diff --git a/notebooks/covid-19-ecdc.ipynb b/notebooks/covid-19-ecdc.ipynb
index 002206e424ed3d8fa74d94c0a91c382a2b98983c..d647d5059afcd59fdfa8311a3b58ed862b7075d2 100644
--- a/notebooks/covid-19-ecdc.ipynb
+++ b/notebooks/covid-19-ecdc.ipynb
@@ -81,7 +81,7 @@
"metadata": {},
"outputs": [],
"source": [
- "nthresh=50000\n",
+ "nthresh=100000\n",
"country_max_ser = df.set_index(['country_label', 'date'])['positive'].groupby(level='country_label').max()\n",
"countries_over_thresh = country_max_ser[country_max_ser>nthresh].index\n",
"countries_over_thresh = [c for c in countries_over_thresh if c not in set(['Andorra', 'Iceland', 'San Marino'])]\n",
@@ -124,7 +124,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "Deaths in countries with over 50,000 cases, ordered by total number of deaths. "
+ "Deaths in countries with over 100,000 cases, ordered by total number of deaths. "
]
},
{
diff --git a/notebooks/covid-19-italy.ipynb b/notebooks/covid-19-italy.ipynb
index 8d60e6dc6a76155c7c5b587b1ca80689bff419bc..acc41431df77eebf112f7d503c2a1ba31efee83c 100644
--- a/notebooks/covid-19-italy.ipynb
+++ b/notebooks/covid-19-italy.ipynb
@@ -11,7 +11,7 @@
},
{
"cell_type": "code",
- "execution_count": 1,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -21,7 +21,7 @@
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -39,7 +39,7 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -54,7 +54,7 @@
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": null,
"metadata": {
"tags": [
"parameters"
@@ -68,7 +68,7 @@
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -77,7 +77,7 @@
},
{
"cell_type": "code",
- "execution_count": 6,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -86,7 +86,7 @@
},
{
"cell_type": "code",
- "execution_count": 7,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -104,91 +104,14 @@
},
{
"cell_type": "code",
- "execution_count": 8,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
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\"\", \"positive\": 224760, \"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 4873.070459218944, \"tested\": 2944859, \"New cases per day\": 875.0}, {\"index\": 83, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"\", \"country\": \"ITA\", \"date\": \"2020-05-17T17:00:00\", \"deceased_100k\": 52.8004675988759, \"deceased_daily\": \"\", \"deceased\": 31908, \"positive_100k\": 373.0435443510276, \"positive_daily\": \"\", \"positive\": 225435, \"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 4972.523916131319, \"tested\": 3004960, \"New cases per day\": 675.0}]}}, {\"mode\": \"vega-lite\"});\n",
- "</script>"
- ],
- "text/plain": [
- "alt.HConcatChart(...)"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- },
- {
- "data": {
- "text/html": [
- "\n",
- "<p style=\"font-size: smaller\">Data Sources: \n",
- " <a href=\"https://github.com/pcm-dpc/COVID-19\">Italian Civil Protection</a>, <a href=\"https://wikidata.org\">Wikidata</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>"
- ],
- "text/plain": [
- "<IPython.core.display.HTML object>"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
+ "outputs": [],
"source": [
"# make the charts\n",
"base = alt.Chart(df_national).mark_bar(size=10).encode(alt.X('date'))\n",
"daily = base.encode(alt.Y('New cases per day'))\n",
- "total = base.mark_line(color='orange', size=5).encode(alt.Y('positive', title=\"Cases (orange)\"))\n",
+ "total = base.mark_line(color='orange', size=2).encode(alt.Y('positive', title=\"Cases (orange)\"))\n",
"tests = base.encode(alt.Y('tested', title=\"Tests (blue)\"))\n",
"totals = alt.layer(tests, total)\n",
"chart = alt.hconcat(totals, daily, \n",
@@ -202,7 +125,7 @@
},
{
"cell_type": "code",
- "execution_count": 9,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -211,7 +134,7 @@
},
{
"cell_type": "code",
- "execution_count": 10,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -229,86 +152,9 @@
},
{
"cell_type": "code",
- "execution_count": 11,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "data": {
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- "\n",
- "<div id=\"altair-viz-d2a0206789214fb4bb47cd20c49edc38\"></div>\n",
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- " const paths = {\n",
- " \"vega\": \"https://cdn.jsdelivr.net/npm//vega@5?noext\",\n",
- " \"vega-lib\": \"https://cdn.jsdelivr.net/npm//vega-lib?noext\",\n",
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- " \"vega-embed\": \"https://cdn.jsdelivr.net/npm//vega-embed@6?noext\",\n",
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- "\n",
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- "\n",
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- " throw err;\n",
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- "\n",
- " function displayChart(vegaEmbed) {\n",
- " vegaEmbed(outputDiv, spec, embedOpt)\n",
- " .catch(err => showError(`Javascript Error: ${err.message}<br>This usually means there's a typo in your chart specification. See the javascript console for the full traceback.`));\n",
- " }\n",
- "\n",
- " if(typeof define === \"function\" && define.amd) {\n",
- " requirejs.config({paths});\n",
- " require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
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- " displayChart(vegaEmbed);\n",
- " } else {\n",
- " loadScript(\"vega\")\n",
- " .then(() => loadScript(\"vega-lite\"))\n",
- " .then(() => loadScript(\"vega-embed\"))\n",
- " .catch(showError)\n",
- " .then(() => displayChart(vegaEmbed));\n",
- " }\n",
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- " <a href=\"https://github.com/pcm-dpc/COVID-19\">Italian Civil Protection</a>, <a href=\"https://wikidata.org\">Wikidata</a>\n",
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- "<p style=\"font-size: smaller\">Data Sources: \n",
- " <a href=\"https://github.com/pcm-dpc/COVID-19\">Italian Civil Protection</a>, <a href=\"https://wikidata.org\">Wikidata</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",
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"source": [
"# Total cases and deaths per 100k population\n",
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- "<p style=\"font-size: smaller\">Data Sources: \n",
- " <a href=\"https://github.com/pcm-dpc/COVID-19\">Italian Civil Protection</a>, <a href=\"https://wikidata.org\">Wikidata</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>"
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"base = alt.Chart(tdf_diff).encode(alt.X('date')).properties(\n",
@@ -557,69 +249,9 @@
},
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+ "outputs": [],
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"\n",
@@ -659,69 +291,9 @@
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\"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 2961.4827141763644, \"tested\": 1789662, \"New cases per day\": 1739.0, \"sinceDay0\": 62}, {\"level_0\": 64, \"index\": 64, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Italy\", \"country\": \"ITA\", \"date\": \"2020-04-28T17:00:00\", \"deceased_100k\": 45.27290939694264, \"deceased_daily\": \"\", \"deceased\": 27359, \"positive_100k\": 333.44484842395286, \"positive_daily\": \"\", \"positive\": 201505, \"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 3056.254820868192, \"tested\": 1846934, \"New cases per day\": 2091.0, \"sinceDay0\": 63}, {\"level_0\": 65, \"index\": 65, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Italy\", \"country\": \"ITA\", \"date\": \"2020-04-29T17:00:00\", \"deceased_100k\": 45.807400779493626, \"deceased_daily\": \"\", \"deceased\": 27682, \"positive_100k\": 336.8967029874246, \"positive_daily\": \"\", \"positive\": 203591, \"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 3161.8739585588482, \"tested\": 1910761, \"New cases per day\": 2086.0, \"sinceDay0\": 64}, {\"level_0\": 66, \"index\": 66, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Italy\", \"country\": \"ITA\", \"date\": \"2020-04-30T17:00:00\", \"deceased_100k\": 46.27901082292097, \"deceased_daily\": \"\", \"deceased\": 27967, \"positive_100k\": 339.99443632530523, \"positive_daily\": \"\", \"positive\": 205463, \"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 3275.1530362180133, \"tested\": 1979217, \"New cases per day\": 1872.0, \"sinceDay0\": 65}, {\"level_0\": 67, \"index\": 67, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Italy\", \"country\": \"ITA\", \"date\": \"2020-05-01T17:00:00\", \"deceased_100k\": 46.724144513033096, \"deceased_daily\": \"\", \"deceased\": 28236, \"positive_100k\": 343.2460634668306, \"positive_daily\": \"\", \"positive\": 207428, \"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 3397.9503628939997, \"tested\": 2053425, \"New cases per day\": 1965.0, \"sinceDay0\": 66}, {\"level_0\": 68, \"index\": 68, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Italy\", \"country\": \"ITA\", \"date\": \"2020-05-02T17:00:00\", \"deceased_100k\": 47.50850647999646, \"deceased_daily\": \"\", \"deceased\": 28710, \"positive_100k\": 346.39013042301286, \"positive_daily\": \"\", \"positive\": 209328, \"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 3489.6445935129327, \"tested\": 2108837, \"New cases per day\": 1900.0, \"sinceDay0\": 67}, {\"level_0\": 69, \"index\": 69, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Italy\", \"country\": \"ITA\", \"date\": \"2020-05-03T17:00:00\", \"deceased_100k\": 47.79643682229947, \"deceased_daily\": \"\", \"deceased\": 28884, \"positive_100k\": 348.6886088451903, \"positive_daily\": \"\", \"positive\": 210717, \"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 3564.0017770266436, \"tested\": 2153772, \"New cases per day\": 1389.0, \"sinceDay0\": 68}, {\"level_0\": 70, \"index\": 70, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Italy\", \"country\": \"ITA\", \"date\": \"2020-05-04T17:00:00\", \"deceased_100k\": 48.1191173783287, \"deceased_daily\": \"\", \"deceased\": 29079, \"positive_100k\": 350.709085557558, \"positive_daily\": \"\", \"positive\": 211938, \"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 3626.2725052519568, \"tested\": 2191403, \"New cases per day\": 1221.0, \"sinceDay0\": 69}, {\"level_0\": 71, \"index\": 71, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Italy\", \"country\": \"ITA\", \"date\": \"2020-05-05T17:00:00\", \"deceased_100k\": 48.509643589728185, \"deceased_daily\": \"\", \"deceased\": 29315, \"positive_100k\": 352.4879655459243, \"positive_daily\": \"\", \"positive\": 213013, \"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 3717.7201748306416, \"tested\": 2246666, \"New cases per day\": 1075.0, \"sinceDay0\": 70}, {\"level_0\": 72, \"index\": 72, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Italy\", \"country\": \"ITA\", \"date\": \"2020-05-06T17:00:00\", \"deceased_100k\": 49.12025448806043, \"deceased_daily\": \"\", \"deceased\": 29684, \"positive_100k\": 354.8774564326228, \"positive_daily\": \"\", \"positive\": 214457, \"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 3824.060793149138, \"tested\": 2310929, \"New cases per day\": 1444.0, \"sinceDay0\": 71}, {\"level_0\": 73, \"index\": 73, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Italy\", \"country\": \"ITA\", \"date\": \"2020-05-07T17:00:00\", \"deceased_100k\": 49.57366203858356, \"deceased_daily\": \"\", \"deceased\": 29958, \"positive_100k\": 357.1957921197867, \"positive_daily\": \"\", \"positive\": 215858, \"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 3940.488902080732, \"tested\": 2381288, \"New cases per day\": 1401.0, \"sinceDay0\": 72}, {\"level_0\": 74, \"index\": 74, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Italy\", \"country\": \"ITA\", \"date\": \"2020-05-08T17:00:00\", \"deceased_100k\": 49.97577165455846, \"deceased_daily\": \"\", \"deceased\": 30201, \"positive_100k\": 359.39167467286774, \"positive_daily\": \"\", \"positive\": 217185, \"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 4046.021991623114, \"tested\": 2445063, \"New cases per day\": 1327.0, \"sinceDay0\": 73}, {\"level_0\": 75, \"index\": 75, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Italy\", \"country\": \"ITA\", \"date\": \"2020-05-09T17:00:00\", \"deceased_100k\": 50.296797438505486, \"deceased_daily\": \"\", \"deceased\": 30395, \"positive_100k\": 361.1837928378916, \"positive_daily\": \"\", \"positive\": 218268, \"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 4160.484231321053, \"tested\": 2514234, \"New cases per day\": 1083.0, \"sinceDay0\": 74}, {\"level_0\": 76, \"index\": 76, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Italy\", \"country\": \"ITA\", \"date\": \"2020-05-10T17:00:00\", \"deceased_100k\": 50.56983483206868, \"deceased_daily\": \"\", \"deceased\": 30560, \"positive_100k\": 362.51092004781697, \"positive_daily\": \"\", \"positive\": 219070, \"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 4245.999542985046, \"tested\": 2565912, \"New cases per day\": 802.0, \"sinceDay0\": 75}, {\"level_0\": 77, \"index\": 77, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Italy\", \"country\": \"ITA\", \"date\": \"2020-05-11T17:00:00\", \"deceased_100k\": 50.866039034782695, \"deceased_daily\": \"\", \"deceased\": 30739, \"positive_100k\": 363.7420704769747, \"positive_daily\": \"\", \"positive\": 219814, \"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 4313.414957613923, \"tested\": 2606652, \"New cases per day\": 744.0, \"sinceDay0\": 76}, {\"level_0\": 78, \"index\": 78, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Italy\", \"country\": \"ITA\", \"date\": \"2020-05-12T17:00:00\", \"deceased_100k\": 51.1506598329213, \"deceased_daily\": \"\", \"deceased\": 30911, \"positive_100k\": 366.06206093622075, \"positive_daily\": \"\", \"positive\": 221216, \"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 4424.289651437651, \"tested\": 2673655, \"New cases per day\": 1402.0, \"sinceDay0\": 77}, {\"level_0\": 79, \"index\": 79, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Italy\", \"country\": \"ITA\", \"date\": \"2020-05-13T17:00:00\", \"deceased_100k\": 51.47334038895053, \"deceased_daily\": \"\", \"deceased\": 31106, \"positive_100k\": 367.5314985452154, \"positive_daily\": \"\", \"positive\": 222104, \"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 4526.840841687906, \"tested\": 2735628, \"New cases per day\": 888.0, \"sinceDay0\": 78}, {\"level_0\": 80, \"index\": 80, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Italy\", \"country\": \"ITA\", \"date\": \"2020-05-14T17:00:00\", \"deceased_100k\": 51.90689067448726, \"deceased_daily\": \"\", \"deceased\": 31368, \"positive_100k\": 369.17303245075897, \"positive_daily\": \"\", \"positive\": 223096, \"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 4645.779239868199, \"tested\": 2807504, \"New cases per day\": 992.0, \"sinceDay0\": 79}, {\"level_0\": 81, \"index\": 81, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Italy\", \"country\": \"ITA\", \"date\": \"2020-05-15T17:00:00\", \"deceased_100k\": 52.30734551837994, \"deceased_daily\": \"\", \"deceased\": 31610, \"positive_100k\": 370.47864762361576, \"positive_daily\": \"\", \"positive\": 223885, \"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 4758.594981344348, \"tested\": 2875680, \"New cases per day\": 789.0, \"sinceDay0\": 80}, {\"level_0\": 82, \"index\": 82, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Italy\", \"country\": \"ITA\", \"date\": \"2020-05-16T17:00:00\", \"deceased_100k\": 52.56052564695672, \"deceased_daily\": \"\", \"deceased\": 31763, \"positive_100k\": 371.9265731955418, \"positive_daily\": \"\", \"positive\": 224760, \"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 4873.070459218944, \"tested\": 2944859, \"New cases per day\": 875.0, \"sinceDay0\": 81}, {\"level_0\": 83, \"index\": 83, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Italy\", \"country\": \"ITA\", \"date\": \"2020-05-17T17:00:00\", \"deceased_100k\": 52.8004675988759, \"deceased_daily\": \"\", \"deceased\": 31908, \"positive_100k\": 373.0435443510276, \"positive_daily\": \"\", \"positive\": 225435, \"region_iso\": \"\", \"region_label\": \"\", \"tested_100k\": 4972.523916131319, \"tested\": 3004960, \"New cases per day\": 675.0, \"sinceDay0\": 82}]}}, {\"mode\": \"vega-lite\"});\n",
- "</script>"
- ],
- "text/plain": [
- "alt.LayerChart(...)"
- ]
- },
- "execution_count": 16,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "outputs": [],
"source": [
"since_10th_death = helper.make_since_df(df_regions, start_case=10, column='deceased', region_column='region_label')\n",
"\n",
diff --git a/notebooks/covid-19-us-nyt.ipynb b/notebooks/covid-19-us-nyt.ipynb
index d5f45721879b5cf9ce571de23abf9a38e363672f..ff37ece54901b14cefe5b367dbe3952489551c90 100644
--- a/notebooks/covid-19-us-nyt.ipynb
+++ b/notebooks/covid-19-us-nyt.ipynb
@@ -200,7 +200,7 @@
" pos_day=(12, 20000), \n",
" pos_3days=(40,20000),\n",
" pos_week=(44,100),\n",
- " max_days=45, \n",
+ " max_days=150, \n",
" max_case=50000,\n",
" start_case=10\n",
")\n",
diff --git a/notebooks/covidtracking.ipynb b/notebooks/covidtracking.ipynb
index 7dbee2a547976e96aaa7b3886c7f7410037afacd..48108754cda7718a1145a680b235f34e76410557 100644
--- a/notebooks/covidtracking.ipynb
+++ b/notebooks/covidtracking.ipynb
@@ -112,14 +112,16 @@
" columns =['labelX', 'labelY','labelText']\n",
")\n",
"\n",
+ "startCase = 1000\n",
+ "\n",
"# make dataframe of states with points >=10 deceaseds\n",
- "deceased10_df = data_df.loc[data_df['deceased']>=10]\n",
+ "deceased10_df = data_df.loc[data_df['deceased']>=startCase]\n",
"\n",
"# group deceased10 dataframe by state and then increasing order of date\n",
"deceased10_df = deceased10_df.sort_values(by=['state','date'])\n",
"\n",
"# add US to that dataframe\n",
- "nationdeceased10_df = nation_df.loc[nation_df['deceased']>=10]\n",
+ "nationdeceased10_df = nation_df.loc[nation_df['deceased']>=startCase]\n",
"deceased10_df= pd.concat ([deceased10_df,nationdeceased10_df])\n",
"\n",
"deceased10_df = deceased10_df.reset_index()\n",
@@ -133,8 +135,8 @@
"deceased10_df = deceased10_df.astype({'sinceDay0': 'int32'})\n",
"\n",
"#Now create plotlines for each state since 10 deceaseds\n",
- "lineChart = alt.Chart(deceased10_df,title='US States: Cumulative Deaths Since 10th Death').mark_line(interpolate='basis').encode(\n",
- " alt.X('sinceDay0:Q', axis=alt.Axis(title='Days Since 10th Death')),\n",
+ "lineChart = alt.Chart(deceased10_df,title='US States: Cumulative Deaths Since 1000th Death').mark_line(interpolate='basis').encode(\n",
+ " alt.X('sinceDay0:Q', axis=alt.Axis(title='Days Since 1000th Death')),\n",
" alt.Y('deceased:Q',\n",
" axis = alt.Axis(title='Cumulative Deaths'),\n",
" scale=alt.Scale(type='log')),\n",
@@ -146,7 +148,6 @@
"\n",
"# Compute theoretical trends of doubling every day, 3 days, week\n",
"days = {'day':[1,2,3,4,5,10,15,20, max(deceased10_df.sinceDay0)+5]}\n",
- "startCase = 10\n",
"logRuleDay_df = pd.DataFrame(days, columns=['day'])\n",
"logRuleDay_df['case']= startCase * pow(2,logRuleDay_df['day'])\n",
"logRuleDay_df['doubling period']='every day'\n",
@@ -166,7 +167,7 @@
"ruleChart = alt.Chart(logRules_df).mark_line(opacity=0.2,clip=True).encode(\n",
" alt.X('day:Q',\n",
" scale=alt.Scale(domain=[1,max(deceased10_df.sinceDay0)+5])),\n",
- " alt.Y('case', scale=alt.Scale(type='log',domain=[10,15000]),\n",
+ " alt.Y('case', scale=alt.Scale(type='log',domain=[startCase,150000]),\n",
" ),\n",
" color = 'doubling period',\n",
" tooltip = ['doubling period']) \n",
@@ -231,11 +232,13 @@
" columns =['labelX', 'labelY','labelText']\n",
")\n",
"\n",
+ "startCase = 10000\n",
+ "\n",
"# make dataframe with only points >=100 positives\n",
- "positive100_df = data_df.loc[data_df['positive']>=100]\n",
+ "positive100_df = data_df.loc[data_df['positive']>=startCase]\n",
"\n",
"## add US to that dataframe\n",
- "nationpos100_df = nation_df.loc[nation_df['positive']>=100]\n",
+ "nationpos100_df = nation_df.loc[nation_df['positive']>=startCase]\n",
"positive100_df= pd.concat ([positive100_df,nationpos100_df])\n",
"\n",
"# group positive100 dataframe by state and then increasing order of date\n",
@@ -252,8 +255,8 @@
"\n",
" \n",
"# Now create plotlines for each state since 10 deaths\n",
- "lineChart = alt.Chart(positive100_df, title=\"US States: total cases since 100th case\").mark_line(interpolate='basis').encode(\n",
- " alt.X('sinceDay0:Q', axis=alt.Axis(title='Days since 100th case')),\n",
+ "lineChart = alt.Chart(positive100_df, title=\"US States: total cases since 10000th case\").mark_line(interpolate='basis').encode(\n",
+ " alt.X('sinceDay0:Q', axis=alt.Axis(title='Days since 10000th case')),\n",
" alt.Y('positive:Q',\n",
" axis = alt.Axis(title='Cumulative positive cases'),\n",
" scale=alt.Scale(type='log')),\n",
@@ -265,7 +268,7 @@
"# make dataframe with lines to indicate doubling every day, 3 days, week \n",
"\n",
"days = {'day':[1,2,3,4,5,10,15,20, max(positive100_df.sinceDay0)+5]}\n",
- "startCase = 100\n",
+ "\n",
"logRuleDay_df = pd.DataFrame (days, columns=['day'])\n",
"logRuleDay_df['case']= startCase * pow(2,logRuleDay_df['day'])\n",
"logRuleDay_df['doubling period']='every day'\n",
@@ -284,7 +287,7 @@
"ruleChart = alt.Chart(logRules_df).mark_line(opacity=0.2,clip=True).encode(\n",
" alt.X('day:Q',\n",
" scale=alt.Scale(domain=[1, max(positive100_df.sinceDay0)+5])),\n",
- " alt.Y('case', scale=alt.Scale(domain=[100,200000], type='log'),\n",
+ " alt.Y('case', scale=alt.Scale(domain=[startCase,2000000], type='log'),\n",
" ),\n",
" color = 'doubling period')\n",
"\n",
@@ -351,7 +354,7 @@
"source": [
"base = alt.Chart(\n",
" daily_totals\n",
- ").mark_bar(size=7).encode(\n",
+ ").mark_bar(size=2).encode(\n",
" alt.X('date', axis=alt.Axis(title='')\n",
" )\n",
").properties(\n",