From 8f1b44e816506e99bc1278e83b40f5b4b6391e58 Mon Sep 17 00:00:00 2001
From: Chandrasekhar Ramakrishnan <cramakri@ethz.ch>
Date: Fri, 20 Mar 2020 18:47:14 +0000
Subject: [PATCH] feat: display number of tests per 100k pop in US states
---
.../examples/covidtracking-example.ipynb | 312 ++++++++++++++----
1 file changed, 255 insertions(+), 57 deletions(-)
diff --git a/notebooks/examples/covidtracking-example.ipynb b/notebooks/examples/covidtracking-example.ipynb
index 74c3ce4d..a2d141e1 100644
--- a/notebooks/examples/covidtracking-example.ipynb
+++ b/notebooks/examples/covidtracking-example.ipynb
@@ -2,25 +2,12 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 60,
+ "execution_count": 1,
"metadata": {},
- "outputs": [
- {
- "ename": "ModuleNotFoundError",
- "evalue": "No module named 'matplotlib'",
- "output_type": "error",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)",
- "\u001b[0;32m<ipython-input-60-ffb398b1b277>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpandas\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mpd\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0maltair\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0malt\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0;32mimport\u001b[0m \u001b[0mmatplotlib\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
- "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'matplotlib'"
- ]
- }
- ],
+ "outputs": [],
"source": [
"import pandas as pd\n",
- "import altair as alt\n",
- "import matplotlib"
+ "import altair as alt"
]
},
{
@@ -189,7 +176,7 @@
},
{
"cell_type": "code",
- "execution_count": 222,
+ "execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
@@ -199,7 +186,7 @@
},
{
"cell_type": "code",
- "execution_count": 223,
+ "execution_count": 5,
"metadata": {},
"outputs": [
{
@@ -309,7 +296,7 @@
"4 2020-03-19T20:00:00Z "
]
},
- "execution_count": 223,
+ "execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
@@ -327,57 +314,32 @@
},
{
"cell_type": "code",
- "execution_count": 257,
+ "execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
"# compute daily differences\n",
"tdf = data_df.sort_values(['state', 'date'], ascending=[True, False]).set_index(['state', 'date'])\n",
"diffs_df = tdf[['positive', 'negative', 'death']].groupby(level='state').diff(periods=-1).dropna(how='all')\n",
- "tdf_diff=tdf.join(diffs_df, rsuffix='_diff').reset_index()"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 276,
- "metadata": {},
- "outputs": [],
- "source": [
+ "tdf_diff=tdf.join(diffs_df, rsuffix='_diff').reset_index()\n",
+ "\n",
"# \"Normalizing\" the totals\n",
"tdf_diff['total_10'] = tdf_diff['total']/10."
]
},
{
"cell_type": "code",
- "execution_count": 278,
+ "execution_count": 11,
"metadata": {},
"outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "/opt/conda/lib/python3.7/site-packages/ipykernel_launcher.py:7: SettingWithCopyWarning: \n",
- "A value is trying to be set on a copy of a slice from a DataFrame.\n",
- "Try using .loc[row_indexer,col_indexer] = value instead\n",
- "\n",
- "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
- " import sys\n",
- "/opt/conda/lib/python3.7/site-packages/ipykernel_launcher.py:9: SettingWithCopyWarning: \n",
- "A value is trying to be set on a copy of a slice from a DataFrame.\n",
- "Try using .loc[row_indexer,col_indexer] = value instead\n",
- "\n",
- "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
- " if __name__ == '__main__':\n"
- ]
- },
{
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-a2f753a0d34f48da9107b4032abab8e2\"></div>\n",
+ "<div id=\"altair-viz-65df72664b9f476eaf839e817659dd24\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-a2f753a0d34f48da9107b4032abab8e2\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-65df72664b9f476eaf839e817659dd24\");\n",
" const paths = {\n",
" \"vega\": \"https://cdn.jsdelivr.net/npm//vega@5?noext\",\n",
" \"vega-lib\": \"https://cdn.jsdelivr.net/npm//vega-lib?noext\",\n",
@@ -425,7 +387,7 @@
"alt.HConcatChart(...)"
]
},
- "execution_count": 278,
+ "execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
@@ -435,11 +397,10 @@
"\n",
"charts=[]\n",
"for state in ['WA', 'CA', 'NY']: \n",
- " state_df = tdf_diff[tdf_diff['state'] == state]\n",
- "\n",
- " state_df['daily_positive'] = state_df['positive'][::-1].diff()\n",
+ " state_df = tdf_diff[tdf_diff['state'] == state].copy()\n",
"\n",
- " state_df['total_10'] = state_df['total']/10.\n",
+ " state_df.loc[:,'daily_positive'] = state_df['positive'][::-1].diff()\n",
+ " state_df.loc[:,'total_10'] = state_df['total']/10.\n",
"\n",
" base = alt.Chart(state_df, title=state).encode(alt.X('date', axis=alt.Axis(title='Date'))).properties(width=250, height=150)\n",
" dailies = base.mark_bar(size=10).encode(alt.Y('daily_positive', axis=alt.Axis(title='Daily positive')))\n",
@@ -454,12 +415,249 @@
"alt.hconcat(*charts)"
]
},
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### Counts per 100k"
+ ]
+ },
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 55,
"metadata": {},
"outputs": [],
- "source": []
+ "source": [
+ "pop_df = pd.read_csv('../../data/geodata/us_pop_fung_2019.csv').set_index('ST')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 56,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Most recent test date 2020-03-19 00:00:00\n",
+ "56 states/territories have data on this date.\n"
+ ]
+ }
+ ],
+ "source": [
+ "most_recent_test_date = data_df['date'].max()\n",
+ "most_recent_df = data_df[data_df['date'] == most_recent_test_date].set_index('state')\n",
+ "print(\"Most recent test date\", most_recent_test_date)\n",
+ "print(len(most_recent_df), \"states/territories have data on this date.\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 57,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "most_recent_df['total/100k'] = (most_recent_df['total'] / pop_df['Population']) * 100000\n",
+ "most_recent_df = most_recent_df.reset_index()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 58,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<div>\n",
+ "<style scoped>\n",
+ " .dataframe tbody tr th:only-of-type {\n",
+ " vertical-align: middle;\n",
+ " }\n",
+ "\n",
+ " .dataframe tbody tr th {\n",
+ " vertical-align: top;\n",
+ " }\n",
+ "\n",
+ " .dataframe thead th {\n",
+ " text-align: right;\n",
+ " }\n",
+ "</style>\n",
+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th></th>\n",
+ " <th>state</th>\n",
+ " <th>date</th>\n",
+ " <th>positive</th>\n",
+ " <th>negative</th>\n",
+ " <th>pending</th>\n",
+ " <th>death</th>\n",
+ " <th>total</th>\n",
+ " <th>dateChecked</th>\n",
+ " <th>total/100k</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>0</th>\n",
+ " <td>AK</td>\n",
+ " <td>2020-03-19</td>\n",
+ " <td>6</td>\n",
+ " <td>400.0</td>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>406</td>\n",
+ " <td>2020-03-19T20:00:00Z</td>\n",
+ " <td>55.498978</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>1</th>\n",
+ " <td>AL</td>\n",
+ " <td>2020-03-19</td>\n",
+ " <td>68</td>\n",
+ " <td>28.0</td>\n",
+ " <td>NaN</td>\n",
+ " <td>0.0</td>\n",
+ " <td>96</td>\n",
+ " <td>2020-03-19T20:00:00Z</td>\n",
+ " <td>1.957911</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2</th>\n",
+ " <td>AR</td>\n",
+ " <td>2020-03-19</td>\n",
+ " <td>46</td>\n",
+ " <td>310.0</td>\n",
+ " <td>113.0</td>\n",
+ " <td>NaN</td>\n",
+ " <td>469</td>\n",
+ " <td>2020-03-19T20:00:00Z</td>\n",
+ " <td>15.540994</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>3</th>\n",
+ " <td>AS</td>\n",
+ " <td>2020-03-19</td>\n",
+ " <td>0</td>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>0.0</td>\n",
+ " <td>0</td>\n",
+ " <td>2020-03-19T20:00:00Z</td>\n",
+ " <td>NaN</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>4</th>\n",
+ " <td>AZ</td>\n",
+ " <td>2020-03-19</td>\n",
+ " <td>44</td>\n",
+ " <td>175.0</td>\n",
+ " <td>130.0</td>\n",
+ " <td>0.0</td>\n",
+ " <td>349</td>\n",
+ " <td>2020-03-19T20:00:00Z</td>\n",
+ " <td>4.794801</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " state date positive negative pending death total \\\n",
+ "0 AK 2020-03-19 6 400.0 NaN NaN 406 \n",
+ "1 AL 2020-03-19 68 28.0 NaN 0.0 96 \n",
+ "2 AR 2020-03-19 46 310.0 113.0 NaN 469 \n",
+ "3 AS 2020-03-19 0 NaN NaN 0.0 0 \n",
+ "4 AZ 2020-03-19 44 175.0 130.0 0.0 349 \n",
+ "\n",
+ " dateChecked total/100k \n",
+ "0 2020-03-19T20:00:00Z 55.498978 \n",
+ "1 2020-03-19T20:00:00Z 1.957911 \n",
+ "2 2020-03-19T20:00:00Z 15.540994 \n",
+ "3 2020-03-19T20:00:00Z NaN \n",
+ "4 2020-03-19T20:00:00Z 4.794801 "
+ ]
+ },
+ "execution_count": 58,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "most_recent_df.head()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 60,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div id=\"altair-viz-e7f6c101686c406b93be99359dbeb66b\"></div>\n",
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15.540993927745976}, {\"state\": \"GA\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 287, \"negative\": 1544.0, \"pending\": null, \"death\": 10.0, \"total\": 1831, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 17.245239263802524}, {\"state\": \"LA\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 347, \"negative\": 458.0, \"pending\": null, \"death\": 8.0, \"total\": 805, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 17.31631902811783}, {\"state\": \"OK\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 44, \"negative\": 466.0, \"pending\": 250.0, \"death\": 1.0, \"total\": 760, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 19.206610308743734}, {\"state\": \"CT\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 96, \"negative\": 604.0, \"pending\": null, \"death\": 1.0, \"total\": 700, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 19.633763004212565}, {\"state\": \"MS\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 50, \"negative\": 552.0, \"pending\": null, \"death\": null, \"total\": 602, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 20.227481890187622}, {\"state\": \"VA\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 94, \"negative\": 1829.0, \"pending\": null, \"death\": 2.0, \"total\": 1923, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 22.52938573506778}, {\"state\": \"NC\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 97, \"negative\": 2408.0, \"pending\": null, \"death\": 0.0, \"total\": 2505, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 23.88424806666308}, {\"state\": \"MI\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 336, \"negative\": 2113.0, \"pending\": null, \"death\": 3.0, \"total\": 2449, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 24.522229566319012}, {\"state\": \"CA\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 924, \"negative\": 8787.0, \"pending\": null, \"death\": 18.0, \"total\": 9711, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 24.577204881638778}, {\"state\": \"IL\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 426, \"negative\": 2725.0, \"pending\": null, \"death\": 4.0, \"total\": 3151, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 24.86619721032991}, {\"state\": \"ID\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 11, \"negative\": 457.0, \"pending\": null, \"death\": null, \"total\": 468, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 26.1151241723933}, {\"state\": \"DC\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 39, \"negative\": 153.0, \"pending\": 11.0, \"death\": 0.0, \"total\": 203, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 28.76376728837023}, {\"state\": \"WI\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 155, \"negative\": 2192.0, \"pending\": null, \"death\": null, \"total\": 2347, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 40.309602478963264}, {\"state\": \"CO\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 216, \"negative\": 2112.0, \"pending\": null, \"death\": 2.0, \"total\": 2328, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 40.42553782635634}, {\"state\": \"OR\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 88, \"negative\": 1329.0, \"pending\": 437.0, \"death\": 3.0, \"total\": 1854, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 43.95722160959775}, {\"state\": \"MA\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 328, \"negative\": 2804.0, \"pending\": null, \"death\": null, \"total\": 3132, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 45.067971047713776}, {\"state\": \"WY\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 18, \"negative\": 271.0, \"pending\": null, \"death\": null, \"total\": 289, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 49.934428665472154}, {\"state\": \"UT\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 78, \"negative\": 1526.0, \"pending\": null, 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65.52863071638016}, {\"state\": \"ND\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 15, \"negative\": 493.0, \"pending\": null, \"death\": 0.0, \"total\": 508, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 66.66124278602003}, {\"state\": \"MT\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 12, \"negative\": 761.0, \"pending\": 0.0, \"death\": null, \"total\": 773, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 72.3255905342363}, {\"state\": \"RI\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 33, \"negative\": 540.0, \"pending\": 334.0, \"death\": null, \"total\": 907, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 85.61765064033885}, {\"state\": \"VT\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 22, \"negative\": 645.0, \"pending\": null, \"death\": null, \"total\": 667, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 106.89290997116937}, {\"state\": \"SD\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 11, \"negative\": 551.0, \"pending\": 385.0, \"death\": 1.0, \"total\": 947, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 107.04689603564763}, {\"state\": \"NY\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 4152, \"negative\": 18132.0, \"pending\": null, \"death\": 12.0, \"total\": 22284, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 114.5497217707339}, {\"state\": \"NM\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 35, \"negative\": 2762.0, \"pending\": null, \"death\": null, \"total\": 2797, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 133.39189795639035}, {\"state\": \"ME\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 53, \"negative\": 2004.0, \"pending\": null, \"death\": null, \"total\": 2057, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 153.02645713622553}, {\"state\": \"WA\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 1187, \"negative\": 15918.0, \"pending\": null, \"death\": 66.0, \"total\": 17105, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": 224.62561194228203}, {\"state\": \"AS\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 0, \"negative\": null, \"pending\": null, \"death\": 0.0, \"total\": 0, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": null}, {\"state\": \"GU\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 12, \"negative\": 69.0, \"pending\": null, \"death\": null, \"total\": 81, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": null}, {\"state\": \"MP\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 0, \"negative\": null, \"pending\": null, \"death\": 0.0, \"total\": 0, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": null}, {\"state\": \"PR\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 5, \"negative\": 56.0, \"pending\": 29.0, \"death\": null, \"total\": 90, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": null}, {\"state\": \"VI\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 3, \"negative\": null, \"pending\": null, \"death\": 0.0, \"total\": 3, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"total/100k\": null}]}}, {\"mode\": \"vega-lite\"});\n",
+ "</script>"
+ ],
+ "text/plain": [
+ "alt.Chart(...)"
+ ]
+ },
+ "execution_count": 60,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "chart = alt.Chart(most_recent_df.sort_values('total/100k'), title=\"Tests per 100k\")\n",
+ "chart.mark_bar().encode(alt.X('state', sort='y'), alt.Y('total/100k'))"
+ ]
}
],
"metadata": {
--
GitLab