diff --git a/.renku/workflow/a391937483df408c9a1507565b2e0574_papermill.cwl b/.renku/workflow/a391937483df408c9a1507565b2e0574_papermill.cwl
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index 0000000000000000000000000000000000000000..c1a222f308dfdb4e8d6b388a6cdc1ff99aebdbe0
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+++ b/.renku/workflow/a391937483df408c9a1507565b2e0574_papermill.cwl
@@ -0,0 +1,77 @@
+arguments: []
+baseCommand:
+- papermill
+class: CommandLineTool
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default:
+ class: File
+ path: ../../notebooks/openzh-covid-19-dashboard.ipynb
+ inputBinding:
+ position: 1
+ prefix: --report-mode
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: File
+ input_2:
+ default: runs/openzh-covid-19-dashboard.run.ipynb
+ inputBinding:
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+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_3:
+ default: data_path
+ inputBinding:
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+ prefix: -p
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_4:
+ default:
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+ listing: []
+ path: ../../data/openzh-covid-19
+ inputBinding:
+ position: 4
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: Directory
+ input_5:
+ default:
+ class: File
+ path: ../../data/ch-population-statistics/ch-population-by-age-canton.xls
+ streamable: false
+ type: File
+outputs:
+ output_0:
+ outputBinding:
+ glob: $(inputs.input_2)
+ streamable: false
+ type: File
+permanentFailCodes: []
+requirements:
+- class: InlineJavascriptRequirement
+- class: InitialWorkDirRequirement
+ listing:
+ - entry: '$({"listing": [], "class": "Directory"})'
+ entryname: runs
+ writable: true
+ - entry: $(inputs.input_1)
+ entryname: notebooks/openzh-covid-19-dashboard.ipynb
+ writable: false
+ - entry: $(inputs.input_4)
+ entryname: data/openzh-covid-19
+ writable: false
+ - entry: $(inputs.input_5)
+ entryname: data/ch-population-statistics/ch-population-by-age-canton.xls
+ writable: false
+successCodes: []
+temporaryFailCodes: []
diff --git a/notebooks/covidtracking-dashboard.ipynb b/notebooks/covidtracking-dashboard.ipynb
new file mode 100644
index 0000000000000000000000000000000000000000..f6c7a925927adf33f6eca172be63c95d4f9dd3a0
--- /dev/null
+++ b/notebooks/covidtracking-dashboard.ipynb
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+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 133,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import pandas as pd\n",
+ "import altair as alt"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 134,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "data_df = pd.read_json('../../data/covidtracking/states-daily.json')\n",
+ "data_df['date'] = pd.to_datetime(data_df['date'], format=\"%Y%m%d\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### Daily Cumulative Totals of Covid-19 Cases in U.S."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 135,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "daily_totals = data_df.groupby('date').sum()\n",
+ "daily_totals.reset_index(level=0, inplace=True)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 136,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div id=\"altair-viz-57fe38220740452bba1ebc966acdc68c\"></div>\n",
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+ " (function(spec, embedOpt){\n",
+ " const outputDiv = document.getElementById(\"altair-viz-57fe38220740452bba1ebc966acdc68c\");\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",
+ " \"vega-lite\": \"https://cdn.jsdelivr.net/npm//vega-lite@4.0.2?noext\",\n",
+ " \"vega-embed\": \"https://cdn.jsdelivr.net/npm//vega-embed@6?noext\",\n",
+ " };\n",
+ "\n",
+ " function loadScript(lib) {\n",
+ " return new Promise(function(resolve, reject) {\n",
+ " var s = document.createElement('script');\n",
+ " s.src = paths[lib];\n",
+ " s.async = true;\n",
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+ " document.getElementsByTagName(\"head\")[0].appendChild(s);\n",
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+ " }\n",
+ "\n",
+ " function showError(err) {\n",
+ " outputDiv.innerHTML = `<div class=\"error\" style=\"color:red;\">${err}</div>`;\n",
+ " throw err;\n",
+ " }\n",
+ "\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: ${err.message}`));\n",
+ " } else if (typeof vegaEmbed === \"function\") {\n",
+ " displayChart(vegaEmbed);\n",
+ " } else {\n",
+ " loadScript(\"vega\")\n",
+ " .then(() => loadScript(\"vega-lite\"))\n",
+ " .then(() => loadScript(\"vega-embed\"))\n",
+ " .catch(showError)\n",
+ " .then(() => displayChart(vegaEmbed));\n",
+ " }\n",
+ " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}}, \"data\": {\"name\": \"data-4d03f2a19b6ccedad6d0f5f4840015a0\"}, \"mark\": {\"type\": \"bar\", \"size\": 15}, \"encoding\": {\"x\": {\"type\": \"temporal\", \"axis\": {\"title\": \"Date\"}, \"field\": \"date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"positive\"}}, \"title\": \"Cumulative positive cases\", \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": {\"data-4d03f2a19b6ccedad6d0f5f4840015a0\": [{\"date\": \"2020-03-04T00:00:00\", \"positive\": 118.0, \"negative\": 748.0, \"pending\": 103.0, \"hospitalized\": 0.0, \"death\": 0.0, \"total\": 969}, {\"date\": \"2020-03-05T00:00:00\", \"positive\": 176.0, \"negative\": 953.0, \"pending\": 197.0, \"hospitalized\": 0.0, \"death\": 0.0, \"total\": 1326}, {\"date\": \"2020-03-06T00:00:00\", \"positive\": 223.0, \"negative\": 1571.0, \"pending\": 458.0, \"hospitalized\": 0.0, \"death\": 0.0, \"total\": 2252}, {\"date\": \"2020-03-07T00:00:00\", \"positive\": 341.0, \"negative\": 1809.0, \"pending\": 602.0, \"hospitalized\": 0.0, \"death\": 0.0, \"total\": 2752}, {\"date\": \"2020-03-08T00:00:00\", \"positive\": 417.0, \"negative\": 2335.0, \"pending\": 347.0, \"hospitalized\": 0.0, \"death\": 0.0, \"total\": 3099}, {\"date\": \"2020-03-09T00:00:00\", \"positive\": 584.0, \"negative\": 3367.0, \"pending\": 313.0, \"hospitalized\": 0.0, \"death\": 0.0, \"total\": 4264}, {\"date\": \"2020-03-10T00:00:00\", \"positive\": 778.0, \"negative\": 3807.0, \"pending\": 469.0, \"hospitalized\": 0.0, \"death\": 0.0, \"total\": 5054}, {\"date\": \"2020-03-11T00:00:00\", \"positive\": 1053.0, \"negative\": 5978.0, \"pending\": 563.0, \"hospitalized\": 0.0, \"death\": 27.0, \"total\": 7617}, {\"date\": \"2020-03-12T00:00:00\", \"positive\": 1315.0, \"negative\": 7949.0, \"pending\": 673.0, \"hospitalized\": 0.0, \"death\": 36.0, \"total\": 9966}, {\"date\": \"2020-03-13T00:00:00\", \"positive\": 1922.0, \"negative\": 13613.0, \"pending\": 1130.0, \"hospitalized\": 0.0, \"death\": 39.0, \"total\": 16665}, {\"date\": \"2020-03-14T00:00:00\", \"positive\": 2450.0, \"negative\": 17102.0, \"pending\": 1236.0, \"hospitalized\": 0.0, \"death\": 49.0, \"total\": 20789}, {\"date\": \"2020-03-15T00:00:00\", \"positive\": 3173.0, \"negative\": 22548.0, \"pending\": 2242.0, \"hospitalized\": 0.0, \"death\": 60.0, \"total\": 27963}, {\"date\": \"2020-03-16T00:00:00\", \"positive\": 4019.0, \"negative\": 36104.0, \"pending\": 1691.0, \"hospitalized\": 0.0, \"death\": 71.0, \"total\": 41714}, {\"date\": \"2020-03-17T00:00:00\", \"positive\": 5723.0, \"negative\": 47604.0, \"pending\": 1687.0, \"hospitalized\": 0.0, \"death\": 90.0, \"total\": 54957}, {\"date\": \"2020-03-18T00:00:00\", \"positive\": 7731.0, \"negative\": 66225.0, \"pending\": 2538.0, \"hospitalized\": 0.0, \"death\": 112.0, \"total\": 76495}, {\"date\": \"2020-03-19T00:00:00\", \"positive\": 11723.0, \"negative\": 89119.0, \"pending\": 3025.0, \"hospitalized\": 0.0, \"death\": 160.0, \"total\": 103867}, {\"date\": \"2020-03-20T00:00:00\", \"positive\": 17038.0, \"negative\": 118147.0, \"pending\": 3336.0, \"hospitalized\": 0.0, \"death\": 219.0, \"total\": 138521}, {\"date\": \"2020-03-21T00:00:00\", \"positive\": 23203.0, \"negative\": 155909.0, \"pending\": 3477.0, \"hospitalized\": 1964.0, \"death\": 272.0, \"total\": 182589}, {\"date\": \"2020-03-22T00:00:00\", \"positive\": 31888.0, \"negative\": 193463.0, \"pending\": 2842.0, \"hospitalized\": 2554.0, \"death\": 398.0, \"total\": 228216}, {\"date\": \"2020-03-23T00:00:00\", \"positive\": 42164.0, \"negative\": 237321.0, \"pending\": 14571.0, \"hospitalized\": 3325.0, \"death\": 471.0, \"total\": 294056}]}}, {\"mode\": \"vega-lite\"});\n",
+ "</script>"
+ ],
+ "text/plain": [
+ "alt.Chart(...)"
+ ]
+ },
+ "execution_count": 136,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "alt.Chart(daily_totals, title='Cumulative positive cases').mark_bar(size=15).encode(alt.X('date', axis=alt.Axis(title='Date')), alt.Y('positive'))"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Counts and rates by state"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 137,
+ "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()\n",
+ "\n",
+ "# \"Normalizing\" the totals\n",
+ "tdf_diff['total_10'] = tdf_diff['total']/10."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 138,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "tdf_diff_daily_cumulative=tdf_diff.groupby('date').sum()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 139,
+ "metadata": {},
+ "outputs": [
+ {
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\"2020-03-19T20:00:00Z\", \"positive_diff\": 313.0, \"negative_diff\": 806.0, \"death_diff\": 5.0, \"total_10\": 971.1, \"daily_positive\": 313.0}, {\"state\": \"CA\", \"date\": \"2020-03-18T00:00:00\", \"positive\": 611.0, \"negative\": 7981.0, \"pending\": null, \"hospitalized\": null, \"death\": 13.0, \"total\": 8592, \"dateChecked\": \"2020-03-18T20:00:00Z\", \"positive_diff\": 128.0, \"negative_diff\": 0.0, \"death_diff\": 2.0, \"total_10\": 859.2, \"daily_positive\": 128.0}, {\"state\": \"CA\", \"date\": \"2020-03-17T00:00:00\", \"positive\": 483.0, \"negative\": 7981.0, \"pending\": null, \"hospitalized\": null, \"death\": 11.0, \"total\": 8407, \"dateChecked\": \"2020-03-17T20:00:00Z\", \"positive_diff\": 148.0, \"negative_diff\": 0.0, \"death_diff\": 5.0, \"total_10\": 840.7, \"daily_positive\": 148.0}, {\"state\": \"CA\", \"date\": \"2020-03-16T00:00:00\", \"positive\": 335.0, \"negative\": 7981.0, \"pending\": null, \"hospitalized\": null, \"death\": 6.0, \"total\": 8316, \"dateChecked\": \"2020-03-16T20:00:00Z\", \"positive_diff\": 42.0, \"negative_diff\": 7065.0, \"death_diff\": 1.0, \"total_10\": 831.6, \"daily_positive\": 42.0}, {\"state\": \"CA\", \"date\": \"2020-03-15T00:00:00\", \"positive\": 293.0, \"negative\": 916.0, \"pending\": null, \"hospitalized\": null, \"death\": 5.0, \"total\": 1209, \"dateChecked\": \"2020-03-15T20:00:00Z\", \"positive_diff\": 41.0, \"negative_diff\": 0.0, \"death_diff\": 0.0, \"total_10\": 120.9, \"daily_positive\": 41.0}, {\"state\": \"CA\", \"date\": \"2020-03-14T00:00:00\", \"positive\": 252.0, \"negative\": 916.0, \"pending\": null, \"hospitalized\": null, \"death\": 5.0, \"total\": 1168, \"dateChecked\": \"2020-03-14T20:00:00Z\", \"positive_diff\": 50.0, \"negative_diff\": 0.0, \"death_diff\": 1.0, \"total_10\": 116.8, \"daily_positive\": 50.0}, {\"state\": \"CA\", \"date\": \"2020-03-13T00:00:00\", \"positive\": 202.0, \"negative\": 916.0, \"pending\": null, \"hospitalized\": null, \"death\": 4.0, \"total\": 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10356.0, \"negative\": 35081.0, \"pending\": null, \"hospitalized\": 1603.0, \"death\": 44.0, \"total\": 45437, \"dateChecked\": \"2020-03-21T20:00:00Z\", \"positive_diff\": 3254.0, \"negative_diff\": 9756.0, \"death_diff\": 9.0, \"total_10\": 4543.7, \"daily_positive\": 3254.0}, {\"state\": \"NY\", \"date\": \"2020-03-20T00:00:00\", \"positive\": 7102.0, \"negative\": 25325.0, \"pending\": null, \"hospitalized\": null, \"death\": 35.0, \"total\": 32427, \"dateChecked\": \"2020-03-20T20:00:00Z\", \"positive_diff\": 2950.0, \"negative_diff\": 7193.0, \"death_diff\": 23.0, \"total_10\": 3242.7, \"daily_positive\": 2950.0}, {\"state\": \"NY\", \"date\": \"2020-03-19T00:00:00\", \"positive\": 4152.0, \"negative\": 18132.0, \"pending\": null, \"hospitalized\": null, \"death\": 12.0, \"total\": 22284, \"dateChecked\": \"2020-03-19T20:00:00Z\", \"positive_diff\": 1770.0, \"negative_diff\": 5917.0, \"death_diff\": 0.0, \"total_10\": 2228.4, \"daily_positive\": 1770.0}, {\"state\": \"NY\", \"date\": \"2020-03-18T00:00:00\", \"positive\": 2382.0, \"negative\": 12215.0, \"pending\": null, \"hospitalized\": null, \"death\": 12.0, \"total\": 14597, \"dateChecked\": \"2020-03-18T20:00:00Z\", \"positive_diff\": 682.0, \"negative_diff\": 6709.0, \"death_diff\": 5.0, \"total_10\": 1459.7, \"daily_positive\": 682.0}, {\"state\": \"NY\", \"date\": \"2020-03-17T00:00:00\", \"positive\": 1700.0, \"negative\": 5506.0, \"pending\": null, \"hospitalized\": null, \"death\": 7.0, \"total\": 7206, \"dateChecked\": \"2020-03-17T20:00:00Z\", \"positive_diff\": 750.0, \"negative_diff\": 963.0, \"death_diff\": 0.0, \"total_10\": 720.6, \"daily_positive\": 750.0}, {\"state\": \"NY\", \"date\": \"2020-03-16T00:00:00\", \"positive\": 950.0, \"negative\": 4543.0, \"pending\": null, \"hospitalized\": null, \"death\": 7.0, \"total\": 5493, \"dateChecked\": \"2020-03-16T20:00:00Z\", \"positive_diff\": 221.0, \"negative_diff\": 0.0, \"death_diff\": 4.0, \"total_10\": 549.3, \"daily_positive\": 221.0}, {\"state\": \"NY\", \"date\": \"2020-03-15T00:00:00\", \"positive\": 729.0, \"negative\": 4543.0, \"pending\": null, \"hospitalized\": null, \"death\": 3.0, \"total\": 5272, \"dateChecked\": \"2020-03-15T20:00:00Z\", \"positive_diff\": 205.0, \"negative_diff\": 1764.0, \"death_diff\": null, \"total_10\": 527.2, \"daily_positive\": 205.0}, {\"state\": \"NY\", \"date\": \"2020-03-14T00:00:00\", \"positive\": 524.0, \"negative\": 2779.0, \"pending\": null, \"hospitalized\": null, \"death\": null, \"total\": 3303, \"dateChecked\": \"2020-03-14T20:00:00Z\", \"positive_diff\": 103.0, \"negative_diff\": 0.0, \"death_diff\": null, \"total_10\": 330.3, \"daily_positive\": 103.0}, {\"state\": \"NY\", \"date\": \"2020-03-13T00:00:00\", \"positive\": 421.0, \"negative\": 2779.0, \"pending\": null, \"hospitalized\": null, \"death\": null, \"total\": 3200, \"dateChecked\": \"2020-03-13T20:00:00Z\", \"positive_diff\": 205.0, \"negative_diff\": null, \"death_diff\": null, \"total_10\": 320.0, \"daily_positive\": 205.0}, {\"state\": \"NY\", \"date\": \"2020-03-12T00:00:00\", \"positive\": 216.0, \"negative\": null, \"pending\": null, \"hospitalized\": null, \"death\": null, \"total\": 216, \"dateChecked\": \"2020-03-12T20:00:00Z\", \"positive_diff\": 0.0, \"negative_diff\": null, \"death_diff\": null, \"total_10\": 21.6, \"daily_positive\": 0.0}, {\"state\": \"NY\", \"date\": \"2020-03-11T00:00:00\", \"positive\": 216.0, \"negative\": null, \"pending\": null, \"hospitalized\": null, \"death\": null, \"total\": 216, \"dateChecked\": \"2020-03-11T20:00:00Z\", \"positive_diff\": 43.0, \"negative_diff\": null, \"death_diff\": null, \"total_10\": 21.6, \"daily_positive\": 43.0}, {\"state\": \"NY\", \"date\": \"2020-03-10T00:00:00\", \"positive\": 173.0, \"negative\": 92.0, \"pending\": null, \"hospitalized\": null, \"death\": null, \"total\": 265, \"dateChecked\": \"2020-03-10T20:00:00Z\", \"positive_diff\": 31.0, \"negative_diff\": 0.0, \"death_diff\": null, \"total_10\": 26.5, \"daily_positive\": 31.0}, {\"state\": \"NY\", \"date\": \"2020-03-09T00:00:00\", \"positive\": 142.0, \"negative\": 92.0, \"pending\": null, \"hospitalized\": null, \"death\": null, \"total\": 234, \"dateChecked\": \"2020-03-09T20:00:00Z\", \"positive_diff\": 37.0, \"negative_diff\": 0.0, \"death_diff\": null, \"total_10\": 23.4, \"daily_positive\": 37.0}, {\"state\": \"NY\", \"date\": \"2020-03-08T00:00:00\", \"positive\": 105.0, \"negative\": 92.0, \"pending\": null, \"hospitalized\": null, \"death\": null, \"total\": 197, \"dateChecked\": \"2020-03-08T20:00:00Z\", \"positive_diff\": 29.0, \"negative_diff\": 0.0, \"death_diff\": null, \"total_10\": 19.7, \"daily_positive\": 29.0}, {\"state\": \"NY\", \"date\": \"2020-03-07T00:00:00\", \"positive\": 76.0, \"negative\": 92.0, \"pending\": 236.0, \"hospitalized\": null, \"death\": null, \"total\": 404, \"dateChecked\": \"2020-03-07T21:00:00Z\", \"positive_diff\": 43.0, \"negative_diff\": 0.0, \"death_diff\": null, \"total_10\": 40.4, \"daily_positive\": 43.0}, {\"state\": \"NY\", \"date\": \"2020-03-06T00:00:00\", \"positive\": 33.0, \"negative\": 92.0, \"pending\": 236.0, \"hospitalized\": null, \"death\": null, \"total\": 361, \"dateChecked\": \"2020-03-06T21:00:00Z\", \"positive_diff\": 11.0, \"negative_diff\": 16.0, \"death_diff\": null, \"total_10\": 36.1, \"daily_positive\": 11.0}, {\"state\": \"NY\", \"date\": \"2020-03-05T00:00:00\", \"positive\": 22.0, \"negative\": 76.0, \"pending\": 24.0, \"hospitalized\": null, \"death\": null, \"total\": 122, \"dateChecked\": \"2020-03-05T21:00:00Z\", \"positive_diff\": 16.0, \"negative_diff\": 28.0, \"death_diff\": null, \"total_10\": 12.2, \"daily_positive\": 16.0}, {\"state\": \"NY\", \"date\": \"2020-03-04T00:00:00\", \"positive\": 6.0, \"negative\": 48.0, \"pending\": 24.0, \"hospitalized\": null, \"death\": null, \"total\": 78, \"dateChecked\": \"2020-03-04T21:00:00Z\", \"positive_diff\": null, \"negative_diff\": null, \"death_diff\": null, \"total_10\": 7.8, \"daily_positive\": null}]}}, {\"mode\": \"vega-lite\"});\n",
+ "</script>"
+ ],
+ "text/plain": [
+ "alt.HConcatChart(...)"
+ ]
+ },
+ "execution_count": 139,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "# produce the charts for a few states\n",
+ "\n",
+ "charts=[]\n",
+ "for state in ['WA', 'CA', 'NY']: \n",
+ " state_df = tdf_diff[tdf_diff['state'] == state].copy()\n",
+ "\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",
+ "\n",
+ " totals = base.mark_line(color='red').encode(alt.Y('total_10', axis=alt.Axis(title='Total/10'))) \n",
+ " positives = totals.mark_line(color='orange').encode(alt.Y('positive', axis=alt.Axis(title='Positive')))\n",
+ " cumulative = totals + positives\n",
+ "\n",
+ " charts.append(alt.layer(dailies, cumulative).resolve_scale(y='independent'))\n",
+ "\n",
+ "\n",
+ "alt.hconcat(*charts)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### Total tests and Positives per 100k population"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 140,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Most recent test date 2020-03-23 00:00:00\n",
+ "56 states/territories have data on this date.\n"
+ ]
+ }
+ ],
+ "source": [
+ "pop_df = pd.read_csv('../../data/geodata/us_pop_fung_2019.csv').set_index('ST')\n",
+ "\n",
+ "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.\")\n",
+ "\n",
+ "most_recent_df['total/100k'] = (most_recent_df['total'] / pop_df['Population']) * 100000\n",
+ "most_recent_df['positive/100k'] = (most_recent_df['positive'] / pop_df['Population']) * 100000\n",
+ "most_recent_df = most_recent_df.reset_index()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 141,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "chart = alt.Chart(most_recent_df.sort_values('total/100k'), title=\"Cases per 100k\")\n",
+ "tests = chart.mark_bar().encode(alt.X('state', sort=None), alt.Y('total/100k'))\n",
+ "positives = chart.mark_point(color='orange', filled=True, size=100).encode(alt.X('state', sort=None), alt.Y('positive/100k'))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 142,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div id=\"altair-viz-6d18475c9c4546b48758753710a01e90\"></div>\n",
+ "<script type=\"text/javascript\">\n",
+ " (function(spec, embedOpt){\n",
+ " const outputDiv = document.getElementById(\"altair-viz-6d18475c9c4546b48758753710a01e90\");\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",
+ " \"vega-lite\": \"https://cdn.jsdelivr.net/npm//vega-lite@4.0.2?noext\",\n",
+ " \"vega-embed\": \"https://cdn.jsdelivr.net/npm//vega-embed@6?noext\",\n",
+ " };\n",
+ "\n",
+ " function loadScript(lib) {\n",
+ " return new Promise(function(resolve, reject) {\n",
+ " var s = document.createElement('script');\n",
+ " s.src = paths[lib];\n",
+ " s.async = true;\n",
+ " s.onload = () => resolve(paths[lib]);\n",
+ " s.onerror = () => reject(`Error loading script: ${paths[lib]}`);\n",
+ " document.getElementsByTagName(\"head\")[0].appendChild(s);\n",
+ " });\n",
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+ "\n",
+ " function showError(err) {\n",
+ " outputDiv.innerHTML = `<div class=\"error\" style=\"color:red;\">${err}</div>`;\n",
+ " throw err;\n",
+ " }\n",
+ "\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",
+ " } else if (typeof vegaEmbed === \"function\") {\n",
+ " 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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\"total/100k\": null, \"positive/100k\": null}]}}, {\"mode\": \"vega-lite\"});\n",
+ "</script>"
+ ],
+ "text/plain": [
+ "alt.LayerChart(...)"
+ ]
+ },
+ "execution_count": 142,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "tests + positives"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "metadata": {
+ "hide_input": true,
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.7.3"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
diff --git a/notebooks/openzh-covid-19-dashboard.ipynb b/notebooks/openzh-covid-19-dashboard.ipynb
new file mode 100644
index 0000000000000000000000000000000000000000..075f70fd49f599b55af6399b499a7c657e5b5ea2
--- /dev/null
+++ b/notebooks/openzh-covid-19-dashboard.ipynb
@@ -0,0 +1,403 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
+ "jupyter": {
+ "source_hidden": true
+ }
+ },
+ "outputs": [],
+ "source": [
+ "from pathlib import Path\n",
+ "\n",
+ "import altair as alt\n",
+ "import pandas as pd\n",
+ "from IPython.display import display, HTML"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "jupyter": {
+ "source_hidden": true
+ },
+ "tags": [
+ "parameters"
+ ]
+ },
+ "outputs": [],
+ "source": [
+ "save_figures = False\n",
+ "data_path = '../data/openzh-covid-19'"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {
+ "jupyter": {
+ "source_hidden": true
+ }
+ },
+ "outputs": [],
+ "source": [
+ "html_credits=HTML('''\n",
+ "<p style=\"font-size: smaller\">Data Sources: \n",
+ " <a href=\"https://github.com/openZH/covid_19\">OpenData Zuerich</a>,\n",
+ " <a href=\"https://www.bfs.admin.ch\">Federal Statistical Office</a>\n",
+ "<br>\n",
+ "Analysis:\n",
+ " <a href=\"https://renkulab.io/projects/covid-19/covid-19-public-data\">Covid-19 Public Data Collaboration Project</a>\n",
+ "</p>''')"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Summary data for Covid-19 cases in Switzerland\n",
+ "\n",
+ "The data for Switzerland comes from the effort initiated by [OpenData Zürich](https://github.com/openZH/covid_19) and collected during the [Case data #covid19mon hackathon challenge](https://db.schoolofdata.ch/project/73). \n",
+ "\n",
+ "Below we make plots of total cases, total cases per 10k population and total deaths. You can click on the canton abbreviations in the legend to highlight individual lines. "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "metadata": {
+ "jupyter": {
+ "source_hidden": true
+ }
+ },
+ "outputs": [],
+ "source": [
+ "# read in cantonal data and produce one dataframe\n",
+ "df_list = []\n",
+ "\n",
+ "for f in Path(data_path).glob('COVID19_Fallzahlen_Kanton_*total.csv'):\n",
+ " df_list.append(pd.read_csv(f))\n",
+ "\n",
+ "df = pd.concat(df_list)\n",
+ "\n",
+ "df['date'] = pd.to_datetime(df['date'], dayfirst=True)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "metadata": {
+ "jupyter": {
+ "source_hidden": true
+ }
+ },
+ "outputs": [],
+ "source": [
+ "# read in population data\n",
+ "df_pop = pd.read_excel(\n",
+ " Path(data_path) / '../ch-population-statistics/ch-population-by-age-canton.xls', \n",
+ " header=1, \n",
+ " skipfooter=5\n",
+ ")\n",
+ "df_pop = df_pop.where(\n",
+ " df_pop.Region.str.startswith('-')\n",
+ ").dropna().sort_values('Region').reset_index(drop=True)\n",
+ "\n",
+ "# match the cantons in the two datasets\n",
+ "df_pop['abbreviation_canton_and_fl'] = ['AG', 'AI', 'AR', 'BL', 'BS', 'BE', 'FR', 'GE', 'GL', 'GR', 'JU', 'LU', 'NE', 'NW', 'OW', 'SH', 'SZ', 'SO', 'SG', 'TG', 'TI', 'UR', 'VS', 'VD', 'ZG', 'ZH']\n",
+ "\n",
+ "pop_d = df_pop[['abbreviation_canton_and_fl', 'Total']].set_index('abbreviation_canton_and_fl').to_dict()\n",
+ "\n",
+ "\n",
+ "# calculate cases and deaths per 10k\n",
+ "\n",
+ "for x in ['conf', 'deceased']:\n",
+ " df[f'ncumul_{x}_10k'] = df.apply(\n",
+ " lambda row: row[f'ncumul_{x}']/pop_d['Total'][row.abbreviation_canton_and_fl]*10000, axis=1\n",
+ " )"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "metadata": {
+ "jupyter": {
+ "source_hidden": true
+ }
+ },
+ "outputs": [],
+ "source": [
+ "def generate_canton_chart(column, title, tooltip_title):\n",
+ " \"\"\"Produce a canton chart given a column name\"\"\"\n",
+ " selection = alt.selection_multi(fields=['abbreviation_canton_and_fl'], bind='legend')\n",
+ " chart = base.mark_line().encode(\n",
+ " alt.X('date', title='Date'), \n",
+ " alt.Y(column, \n",
+ " title=title, scale=alt.Scale(type='linear')),\n",
+ " color=alt.Color('abbreviation_canton_and_fl', legend=alt.Legend(title=\"Canton\")),\n",
+ " tooltip=[alt.Tooltip('abbreviation_canton_and_fl',title='Canton'),\n",
+ " alt.Tooltip(column,title=tooltip_title),\n",
+ " alt.Tooltip('date',title='Date')],\n",
+ " opacity=alt.condition(selection, alt.value(1), alt.value(0.2))\n",
+ " ).add_selection(\n",
+ " selection\n",
+ " )\n",
+ " return chart"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### Total cases"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 11,
+ "metadata": {
+ "jupyter": {
+ "source_hidden": true
+ }
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
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+ " const outputDiv = document.getElementById(\"altair-viz-5771810cda31478ba62c12691bb8a3cf\");\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",
+ " \"vega-lite\": \"https://cdn.jsdelivr.net/npm//vega-lite@4.0.2?noext\",\n",
+ " \"vega-embed\": \"https://cdn.jsdelivr.net/npm//vega-embed@6?noext\",\n",
+ " };\n",
+ "\n",
+ " function loadScript(lib) {\n",
+ " return new Promise(function(resolve, reject) {\n",
+ " var s = document.createElement('script');\n",
+ " s.src = paths[lib];\n",
+ " s.async = true;\n",
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+ " s.onerror = () => reject(`Error loading script: ${paths[lib]}`);\n",
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+ " outputDiv.innerHTML = `<div class=\"error\" style=\"color:red;\">${err}</div>`;\n",
+ " throw err;\n",
+ " }\n",
+ "\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",
+ " } else if (typeof vegaEmbed === \"function\") {\n",
+ " 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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\"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_10k\": 4.207608345914908, \"ncumul_deceased_10k\": null}, {\"date\": \"2020-03-22T00:00:00\", \"time\": \"13:30\", \"abbreviation_canton_and_fl\": \"GL\", \"ncumul_tested\": null, \"ncumul_conf\": 31.0, \"ncumul_hosp\": 3.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.gl.ch/verwaltung/finanzen-und-gesundheit/gesundheit/coronavirus.html/4817#Fallzahlen\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_10k\": 7.672697571962478, \"ncumul_deceased_10k\": null}, {\"date\": \"2020-03-20T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"SH\", \"ncumul_tested\": null, \"ncumul_conf\": 14.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 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+ "</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/openZH/covid_19\">OpenData Zuerich</a>,\n",
+ " <a href=\"https://www.bfs.admin.ch\">Federal Statistical Office</a>\n",
+ "<br>\n",
+ "Analysis:\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"
+ }
+ ],
+ "source": [
+ "base = alt.Chart(df.where(df.ncumul_conf>0).dropna(subset=['abbreviation_canton_and_fl']))\n",
+ "base.configure_header(titleFontSize=25)\n",
+ "base.configure_axis(labelFontSize=15, titleFontSize=15)\n",
+ "\n",
+ "cumul = generate_canton_chart('ncumul_conf', 'Cases', 'Cases')\n",
+ "cumul_10k = generate_canton_chart('ncumul_conf_10k', 'Cases per 10k population', 'Cases/10k')\n",
+ "\n",
+ "chart = alt.hconcat(\n",
+ " cumul, cumul_10k, title='Covid-19 cases in Switzerland by Canton'\n",
+ ").configure_title(\n",
+ " anchor='middle'\n",
+ ")\n",
+ "\n",
+ "display(chart)\n",
+ "if save_figures:\n",
+ " chart.save(str(Path(figures_path) / 'switzerland-cases-by-canton.html'))\n",
+ " \n",
+ "display(html_credits)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### Deaths"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 12,
+ "metadata": {
+ "jupyter": {
+ "source_hidden": true
+ }
+ },
+ "outputs": [
+ {
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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",
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+ " 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",
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+ " loadScript(\"vega\")\n",
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+ " .catch(showError)\n",
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\"https://gd.zh.ch/internet/gesundheitsdirektion/de/themen/coronavirus.html#title-content-internet-gesundheitsdirektion-de-themen-coronavirus-jcr-content-contentPar-textimage_7\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_10k\": 5.082289699717548, \"ncumul_deceased_10k\": 0.01972428085272011}, {\"date\": \"2020-03-23T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"ZH\", \"ncumul_tested\": null, \"ncumul_conf\": 1068.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 5.0, \"source\": \"https://gd.zh.ch/internet/gesundheitsdirektion/de/themen/coronavirus.html#title-content-internet-gesundheitsdirektion-de-themen-coronavirus-jcr-content-contentPar-textimage_7\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, 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\"https://www.vd.ch/toutes-les-actualites/hotline-et-informations-sur-le-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_10k\": 0.2878075943664792, \"ncumul_deceased_10k\": 0.01251337366810779}, {\"date\": \"2020-03-07T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VD\", \"ncumul_tested\": null, \"ncumul_conf\": 30.0, \"ncumul_hosp\": 16.0, \"ncumul_ICU\": 4.0, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 1.0, \"source\": \"https://www.vd.ch/toutes-les-actualites/hotline-et-informations-sur-le-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_10k\": 0.37540121004323374, \"ncumul_deceased_10k\": 0.01251337366810779}, {\"date\": \"2020-03-08T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VD\", 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\"ncumul_conf_10k\": 0.6381820570734973, \"ncumul_deceased_10k\": 0.01251337366810779}, {\"date\": \"2020-03-10T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VD\", \"ncumul_tested\": null, \"ncumul_conf\": 77.0, \"ncumul_hosp\": 36.0, \"ncumul_ICU\": 6.0, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 1.0, \"source\": \"https://www.vd.ch/toutes-les-actualites/hotline-et-informations-sur-le-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_10k\": 0.9635297724442998, \"ncumul_deceased_10k\": 0.01251337366810779}, {\"date\": \"2020-03-11T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VD\", \"ncumul_tested\": null, \"ncumul_conf\": 108.0, \"ncumul_hosp\": 38.0, \"ncumul_ICU\": 7.0, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 1.0, \"source\": \"https://www.vd.ch/toutes-les-actualites/hotline-et-informations-sur-le-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_10k\": 1.3514443561556415, \"ncumul_deceased_10k\": 0.01251337366810779}, {\"date\": \"2020-03-12T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VD\", \"ncumul_tested\": null, \"ncumul_conf\": 156.0, \"ncumul_hosp\": 43.0, \"ncumul_ICU\": 8.0, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 1.0, \"source\": \"https://www.vd.ch/toutes-les-actualites/hotline-et-informations-sur-le-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_10k\": 1.9520862922248154, \"ncumul_deceased_10k\": 0.01251337366810779}, {\"date\": \"2020-03-13T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VD\", 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\"ncumul_conf_10k\": 4.379680783837727, \"ncumul_deceased_10k\": 0.03754012100432337}, {\"date\": \"2020-03-15T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VD\", \"ncumul_tested\": null, \"ncumul_conf\": 406.0, \"ncumul_hosp\": 62.0, \"ncumul_ICU\": 19.0, \"ncumul_vent\": null, \"ncumul_released\": 5.0, \"ncumul_deceased\": 4.0, \"source\": \"https://www.vd.ch/toutes-les-actualites/hotline-et-informations-sur-le-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_10k\": 5.080429709251763, \"ncumul_deceased_10k\": 0.05005349467243116}, {\"date\": \"2020-03-16T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VD\", \"ncumul_tested\": null, \"ncumul_conf\": 508.0, \"ncumul_hosp\": 66.0, \"ncumul_ICU\": 27.0, \"ncumul_vent\": null, \"ncumul_released\": 5.0, \"ncumul_deceased\": 5.0, \"source\": \"https://www.vd.ch/toutes-les-actualites/hotline-et-informations-sur-le-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_10k\": 6.356793823398758, \"ncumul_deceased_10k\": 0.06256686834053896}, {\"date\": \"2020-03-17T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VD\", \"ncumul_tested\": null, \"ncumul_conf\": 608.0, \"ncumul_hosp\": 95.0, \"ncumul_ICU\": 35.0, \"ncumul_vent\": null, \"ncumul_released\": 9.0, \"ncumul_deceased\": 5.0, \"source\": \"https://www.vd.ch/toutes-les-actualites/hotline-et-informations-sur-le-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_10k\": 7.608131190209536, \"ncumul_deceased_10k\": 0.06256686834053896}, {\"date\": \"2020-03-18T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VD\", 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+ "</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/openZH/covid_19\">OpenData Zuerich</a>,\n",
+ " <a href=\"https://www.bfs.admin.ch\">Federal Statistical Office</a>\n",
+ "<br>\n",
+ "Analysis:\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"
+ }
+ ],
+ "source": [
+ "base = alt.Chart(df.where(df.ncumul_deceased>0).dropna(subset=['abbreviation_canton_and_fl']))\n",
+ "base.configure_header(titleFontSize=25)\n",
+ "base.configure_axis(labelFontSize=15, titleFontSize=15)\n",
+ "\n",
+ "deaths = generate_canton_chart('ncumul_deceased', 'Deaths', 'Deaths')\n",
+ "deaths_10k = generate_canton_chart('ncumul_deceased_10k', 'Deaths per 10k population', 'Deaths/10k')\n",
+ "\n",
+ "chart = alt.hconcat(\n",
+ " deaths, deaths_10k, title='Covid-19 deaths in Switzerland by Canton'\n",
+ ").configure_title(\n",
+ " anchor='middle'\n",
+ ")\n",
+ "display(chart) \n",
+ "display(html_credits)\n",
+ "\n",
+ "if save_figures:\n",
+ " chart.save(str(Path(figures_path) / 'switzerland-deaths-by-canton.html'))\n"
+ ]
+ }
+ ],
+ "metadata": {
+ "hide_input": true,
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.7.3"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
diff --git a/runs/openzh-covid-19-dashboard.run.ipynb b/runs/openzh-covid-19-dashboard.run.ipynb
new file mode 100644
index 0000000000000000000000000000000000000000..869abae72b8fef613fd7d12bc29029eec3cf7ef7
--- /dev/null
+++ b/runs/openzh-covid-19-dashboard.run.ipynb
@@ -0,0 +1,530 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {
+ "jupyter": {
+ "source_hidden": true
+ },
+ "papermill": {
+ "duration": 0.45671,
+ "end_time": "2020-03-24T14:57:54.300303",
+ "exception": false,
+ "start_time": "2020-03-24T14:57:53.843593",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "from pathlib import Path\n",
+ "\n",
+ "import altair as alt\n",
+ "import pandas as pd\n",
+ "from IPython.display import display, HTML"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {
+ "jupyter": {
+ "source_hidden": true
+ },
+ "papermill": {
+ "duration": 0.022277,
+ "end_time": "2020-03-24T14:57:54.341008",
+ "exception": false,
+ "start_time": "2020-03-24T14:57:54.318731",
+ "status": "completed"
+ },
+ "tags": [
+ "parameters"
+ ]
+ },
+ "outputs": [],
+ "source": [
+ "save_figures = False\n",
+ "data_path = '../data/openzh-covid-19'"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
+ "jupyter": {
+ "source_hidden": true
+ },
+ "papermill": {
+ "duration": 0.020688,
+ "end_time": "2020-03-24T14:57:54.371847",
+ "exception": false,
+ "start_time": "2020-03-24T14:57:54.351159",
+ "status": "completed"
+ },
+ "tags": [
+ "injected-parameters"
+ ]
+ },
+ "outputs": [],
+ "source": [
+ "# Parameters\n",
+ "data_path = \"data/openzh-covid-19/\"\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "jupyter": {
+ "source_hidden": true
+ },
+ "papermill": {
+ "duration": 0.021742,
+ "end_time": "2020-03-24T14:57:54.402304",
+ "exception": false,
+ "start_time": "2020-03-24T14:57:54.380562",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "html_credits=HTML('''\n",
+ "<p style=\"font-size: smaller\">Data Sources: \n",
+ " <a href=\"https://github.com/openZH/covid_19\">OpenData Zuerich</a>,\n",
+ " <a href=\"https://www.bfs.admin.ch\">Federal Statistical Office</a>\n",
+ "<br>\n",
+ "Analysis:\n",
+ " <a href=\"https://renkulab.io/projects/covid-19/covid-19-public-data\">Covid-19 Public Data Collaboration Project</a>\n",
+ "</p>''')"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "papermill": {
+ "duration": 0.007116,
+ "end_time": "2020-03-24T14:57:54.419890",
+ "exception": false,
+ "start_time": "2020-03-24T14:57:54.412774",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "source": [
+ "## Summary data for Covid-19 cases in Switzerland\n",
+ "\n",
+ "The data for Switzerland comes from the effort initiated by [OpenData Zürich](https://github.com/openZH/covid_19) and collected during the [Case data #covid19mon hackathon challenge](https://db.schoolofdata.ch/project/73). \n",
+ "\n",
+ "Below we make plots of total cases, total cases per 10k population and total deaths. You can click on the canton abbreviations in the legend to highlight individual lines. "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {
+ "jupyter": {
+ "source_hidden": true
+ },
+ "papermill": {
+ "duration": 0.139939,
+ "end_time": "2020-03-24T14:57:54.566467",
+ "exception": false,
+ "start_time": "2020-03-24T14:57:54.426528",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# read in cantonal data and produce one dataframe\n",
+ "df_list = []\n",
+ "\n",
+ "for f in Path(data_path).glob('COVID19_Fallzahlen_Kanton_*total.csv'):\n",
+ " df_list.append(pd.read_csv(f))\n",
+ "\n",
+ "df = pd.concat(df_list)\n",
+ "\n",
+ "df['date'] = pd.to_datetime(df['date'], dayfirst=True)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {
+ "jupyter": {
+ "source_hidden": true
+ },
+ "papermill": {
+ "duration": 24.837972,
+ "end_time": "2020-03-24T14:58:19.420495",
+ "exception": false,
+ "start_time": "2020-03-24T14:57:54.582523",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# read in population data\n",
+ "df_pop = pd.read_excel(\n",
+ " Path(data_path) / '../ch-population-statistics/ch-population-by-age-canton.xls', \n",
+ " header=1, \n",
+ " skipfooter=5\n",
+ ")\n",
+ "df_pop = df_pop.where(\n",
+ " df_pop.Region.str.startswith('-')\n",
+ ").dropna().sort_values('Region').reset_index(drop=True)\n",
+ "\n",
+ "# match the cantons in the two datasets\n",
+ "df_pop['abbreviation_canton_and_fl'] = ['AG', 'AI', 'AR', 'BL', 'BS', 'BE', 'FR', 'GE', 'GL', 'GR', 'JU', 'LU', 'NE', 'NW', 'OW', 'SH', 'SZ', 'SO', 'SG', 'TG', 'TI', 'UR', 'VS', 'VD', 'ZG', 'ZH']\n",
+ "\n",
+ "pop_d = df_pop[['abbreviation_canton_and_fl', 'Total']].set_index('abbreviation_canton_and_fl').to_dict()\n",
+ "\n",
+ "\n",
+ "# calculate cases and deaths per 10k\n",
+ "\n",
+ "for x in ['conf', 'deceased']:\n",
+ " df[f'ncumul_{x}_10k'] = df.apply(\n",
+ " lambda row: row[f'ncumul_{x}']/pop_d['Total'][row.abbreviation_canton_and_fl]*10000, axis=1\n",
+ " )"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {
+ "jupyter": {
+ "source_hidden": true
+ },
+ "papermill": {
+ "duration": 0.035005,
+ "end_time": "2020-03-24T14:58:19.473972",
+ "exception": false,
+ "start_time": "2020-03-24T14:58:19.438967",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "def generate_canton_chart(column, title, tooltip_title):\n",
+ " \"\"\"Produce a canton chart given a column name\"\"\"\n",
+ " selection = alt.selection_multi(fields=['abbreviation_canton_and_fl'], bind='legend')\n",
+ " chart = base.mark_line().encode(\n",
+ " alt.X('date', title='Date'), \n",
+ " alt.Y(column, \n",
+ " title=title, scale=alt.Scale(type='linear')),\n",
+ " color=alt.Color('abbreviation_canton_and_fl', legend=alt.Legend(title=\"Canton\")),\n",
+ " tooltip=[alt.Tooltip('abbreviation_canton_and_fl',title='Canton'),\n",
+ " alt.Tooltip(column,title=tooltip_title),\n",
+ " alt.Tooltip('date',title='Date')],\n",
+ " opacity=alt.condition(selection, alt.value(1), alt.value(0.2))\n",
+ " ).add_selection(\n",
+ " selection\n",
+ " )\n",
+ " return chart"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "papermill": {
+ "duration": 0.008325,
+ "end_time": "2020-03-24T14:58:19.494916",
+ "exception": false,
+ "start_time": "2020-03-24T14:58:19.486591",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "source": [
+ "### Total cases"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "metadata": {
+ "jupyter": {
+ "source_hidden": true
+ },
+ "papermill": {
+ "duration": 0.16326,
+ "end_time": "2020-03-24T14:58:19.665324",
+ "exception": false,
+ "start_time": "2020-03-24T14:58:19.502064",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [
+ {
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+ "</script>"
+ ],
+ "text/plain": [
+ "alt.HConcatChart(...)"
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+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<p style=\"font-size: smaller\">Data Sources: \n",
+ " <a href=\"https://github.com/openZH/covid_19\">OpenData Zuerich</a>,\n",
+ " <a href=\"https://www.bfs.admin.ch\">Federal Statistical Office</a>\n",
+ "<br>\n",
+ "Analysis:\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>"
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+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "base = alt.Chart(df.where(df.ncumul_conf>0).dropna(subset=['abbreviation_canton_and_fl']))\n",
+ "base.configure_header(titleFontSize=25)\n",
+ "base.configure_axis(labelFontSize=15, titleFontSize=15)\n",
+ "\n",
+ "cumul = generate_canton_chart('ncumul_conf', 'Cases', 'Cases')\n",
+ "cumul_10k = generate_canton_chart('ncumul_conf_10k', 'Cases per 10k population', 'Cases/10k')\n",
+ "\n",
+ "chart = alt.hconcat(\n",
+ " cumul, cumul_10k, title='Covid-19 cases in Switzerland by Canton'\n",
+ ").configure_title(\n",
+ " anchor='middle'\n",
+ ")\n",
+ "\n",
+ "display(chart)\n",
+ "if save_figures:\n",
+ " chart.save(str(Path(figures_path) / 'switzerland-cases-by-canton.html'))\n",
+ " \n",
+ "display(html_credits)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "papermill": {
+ "duration": 0.024948,
+ "end_time": "2020-03-24T14:58:19.707431",
+ "exception": false,
+ "start_time": "2020-03-24T14:58:19.682483",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "source": [
+ "### Deaths"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "metadata": {
+ "jupyter": {
+ "source_hidden": true
+ },
+ "papermill": {
+ "duration": 0.119744,
+ "end_time": "2020-03-24T14:58:19.839516",
+ "exception": false,
+ "start_time": "2020-03-24T14:58:19.719772",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
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+ " requirejs.config({paths});\n",
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+ " loadScript(\"vega\")\n",
+ " .then(() => loadScript(\"vega-lite\"))\n",
+ " .then(() => loadScript(\"vega-embed\"))\n",
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\"https://www.ar.ch/verwaltung/departement-gesundheit-und-soziales/amt-fuer-gesundheit/informationsseite-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_10k\": 18.58160421183029, \"ncumul_deceased_10k\": 0.6193868070610096}, {\"date\": \"2020-03-24T00:00:00\", \"time\": \"10:00\", \"abbreviation_canton_and_fl\": \"AR\", \"ncumul_tested\": null, \"ncumul_conf\": 33.0, \"ncumul_hosp\": 6.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 2.0, \"source\": \"https://www.ar.ch/verwaltung/departement-gesundheit-und-soziales/amt-fuer-gesundheit/informationsseite-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_10k\": 20.439764633013315, \"ncumul_deceased_10k\": 1.2387736141220191}]}}, {\"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/openZH/covid_19\">OpenData Zuerich</a>,\n",
+ " <a href=\"https://www.bfs.admin.ch\">Federal Statistical Office</a>\n",
+ "<br>\n",
+ "Analysis:\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"
+ }
+ ],
+ "source": [
+ "base = alt.Chart(df.where(df.ncumul_deceased>0).dropna(subset=['abbreviation_canton_and_fl']))\n",
+ "base.configure_header(titleFontSize=25)\n",
+ "base.configure_axis(labelFontSize=15, titleFontSize=15)\n",
+ "\n",
+ "deaths = generate_canton_chart('ncumul_deceased', 'Deaths', 'Deaths')\n",
+ "deaths_10k = generate_canton_chart('ncumul_deceased_10k', 'Deaths per 10k population', 'Deaths/10k')\n",
+ "\n",
+ "chart = alt.hconcat(\n",
+ " deaths, deaths_10k, title='Covid-19 deaths in Switzerland by Canton'\n",
+ ").configure_title(\n",
+ " anchor='middle'\n",
+ ")\n",
+ "display(chart) \n",
+ "display(html_credits)\n",
+ "\n",
+ "if save_figures:\n",
+ " chart.save(str(Path(figures_path) / 'switzerland-deaths-by-canton.html'))\n"
+ ]
+ }
+ ],
+ "metadata": {
+ "hide_input": true,
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.7.3"
+ },
+ "papermill": {
+ "duration": 27.263389,
+ "end_time": "2020-03-24T14:58:20.272460",
+ "environment_variables": {},
+ "exception": null,
+ "input_path": "notebooks/openzh-covid-19-dashboard.ipynb",
+ "output_path": "runs/openzh-covid-19-dashboard.run.ipynb",
+ "parameters": {
+ "data_path": "data/openzh-covid-19/"
+ },
+ "start_time": "2020-03-24T14:57:53.009071",
+ "version": "1.1.0"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
\ No newline at end of file