From c485d6efbd843588b38e904c96704b3012514cc3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rok=20Ro=C5=A1kar?= <rok.roskar@sdsc.ethz.ch>
Date: Wed, 1 Apr 2020 11:16:48 +0000
Subject: [PATCH] fix: adjust filtering to reduce dataframe rows
---
notebooks/Dashboard.ipynb | 45 ++--
notebooks/openzh-covid-19-dashboard.ipynb | 240 ++--------------------
2 files changed, 29 insertions(+), 256 deletions(-)
diff --git a/notebooks/Dashboard.ipynb b/notebooks/Dashboard.ipynb
index 17e5794..7284949 100644
--- a/notebooks/Dashboard.ipynb
+++ b/notebooks/Dashboard.ipynb
@@ -161,7 +161,7 @@
"metadata": {},
"outputs": [],
"source": [
- "confirmed_rate_df = helper.growth_df(rates_frames_map, geodata_df, 'confirmed', countries_over_thresh, 2)\n",
+ "confirmed_rate_df = helper.growth_df(rates_frames_map, geodata_df, 'confirmed', countries_over_thresh, 10)\n",
"latest_confirmed_ser = confirmed_rate_df.set_index(\n",
" ['Country/Region', 'Geo Region', 'Date']).drop(\n",
" ['Longitude', 'Latitude'], axis=1).unstack().iloc[:,-1]\n",
@@ -174,16 +174,20 @@
"metadata": {},
"outputs": [],
"source": [
- "base = alt.Chart(confirmed_rate_df).properties(\n",
+ "confirmed_rate_df['Country'] = confirmed_rate_df['Country/Region']\n",
+ "base = alt.Chart(confirmed_rate_df.dropna()).properties(\n",
" width=300, height=200, title=\"Countries with 2 or more cases per 100k\")\n",
+ "confirmed_rate_df['Country'] = confirmed_rate_df['Country/Region']\n",
+ "selection = alt.selection_multi(fields=['Country'], bind='legend')\n",
+ "opacity=alt.condition(selection, alt.value(1), alt.value(0.2))\n",
"line = base.mark_line().encode(\n",
- " x='Date',\n",
- " y='Confirmed/100k',\n",
- " color='Country/Region',\n",
+ " alt.X('Date'),\n",
+ " alt.Y('Confirmed/100k', scale=alt.Scale(type='symlog')),\n",
+ " color=alt.Color('Country'),\n",
" facet=alt.Facet('Geo Region:N', columns=1, sort=alt.SortArray(sort_order), title='Geographic Region'),\n",
- " tooltip=[\"Country/Region:N\", \"Date:T\", \"Confirmed/100k:Q\"]\n",
- ")\n",
- "line\n",
+ " tooltip=[\"Country:N\", \"Date:T\", \"Confirmed/100k:Q\"],\n",
+ " opacity=opacity\n",
+ ").add_selection(selection)\n",
"display(line)\n",
"display(HTML('''\n",
"<p style=\"font-size: smaller\">Data Sources: \n",
@@ -241,6 +245,7 @@
" ).transform_filter(f\"datum['Country/Region'] == '{ref_country}'\")\n",
" ref += ref.mark_text().encode(text='Country/Region:N').transform_filter(f\"datum['Days'] == {label_loc}\")\n",
" charts = []\n",
+ " \n",
" # make our small multiples\n",
" for country in sort_order:\n",
" smallm = line.transform_filter(f\"datum['Country/Region'] == '{country}'\").properties(\n",
@@ -296,6 +301,7 @@
"metadata": {},
"outputs": [],
"source": [
+ "# Same with log scale\n",
"sort_order = growth_in_value_df.groupby(\n",
" 'Country/Region').max().sort_values(\n",
" 'Confirmed', ascending=False).index.tolist()\n",
@@ -303,7 +309,8 @@
" 'Confirmed/100k',\n",
" sort_order,\n",
" 'Italy',\n",
- " \"Growth of cases/100k from case 100, compared to Italy\")\n",
+ " \"Growth of cases/100k from case 100, compared to Italy (log scale)\",\n",
+ " 'log')\n",
"display(chart)\n",
"display(HTML('''\n",
"<p style=\"font-size: smaller\">Data Sources: \n",
@@ -318,25 +325,7 @@
"execution_count": null,
"metadata": {},
"outputs": [],
- "source": [
- "# Same with log scale\n",
- "sort_order = growth_in_value_df.groupby(\n",
- " 'Country/Region').max().sort_values(\n",
- " 'Confirmed', ascending=False).index.tolist()\n",
- "chart = facetted_growth_plot(increase_df, \n",
- " 'Confirmed/100k',\n",
- " sort_order,\n",
- " 'Italy',\n",
- " \"Growth of cases/100k from case 100, compared to Italy (log scale)\",\n",
- " 'log')\n",
- "display(chart)\n",
- "display(HTML('''\n",
- "<p style=\"font-size: smaller\">Data Sources: \n",
- " <a href=\"https://github.com/CSSEGISandData/COVID-19\">JHU CSSE</a>,\n",
- " <a href=\"https://data.worldbank.org/indicator/SP.POP.TOTL\">World Bank</a>,\n",
- " <a href=\"https://worldmap.harvard.edu/data/geonode:country_centroids_az8\">Harvard Worldmap</a>\n",
- "</p>'''))"
- ]
+ "source": []
}
],
"metadata": {
diff --git a/notebooks/openzh-covid-19-dashboard.ipynb b/notebooks/openzh-covid-19-dashboard.ipynb
index 6473278..ebe3192 100644
--- a/notebooks/openzh-covid-19-dashboard.ipynb
+++ b/notebooks/openzh-covid-19-dashboard.ipynb
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 1,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -12,7 +12,7 @@
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -25,7 +25,7 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": null,
"metadata": {
"tags": [
"parameters"
@@ -39,7 +39,7 @@
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -66,7 +66,7 @@
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -83,7 +83,7 @@
},
{
"cell_type": "code",
- "execution_count": 6,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -107,87 +107,9 @@
},
{
"cell_type": "code",
- "execution_count": 7,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "data": {
- "text/html": [
- "\n",
- "<div id=\"altair-viz-b21f47c914a34203a17075fd756ca6c4\"></div>\n",
- "<script type=\"text/javascript\">\n",
- " (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-b21f47c914a34203a17075fd756ca6c4\");\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: ${paths[lib]}`);\n",
- " document.getElementsByTagName(\"head\")[0].appendChild(s);\n",
- " });\n",
- " }\n",
- "\n",
- " function showError(err) {\n",
- " outputDiv.innerHTML = `<div class=\"error\" style=\"color:red;\">${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}, \"title\": {\"anchor\": \"middle\"}}, \"hconcat\": [{\"mark\": \"line\", \"encoding\": {\"color\": {\"type\": \"nominal\", \"field\": \"abbreviation_canton_and_fl\", \"legend\": {\"title\": \"Canton\"}}, \"opacity\": {\"condition\": {\"value\": 1, \"selection\": \"selector001\"}, \"value\": 0.2}, \"tooltip\": [{\"type\": \"nominal\", \"field\": \"abbreviation_canton_and_fl\", \"title\": \"Canton\"}, {\"type\": \"quantitative\", \"field\": \"ncumul_conf\", \"title\": \"Cases\"}, {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}], \"x\": {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"ncumul_conf\", \"scale\": {\"type\": \"linear\"}, \"title\": \"Cases\"}}, \"selection\": {\"selector001\": {\"type\": \"multi\", \"fields\": [\"abbreviation_canton_and_fl\"], \"bind\": \"legend\"}}}, {\"mark\": \"line\", \"encoding\": {\"color\": {\"type\": \"nominal\", \"field\": \"abbreviation_canton_and_fl\", \"legend\": {\"title\": \"Canton\"}}, \"opacity\": {\"condition\": {\"value\": 1, \"selection\": \"selector002\"}, \"value\": 0.2}, \"tooltip\": [{\"type\": \"nominal\", \"field\": \"abbreviation_canton_and_fl\", \"title\": \"Canton\"}, {\"type\": \"quantitative\", \"field\": \"ncumul_conf_100k\", \"title\": \"Cases/100k\"}, {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}], \"x\": {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"ncumul_conf_100k\", \"scale\": {\"type\": \"linear\"}, \"title\": \"Cases per 100k population\"}}, \"selection\": {\"selector002\": {\"type\": \"multi\", \"fields\": [\"abbreviation_canton_and_fl\"], \"bind\": \"legend\"}}}], \"data\": {\"name\": \"data-d7ac65f6514987c726d50fe8a6d87b2d\"}, \"title\": \"Covid-19 cases in Switzerland by Canton\", \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": {\"data-d7ac65f6514987c726d50fe8a6d87b2d\": [{\"date\": \"2020-02-28T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 1.0, \"ncumul_hosp\": 3.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://vs.ch/documents/529400/6767345/2020+02+28+-+Medienmitteilung+-+1.+Fall+Coronavirus+VS.pdf/37c4f942-c5d5-6ab5-64fd-83444de4eba5?t=1582923242156\", \"ncumul_ICF\": null, \"ninst_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 0.2907357067058191, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-02-29T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 1.0, \"ncumul_hosp\": 3.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.vs.ch/documents/6756452/7008787/Sit%20Epid%20-%20%C3%89tat%20Stand%2025.03.2020.pdf\", \"ncumul_ICF\": null, \"ninst_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 0.2907357067058191, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-01T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 2.0, \"ncumul_hosp\": 4.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.vs.ch/documents/6756452/7008787/Sit%20Epid%20-%20%C3%89tat%20Stand%2025.03.2020.pdf\", \"ncumul_ICF\": null, \"ninst_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 0.5814714134116382, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-02T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 3.0, \"ncumul_hosp\": 4.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.vs.ch/documents/6756452/7008787/Sit%20Epid%20-%20%C3%89tat%20Stand%2025.03.2020.pdf\", \"ncumul_ICF\": null, \"ninst_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 0.8722071201174572, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-03T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 3.0, \"ncumul_hosp\": 5.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://vs.ch/documents/529400/6789273/2020+03+03+-+Medienmitteilung+-+Best%C3%A4tigung+2.+Fall.pdf/9e063e45-70a1-682e-fc37-31d9685f71f1?t=1583233390225\", \"ncumul_ICF\": null, \"ninst_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 0.8722071201174572, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-04T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 4.0, \"ncumul_hosp\": 6.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.vs.ch/documents/6756452/7008787/Sit%20Epid%20-%20%C3%89tat%20Stand%2025.03.2020.pdf\", \"ncumul_ICF\": null, \"ninst_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 1.1629428268232764, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-05T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 5.0, \"ncumul_hosp\": 3.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.vs.ch/de/web/coronavirus/info?p_p_id=com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN&p_p_lifecycle=0&p_p_state=normal&p_p_mode=view&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN_delta=5&p_r_p_resetCur=false&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN_cur=5#collapse6812036\", \"ncumul_ICF\": null, \"ninst_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 1.4536785335290954, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-06T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 6.0, \"ncumul_hosp\": 3.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.vs.ch/de/web/coronavirus/info?p_p_id=com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN&p_p_lifecycle=0&p_p_state=normal&p_p_mode=view&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN_delta=5&p_r_p_resetCur=false&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN_cur=5#collapse6828733\", \"ncumul_ICF\": null, \"ninst_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 1.7444142402349143, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-08T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 7.0, \"ncumul_hosp\": 3.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.vs.ch/de/web/coronavirus/info?p_p_id=com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN&p_p_lifecycle=0&p_p_state=normal&p_p_mode=view&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN_delta=5&p_r_p_resetCur=false&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN_cur=4\", \"ncumul_ICF\": null, \"ninst_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 2.0351499469407335, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-09T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 12.0, \"ncumul_hosp\": 7.0, \"ncumul_ICU\": 1.0, \"ncumul_vent\": 1.0, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.vs.ch/de/web/coronavirus/info?p_p_id=com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN&p_p_lifecycle=0&p_p_state=normal&p_p_mode=view&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN_delta=5&p_r_p_resetCur=false&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN_cur=4#collapse6846567\", \"ncumul_ICF\": null, \"ninst_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 3.4888284804698286, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-10T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 17.0, \"ncumul_hosp\": 8.0, \"ncumul_ICU\": 1.0, \"ncumul_vent\": 1.0, \"ncumul_released\": 3.0, \"ncumul_deceased\": null, \"source\": \"https://www.vs.ch/de/web/coronavirus/info?p_p_id=com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN&p_p_lifecycle=0&p_p_state=normal&p_p_mode=view&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN_delta=5&p_r_p_resetCur=false&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN_cur=3#collapse6858802\", \"ncumul_ICF\": null, \"ninst_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 4.942507013998925, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-11T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 22.0, \"ncumul_hosp\": 11.0, \"ncumul_ICU\": 1.0, \"ncumul_vent\": 1.0, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": 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- "</script>"
- ],
- "text/plain": [
- "alt.LayerChart(...)"
- ]
- },
- "execution_count": 9,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "outputs": [],
"source": [
"since_100th_case = helper.make_since_df(df, 'ncumul_conf', 'abbreviation_canton_and_fl')\n",
"\n",
--
GitLab