas as pd
+
+from . import CaseConverterImpl as CaseConverter
+from .. import helper
+
+
+class NYTCaseConverter(CaseConverter):
+ """
+ Converter for data from the U.S., collected by
+ the New York Times and hosted at https://github.com/nytimes/covid-19-data/
+ """
+
+ conversion_dict = {
+ "county": "admin2_label",
+ "state": "region_label",
+ "cases": "positive",
+ "deaths": "deceased",
+ }
+ column_list = ["date", "county", "state", "fips", "cases", "deaths"]
+
+ def convert(self, df):
+ # rename the existing columns
+ df_conv = df.rename(columns=self.conversion_dict)
+ df_conv["country"] = "USA"
+ df_conv["country_label"] = "United States of America"
+ df_conv["tested"] = np.nan
+ df_conv["date"] = pd.to_datetime(df_conv["date"])
+ # get population data
+ pop = pd.read_csv(self.atlas_folder / "us_census/co-est2019-alldata.csv")
+ pop["fips"] = pop.STATE * 1000 + pop.COUNTY
+ merged = df_conv.merge(pop[["fips", "POPESTIMATE2019"]]).rename(
+ columns={"POPESTIMATE2019": "population"}
+ )
+
+ # add NYC manually based on https://github.com/nytimes/covid-19-data#geographic-exceptions
+ nyc_county_fips = [61, 47, 81, 5, 85]
+ nyc_pop = nyc_pop = pop.loc[
+ (pop.STATE == 36) & (pop.COUNTY.isin(nyc_county_fips))
+ ]["POPESTIMATE2019"].sum()
+
+ merged = merged.append(
+ df_conv[df_conv.admin2_label == "New York City"], ignore_index=True
+ )
+ merged.loc[merged.admin2_label == "New York City", "population"] = nyc_pop
+
+ return self._set_common_columns(merged)
+
+ def read_data(self, path):
+ """Read in the county data."""
+ return pd.read_csv(Path(path) / "us-counties.csv")
+
+
+NYTCaseConverter._register()
--
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