From 51cc937c0bf78e89852f73756215b0698cdfc430 Mon Sep 17 00:00:00 2001
From: Chandrasekhar Ramakrishnan <cramakri@ethz.ch>
Date: Sun, 15 Mar 2020 18:15:17 +0000
Subject: [PATCH] refactor: moved code into helper.py
---
notebooks/Dashboard.ipynb | 403 ++----------------
requirements.txt | 1 +
src/covid-19/covid_19_dashboard/.editorconfig | 21 +
.../.github/ISSUE_TEMPLATE.md | 15 +
src/covid-19/covid_19_dashboard/.gitignore | 105 +++++
src/covid-19/covid_19_dashboard/.travis.yml | 16 +
.../covid_19_dashboard/CONTRIBUTING.rst | 128 ++++++
src/covid-19/covid_19_dashboard/HISTORY.rst | 8 +
src/covid-19/covid_19_dashboard/LICENSE | 16 +
src/covid-19/covid_19_dashboard/MANIFEST.in | 10 +
src/covid-19/covid_19_dashboard/Makefile | 85 ++++
src/covid-19/covid_19_dashboard/README.rst | 37 ++
.../covid_19_dashboard/__init__.py | 7 +
.../covid_19_dashboard/helper.py | 130 ++++++
src/covid-19/covid_19_dashboard/docs/Makefile | 20 +
src/covid-19/covid_19_dashboard/docs/conf.py | 162 +++++++
.../covid_19_dashboard/docs/contributing.rst | 1 +
.../covid_19_dashboard/docs/history.rst | 1 +
.../covid_19_dashboard/docs/index.rst | 19 +
.../covid_19_dashboard/docs/installation.rst | 51 +++
src/covid-19/covid_19_dashboard/docs/make.bat | 36 ++
.../covid_19_dashboard/docs/readme.rst | 1 +
.../covid_19_dashboard/docs/usage.rst | 7 +
.../covid_19_dashboard/requirements_dev.txt | 10 +
src/covid-19/covid_19_dashboard/setup.cfg | 22 +
src/covid-19/covid_19_dashboard/setup.py | 48 +++
.../covid_19_dashboard/tests/__init__.py | 1 +
.../tests/test_covid_19_dashboard.py | 21 +
src/covid-19/covid_19_dashboard/tox.ini | 20 +
29 files changed, 1023 insertions(+), 379 deletions(-)
create mode 100644 src/covid-19/covid_19_dashboard/.editorconfig
create mode 100644 src/covid-19/covid_19_dashboard/.github/ISSUE_TEMPLATE.md
create mode 100644 src/covid-19/covid_19_dashboard/.gitignore
create mode 100644 src/covid-19/covid_19_dashboard/.travis.yml
create mode 100644 src/covid-19/covid_19_dashboard/CONTRIBUTING.rst
create mode 100644 src/covid-19/covid_19_dashboard/HISTORY.rst
create mode 100644 src/covid-19/covid_19_dashboard/LICENSE
create mode 100644 src/covid-19/covid_19_dashboard/MANIFEST.in
create mode 100644 src/covid-19/covid_19_dashboard/Makefile
create mode 100644 src/covid-19/covid_19_dashboard/README.rst
create mode 100644 src/covid-19/covid_19_dashboard/covid_19_dashboard/__init__.py
create mode 100644 src/covid-19/covid_19_dashboard/covid_19_dashboard/helper.py
create mode 100644 src/covid-19/covid_19_dashboard/docs/Makefile
create mode 100755 src/covid-19/covid_19_dashboard/docs/conf.py
create mode 100644 src/covid-19/covid_19_dashboard/docs/contributing.rst
create mode 100644 src/covid-19/covid_19_dashboard/docs/history.rst
create mode 100644 src/covid-19/covid_19_dashboard/docs/index.rst
create mode 100644 src/covid-19/covid_19_dashboard/docs/installation.rst
create mode 100644 src/covid-19/covid_19_dashboard/docs/make.bat
create mode 100644 src/covid-19/covid_19_dashboard/docs/readme.rst
create mode 100644 src/covid-19/covid_19_dashboard/docs/usage.rst
create mode 100644 src/covid-19/covid_19_dashboard/requirements_dev.txt
create mode 100644 src/covid-19/covid_19_dashboard/setup.cfg
create mode 100644 src/covid-19/covid_19_dashboard/setup.py
create mode 100644 src/covid-19/covid_19_dashboard/tests/__init__.py
create mode 100644 src/covid-19/covid_19_dashboard/tests/test_covid_19_dashboard.py
create mode 100644 src/covid-19/covid_19_dashboard/tox.ini
diff --git a/notebooks/Dashboard.ipynb b/notebooks/Dashboard.ipynb
index 6888426e..6fe07cb7 100644
--- a/notebooks/Dashboard.ipynb
+++ b/notebooks/Dashboard.ipynb
@@ -2,18 +2,19 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 1,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import pandas as pd\n",
"import os\n",
- "from IPython.display import display, HTML, Markdown"
+ "from IPython.display import display, HTML, Markdown\n",
+ "import covid_19_dashboard as helper"
]
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": null,
"metadata": {
"tags": [
"parameters"
@@ -30,7 +31,7 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -39,71 +40,16 @@
},
{
"cell_type": "code",
- "execution_count": 4,
- "metadata": {},
- "outputs": [],
- "source": [
- "def read_jhu_covid_df(name):\n",
- " filename = os.path.join(ts_folder, f\"time_series_19-covid-{name}.csv\")\n",
- " df = pd.read_csv(filename)\n",
- " df = df.set_index(['Province/State', 'Country/Region', 'Lat', 'Long'])\n",
- " df.columns = pd.to_datetime(df.columns)\n",
- " return df\n",
- "\n",
- "\n",
- "jhu_frames_map = {\n",
- " \"confirmed\": read_jhu_covid_df(\"Confirmed\"),\n",
- " \"deaths\": read_jhu_covid_df(\"Deaths\"),\n",
- " \"recovered\": read_jhu_covid_df(\"Recovered\")\n",
- "}"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 5,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
- "def read_rates_covid_df(name):\n",
- " filename = os.path.join(rates_folder, f\"ts_rates_19-covid-{name}.csv\")\n",
- " df = pd.read_csv(filename).drop(\"Unnamed: 0\", axis=1)\n",
- " df = df.set_index(['Country/Region'])\n",
- " df.columns = pd.to_datetime(df.columns)\n",
- " return df\n",
- "\n",
+ "jhu_frames_map = helper.read_jhu_frames_map(ts_folder)\n",
+ "rates_frames_map = helper.read_rates_frames_map(rates_folder)\n",
+ "geodata_df = helper.read_geodata(geodata_path)\n",
"\n",
- "rates_frames_map = {\n",
- " \"confirmed\": read_rates_covid_df(\"confirmed\"),\n",
- " \"deaths\": read_rates_covid_df(\"deaths\"),\n",
- " \"recovered\": read_rates_covid_df(\"recovered\")\n",
- "}"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 6,
- "metadata": {},
- "outputs": [],
- "source": [
- "geodata_df = pd.read_csv(geodata_path)\n",
- "geodata_df = geodata_df.drop('Unnamed: 0', axis=1)\n",
- "geodata_df = geodata_df.rename({'name_jhu':'Country/Region'}, axis=1)\n",
- "geodata_df = geodata_df.set_index('Country/Region')"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 7,
- "metadata": {},
- "outputs": [],
- "source": [
"# Identify countries with 100 or more cases\n",
- "def latest_jhu_country_ser(name):\n",
- " return jhu_frames_map[name].iloc[:,-1].groupby(level='Country/Region').sum()\n",
- "\n",
- "\n",
- "case_count_ser = latest_jhu_country_ser('confirmed')\n",
- "countries_over_thresh = case_count_ser[case_count_ser > 99].index"
+ "countries_over_thresh = helper.countries_with_number_of_cases(jhu_frames_map, 'confirmed', 100)"
]
},
{
@@ -119,22 +65,9 @@
},
{
"cell_type": "code",
- "execution_count": 8,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "data": {
- "text/html": [
- "<em>Data up to Mar 14 2020; countries with 100 or more confirmed cases.</em>"
- ],
- "text/plain": [
- "<IPython.core.display.HTML object>"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
+ "outputs": [],
"source": [
"data_ts = jhu_frames_map['confirmed'].iloc[:,-1].name.strftime(\"%b %d %Y\")\n",
"display(HTML(f\"<em>Data up to {data_ts}; countries with 100 or more confirmed cases.</em>\"))"
@@ -149,161 +82,29 @@
},
{
"cell_type": "code",
- "execution_count": 9,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
- "import altair as alt\n",
- "from vega_datasets import data"
+ "import altair as alt"
]
},
{
"cell_type": "code",
- "execution_count": 24,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
- "def latest_rates_ser(name):\n",
- " return rates_frames_map[name].iloc[:,-1]\n",
- "\n",
- "\n",
- "# Compile the basic df\n",
- "map_df = pd.concat([\n",
- " latest_rates_ser('confirmed'),\n",
- " latest_rates_ser('deaths'),\n",
- " latest_rates_ser('recovered')], axis=1)\n",
- "nominal_df = pd.concat([\n",
- " latest_jhu_country_ser('confirmed'),\n",
- " latest_jhu_country_ser('deaths'),\n",
- " latest_jhu_country_ser('recovered')], axis=1)\n",
- "map_df = pd.concat([map_df, nominal_df, geodata_df[['Longitude', 'Latitude']]], axis=1)\n",
- "# Restrict to countries with 100 or more cases\n",
- "map_df = map_df.loc[countries_over_thresh].dropna()\n",
- "map_df = map_df.reset_index()\n",
- "map_df.columns = ['Country/Region', \n",
- " 'Confirmed/100k', 'Deaths/100k', 'Recovered/100k', \n",
- " 'Confirmed', 'Deaths', 'Recovered',\n",
- " 'Long', 'Lat']"
+ "map_df = helper.compute_map_df(rates_frames_map, jhu_frames_map, geodata_df, countries_over_thresh)"
]
},
{
"cell_type": "code",
- "execution_count": 19,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
- "def map_of_variable(map_df, variable, title):\n",
- " # Data generators for the background\n",
- " sphere = alt.sphere()\n",
- " graticule = alt.graticule()\n",
- "\n",
- " # Source of land data\n",
- " source = alt.topo_feature(data.world_110m.url, 'countries')\n",
- "\n",
- " # Layering and configuring the components\n",
- " p = alt.layer(\n",
- " alt.Chart(sphere).mark_geoshape(fill='#cae6ef'),\n",
- " alt.Chart(graticule).mark_geoshape(stroke='white', strokeWidth=0.5),\n",
- " alt.Chart(source).mark_geoshape(fill='#dddddd', stroke='#aaaaaa'),\n",
- " alt.Chart(map_df).mark_circle(opacity=0.6).encode(\n",
- " longitude='Long:Q',\n",
- " latitude='Lat:Q',\n",
- " size=alt.Size(f'{variable}:Q', title=\"Cases\"),\n",
- " color=alt.value('steelblue'),\n",
- " tooltip=[\"Country/Region:N\", \n",
- " \"Confirmed:Q\", \"Deaths:Q\", \"Recovered:Q\",\n",
- " \"Confirmed/100k:Q\", \"Deaths/100k:Q\", \"Recovered/100k:Q\"]\n",
- " )\n",
- " ).project(\n",
- " 'naturalEarth1'\n",
- " ).properties(width=600, height=400, title=f\"{title} cases per 100k inhabitants\"\n",
- " ).configure_view(stroke=None)\n",
- " return p"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 20,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/html": [
- "\n",
- "<div id=\"altair-viz-c4db865973fa4ab1b0a16c6b2f5f366e\"></div>\n",
- "<script type=\"text/javascript\">\n",
- " (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-c4db865973fa4ab1b0a16c6b2f5f366e\");\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: ${err.message}`));\n",
- " } else if (typeof vegaEmbed === \"function\") {\n",
- " displayChart(vegaEmbed);\n",
- " } else {\n",
- " loadScript(\"vega\")\n",
- " .then(() => loadScript(\"vega-lite\"))\n",
- " .then(() => loadScript(\"vega-embed\"))\n",
- " .catch(showError)\n",
- " .then(() => displayChart(vegaEmbed));\n",
- " }\n",
- " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300, \"stroke\": null}}, \"layer\": [{\"data\": {\"sphere\": true}, \"mark\": {\"type\": \"geoshape\", \"fill\": \"#cae6ef\"}}, {\"data\": {\"graticule\": true}, \"mark\": {\"type\": \"geoshape\", \"stroke\": \"white\", \"strokeWidth\": 0.5}}, {\"data\": {\"url\": \"https://vega.github.io/vega-datasets/data/world-110m.json\", \"format\": {\"feature\": \"countries\", \"type\": \"topojson\"}}, \"mark\": {\"type\": \"geoshape\", \"fill\": \"#dddddd\", \"stroke\": \"#aaaaaa\"}}, {\"data\": {\"name\": \"data-78f0aee81c818a7c0bb35bad1a0ca406\"}, \"mark\": {\"type\": \"circle\", \"opacity\": 0.6}, \"encoding\": {\"color\": {\"value\": \"steelblue\"}, \"latitude\": {\"field\": \"Lat\", \"type\": \"quantitative\"}, \"longitude\": {\"field\": \"Long\", \"type\": \"quantitative\"}, \"size\": {\"type\": \"quantitative\", \"field\": \"Confirmed/100k\", \"title\": \"Cases\"}, \"tooltip\": [{\"type\": \"nominal\", \"field\": \"Country/Region\"}, {\"type\": \"quantitative\", \"field\": \"Confirmed\"}, {\"type\": \"quantitative\", \"field\": \"Deaths\"}, {\"type\": \"quantitative\", \"field\": \"Recovered\"}, {\"type\": \"quantitative\", \"field\": \"Confirmed/100k\"}, {\"type\": \"quantitative\", \"field\": \"Deaths/100k\"}, {\"type\": \"quantitative\", \"field\": \"Recovered/100k\"}]}}], \"height\": 400, \"projection\": {\"type\": \"naturalEarth1\"}, \"title\": \"Confirmed cases per 100k inhabitants\", \"width\": 600, \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": {\"data-78f0aee81c818a7c0bb35bad1a0ca406\": [{\"Country/Region\": \"Australia\", \"Confirmed/100k\": 1.000305333199906, \"Deaths/100k\": 0.012003663998398872, \"Recovered/100k\": 0.09202809065439137, \"Confirmed\": 250.0, \"Deaths\": 3.0, \"Recovered\": 23.0, \"Long\": 134.49100008, \"Lat\": -25.73288704, \"Region\": \"Oceania\"}, {\"Country/Region\": \"Austria\", \"Confirmed/100k\": 7.403608688423027, \"Deaths/100k\": 0.01130321937163821, \"Recovered/100k\": 0.06781931622982926, \"Confirmed\": 655.0, \"Deaths\": 1.0, \"Recovered\": 6.0, \"Long\": 14.1264761, \"Lat\": 47.58549439, \"Region\": \"Europe\"}, {\"Country/Region\": \"Bahrain\", \"Confirmed/100k\": 13.380577391029535, \"Deaths/100k\": 0.0, \"Recovered/100k\": 2.8035495485966644, \"Confirmed\": 210.0, \"Deaths\": 0.0, \"Recovered\": 44.0, \"Long\": 50.54196932, \"Lat\": 26.04205135, \"Region\": \"Asia\"}, {\"Country/Region\": \"Belgium\", \"Confirmed/100k\": 6.0321826135162215, \"Deaths/100k\": 0.035019928090079665, \"Recovered/100k\": 0.008754982022519914, \"Confirmed\": 689.0, \"Deaths\": 4.0, \"Recovered\": 1.0, \"Long\": 4.64065114, \"Lat\": 50.63981576, \"Region\": \"Europe\"}, {\"Country/Region\": \"Brazil\", \"Confirmed/100k\": 0.07208692453324421, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.0, \"Confirmed\": 151.0, \"Deaths\": 0.0, \"Recovered\": 0.0, \"Long\": -53.09783113, \"Lat\": -10.78777702, \"Region\": \"Americas\"}, {\"Country/Region\": \"Canada\", \"Confirmed/100k\": 0.53428524615007, \"Deaths/100k\": 0.002698410334091263, \"Recovered/100k\": 0.021587282672730104, \"Confirmed\": 198.0, \"Deaths\": 1.0, \"Recovered\": 8.0, \"Long\": -98.30777028, \"Lat\": 61.36206324, \"Region\": \"Americas\"}, {\"Country/Region\": \"China\", \"Confirmed/100k\": 5.814264071284455, \"Deaths/100k\": 0.2292619531423894, \"Recovered/100k\": 4.7144816296051655, \"Confirmed\": 80977.0, \"Deaths\": 3193.0, \"Recovered\": 65660.0, \"Long\": 103.81907349, \"Lat\": 36.56176546, \"Region\": \"Asia\"}, {\"Country/Region\": \"Czechia\", \"Confirmed/100k\": 1.7787071810361583, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.0, \"Confirmed\": 189.0, \"Deaths\": 0.0, \"Recovered\": 0.0, \"Long\": 15.31240163, \"Lat\": 49.73341233, \"Region\": \"Europe\"}, {\"Country/Region\": \"Denmark\", \"Confirmed/100k\": 14.420142938804432, \"Deaths/100k\": 0.01724897480718234, \"Recovered/100k\": 0.01724897480718234, \"Confirmed\": 836.0, \"Deaths\": 1.0, \"Recovered\": 1.0, \"Long\": 10.02800992, \"Lat\": 55.98125296, \"Region\": \"Europe\"}, {\"Country/Region\": \"Egypt\", \"Confirmed/100k\": 0.11074580236578434, \"Deaths/100k\": 0.002032033070931823, \"Recovered/100k\": 0.02743244645757961, \"Confirmed\": 109.0, \"Deaths\": 2.0, \"Recovered\": 27.0, \"Long\": 29.86190099, \"Lat\": 26.49593311, \"Region\": \"Africa\"}, {\"Country/Region\": \"Estonia\", \"Confirmed/100k\": 8.706290635665205, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.0, \"Confirmed\": 115.0, \"Deaths\": 0.0, \"Recovered\": 0.0, \"Long\": 25.54248537, \"Lat\": 58.67192972, \"Region\": \"Europe\"}, {\"Country/Region\": \"Finland\", \"Confirmed/100k\": 4.077527387392285, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.018122343943965717, \"Confirmed\": 225.0, \"Deaths\": 0.0, \"Recovered\": 1.0, \"Long\": 26.2746656, \"Lat\": 64.49884603, \"Region\": \"Europe\"}, {\"Country/Region\": \"France\", \"Confirmed/100k\": 6.687840449145809, \"Deaths/100k\": 0.13584675912327426, \"Recovered/100k\": 0.017913858345926282, \"Confirmed\": 4480.0, \"Deaths\": 91.0, \"Recovered\": 12.0, \"Long\": -2.76172945, \"Lat\": 42.17344011, \"Region\": \"Europe\"}, {\"Country/Region\": \"Germany\", \"Confirmed/100k\": 5.528897733624627, \"Deaths/100k\": 0.010852798168510723, \"Recovered/100k\": 0.055469857305721466, \"Confirmed\": 4585.0, \"Deaths\": 9.0, \"Recovered\": 46.0, \"Long\": 10.38578051, \"Lat\": 51.10698181, \"Region\": \"Europe\"}, {\"Country/Region\": \"Greece\", \"Confirmed/100k\": 2.1253454152384283, \"Deaths/100k\": 0.027965071253137214, \"Recovered/100k\": 0.07457352334169924, \"Confirmed\": 228.0, \"Deaths\": 3.0, \"Recovered\": 8.0, \"Long\": 22.95555794, \"Lat\": 39.07469623, \"Region\": \"Europe\"}, {\"Country/Region\": \"Iceland\", \"Confirmed/100k\": 44.1208912420031, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.28282622591027623, \"Confirmed\": 156.0, \"Deaths\": 0.0, \"Recovered\": 1.0, \"Long\": -18.57396167, \"Lat\": 64.99575386, \"Region\": \"Europe\"}, {\"Country/Region\": \"India\", \"Confirmed/100k\": 0.007540935480311991, \"Deaths/100k\": 0.00014786148000611743, \"Recovered/100k\": 0.00029572296001223485, \"Confirmed\": 102.0, \"Deaths\": 2.0, \"Recovered\": 4.0, \"Long\": 79.61197609999998, \"Lat\": 22.88578212, \"Region\": \"Asia\"}, {\"Country/Region\": \"Iran\", \"Confirmed/100k\": 15.561073521653087, \"Deaths/100k\": 0.7469413089582871, \"Recovered/100k\": 3.6173475175246668, \"Confirmed\": 12729.0, \"Deaths\": 611.0, \"Recovered\": 2959.0, \"Long\": 54.27407004, \"Lat\": 32.57503292, \"Region\": \"Asia\"}, {\"Country/Region\": \"Iraq\", \"Confirmed/100k\": 0.2862079014195912, \"Deaths/100k\": 0.026018900129053748, \"Recovered/100k\": 0.06764914033553975, \"Confirmed\": 110.0, \"Deaths\": 10.0, \"Recovered\": 26.0, \"Long\": 43.74353149, \"Lat\": 33.03970582, \"Region\": \"Asia\"}, {\"Country/Region\": \"Ireland\", \"Confirmed/100k\": 2.657872474042476, \"Deaths/100k\": 0.04120732517895311, \"Recovered/100k\": 0.0, \"Confirmed\": 129.0, \"Deaths\": 2.0, \"Recovered\": 0.0, \"Long\": -8.13793569, \"Lat\": 53.17544870000001, \"Region\": \"Europe\"}, {\"Country/Region\": \"Israel\", \"Confirmed/100k\": 2.1724937526734056, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.045025777257479915, \"Confirmed\": 193.0, \"Deaths\": 0.0, \"Recovered\": 4.0, \"Long\": 35.00444693, \"Lat\": 31.46110101, \"Region\": \"Asia\"}, {\"Country/Region\": \"Italy\", \"Confirmed/100k\": 35.0100129431308, \"Deaths/100k\": 2.3845265704519294, \"Recovered/100k\": 3.25328191360756, \"Confirmed\": 21157.0, \"Deaths\": 1441.0, \"Recovered\": 1966.0, \"Long\": 12.07001339, \"Lat\": 42.79662641, \"Region\": \"Europe\"}, {\"Country/Region\": \"Japan\", \"Confirmed/100k\": 0.6109266563976192, \"Deaths/100k\": 0.017387304580527327, \"Recovered/100k\": 0.09325917911373748, \"Confirmed\": 773.0, \"Deaths\": 22.0, \"Recovered\": 118.0, \"Long\": 138.03089558, \"Lat\": 37.59230135, \"Region\": \"Asia\"}, {\"Country/Region\": \"Korea, South\", \"Confirmed/100k\": 15.659842956913007, \"Deaths/100k\": 0.13943961079615835, \"Recovered/100k\": 0.9876972431394551, \"Confirmed\": 8086.0, \"Deaths\": 72.0, \"Recovered\": 510.0, \"Long\": 127.83916086, \"Lat\": 36.38523983, \"Region\": \"Asia\"}, {\"Country/Region\": \"Kuwait\", \"Confirmed/100k\": 2.513711206970521, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.1208515003351212, \"Confirmed\": 104.0, \"Deaths\": 0.0, \"Recovered\": 5.0, \"Long\": 47.58700459, \"Lat\": 29.33431262, \"Region\": \"Asia\"}, {\"Country/Region\": \"Malaysia\", \"Confirmed/100k\": 0.7548705404952363, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.11101037360224064, \"Confirmed\": 238.0, \"Deaths\": 0.0, \"Recovered\": 35.0, \"Long\": 109.69762284, \"Lat\": 3.78986846, \"Region\": \"Asia\"}, {\"Country/Region\": \"Netherlands\", \"Confirmed/100k\": 5.565544970444868, \"Deaths/100k\": 0.06964185573027988, \"Recovered/100k\": 0.011606975955046644, \"Confirmed\": 959.0, \"Deaths\": 12.0, \"Recovered\": 2.0, \"Long\": 5.28144793, \"Lat\": 52.1007899, \"Region\": \"Europe\"}, {\"Country/Region\": \"Norway\", \"Confirmed/100k\": 20.510558609767997, \"Deaths/100k\": 0.056451078742480724, \"Recovered/100k\": 0.018817026247493568, \"Confirmed\": 1090.0, \"Deaths\": 3.0, \"Recovered\": 1.0, \"Long\": 15.34834656, \"Lat\": 68.75015572, \"Region\": \"Europe\"}, {\"Country/Region\": \"Philippines\", \"Confirmed/100k\": 0.10407688667814162, \"Deaths/100k\": 0.007501036877703902, \"Recovered/100k\": 0.0018752592194259754, \"Confirmed\": 111.0, \"Deaths\": 8.0, \"Recovered\": 2.0, \"Long\": 122.88393253, \"Lat\": 11.77536778, \"Region\": \"Asia\"}, {\"Country/Region\": \"Poland\", \"Confirmed/100k\": 0.2712057343529827, \"Deaths/100k\": 0.007899196146203378, \"Recovered/100k\": 0.0, \"Confirmed\": 103.0, \"Deaths\": 3.0, \"Recovered\": 0.0, \"Long\": 19.39012835, \"Lat\": 52.12759564, \"Region\": \"Europe\"}, {\"Country/Region\": \"Portugal\", 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24.12245841, \"Region\": \"Asia\"}, {\"Country/Region\": \"Singapore\", \"Confirmed/100k\": 3.7597478557022965, \"Deaths/100k\": 0.0, \"Recovered/100k\": 1.8621392681544395, \"Confirmed\": 212.0, \"Deaths\": 0.0, \"Recovered\": 105.0, \"Long\": 103.81725592, \"Lat\": 1.35876087, \"Region\": \"Asia\"}, {\"Country/Region\": \"Slovenia\", \"Confirmed/100k\": 8.755076493248433, \"Deaths/100k\": 0.04837058836048858, \"Recovered/100k\": 0.0, \"Confirmed\": 181.0, \"Deaths\": 1.0, \"Recovered\": 0.0, \"Long\": 14.80444238, \"Lat\": 46.11554772, \"Region\": \"Europe\"}, {\"Country/Region\": \"Spain\", \"Confirmed/100k\": 13.678268839257742, \"Deaths/100k\": 0.4173466474190673, \"Recovered/100k\": 1.1065036754649118, \"Confirmed\": 6391.0, \"Deaths\": 195.0, \"Recovered\": 517.0, \"Long\": -3.64755047, \"Lat\": 40.24448698, \"Region\": \"Europe\"}, {\"Country/Region\": \"Sweden\", \"Confirmed/100k\": 9.437135274607376, \"Deaths/100k\": 0.019640239905530446, \"Recovered/100k\": 0.009820119952765223, \"Confirmed\": 961.0, \"Deaths\": 2.0, \"Recovered\": 1.0, \"Long\": 16.74558049, \"Lat\": 62.77966519, \"Region\": \"Europe\"}, {\"Country/Region\": \"Switzerland\", \"Confirmed/100k\": 15.957178869407455, \"Deaths/100k\": 0.15264409514517804, \"Recovered/100k\": 0.04696741389082401, \"Confirmed\": 1359.0, \"Deaths\": 13.0, \"Recovered\": 4.0, \"Long\": 8.20867471, \"Lat\": 46.79785878, \"Region\": \"Europe\"}, {\"Country/Region\": \"US\", \"Confirmed/100k\": 0.8335181673369116, \"Deaths/100k\": 0.01650531024429528, \"Recovered/100k\": 0.0036678467209545055, \"Confirmed\": 2727.0, \"Deaths\": 54.0, \"Recovered\": 12.0, \"Long\": -112.4616737, \"Lat\": 45.6795472, \"Region\": \"Americas\"}, {\"Country/Region\": \"United Kingdom\", \"Confirmed/100k\": 1.719081584498703, \"Deaths/100k\": 0.031584176093152026, \"Recovered/100k\": 0.028576159322375637, \"Confirmed\": 1143.0, \"Deaths\": 21.0, \"Recovered\": 19.0, \"Long\": -2.86563164, \"Lat\": 54.12387156, \"Region\": \"Europe\"}]}}, {\"mode\": \"vega-lite\"});\n",
- "</script>"
- ],
- "text/plain": [
- "alt.LayerChart(...)"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- },
- {
- "data": {
- "text/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>"
- ],
- "text/plain": [
- "<IPython.core.display.HTML object>"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
- "source": [
- "display(map_of_variable(map_df, 'Confirmed/100k', 'Confirmed'))\n",
+ "display(helper.map_of_variable(map_df, 'Confirmed/100k', 'Confirmed'))\n",
"display(HTML('''\n",
"<p style=\"font-size: smaller\">Data Sources: \n",
" <a href=\"https://github.com/CSSEGISandData/COVID-19\">JHU CSSE</a>,\n",
@@ -314,85 +115,9 @@
},
{
"cell_type": "code",
- "execution_count": 21,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "data": {
- "text/html": [
- "\n",
- "<div id=\"altair-viz-ac88b911e4bd44ccb5c59bbecb99bf89\"></div>\n",
- "<script type=\"text/javascript\">\n",
- " (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-ac88b911e4bd44ccb5c59bbecb99bf89\");\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",
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\"Deaths\": 0.0, \"Recovered\": 0.0, \"Long\": -53.09783113, \"Lat\": -10.78777702, \"Region\": \"Americas\"}, {\"Country/Region\": \"Canada\", \"Confirmed/100k\": 0.53428524615007, \"Deaths/100k\": 0.002698410334091263, \"Recovered/100k\": 0.021587282672730104, \"Confirmed\": 198.0, \"Deaths\": 1.0, \"Recovered\": 8.0, \"Long\": -98.30777028, \"Lat\": 61.36206324, \"Region\": \"Americas\"}, {\"Country/Region\": \"China\", \"Confirmed/100k\": 5.814264071284455, \"Deaths/100k\": 0.2292619531423894, \"Recovered/100k\": 4.7144816296051655, \"Confirmed\": 80977.0, \"Deaths\": 3193.0, \"Recovered\": 65660.0, \"Long\": 103.81907349, \"Lat\": 36.56176546, \"Region\": \"Asia\"}, {\"Country/Region\": \"Czechia\", \"Confirmed/100k\": 1.7787071810361583, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.0, \"Confirmed\": 189.0, \"Deaths\": 0.0, \"Recovered\": 0.0, \"Long\": 15.31240163, \"Lat\": 49.73341233, \"Region\": \"Europe\"}, {\"Country/Region\": \"Denmark\", \"Confirmed/100k\": 14.420142938804432, \"Deaths/100k\": 0.01724897480718234, \"Recovered/100k\": 0.01724897480718234, \"Confirmed\": 836.0, \"Deaths\": 1.0, \"Recovered\": 1.0, \"Long\": 10.02800992, \"Lat\": 55.98125296, \"Region\": \"Europe\"}, {\"Country/Region\": \"Egypt\", \"Confirmed/100k\": 0.11074580236578434, \"Deaths/100k\": 0.002032033070931823, \"Recovered/100k\": 0.02743244645757961, \"Confirmed\": 109.0, \"Deaths\": 2.0, \"Recovered\": 27.0, \"Long\": 29.86190099, \"Lat\": 26.49593311, \"Region\": \"Africa\"}, {\"Country/Region\": \"Estonia\", \"Confirmed/100k\": 8.706290635665205, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.0, \"Confirmed\": 115.0, \"Deaths\": 0.0, \"Recovered\": 0.0, \"Long\": 25.54248537, \"Lat\": 58.67192972, \"Region\": \"Europe\"}, {\"Country/Region\": \"Finland\", \"Confirmed/100k\": 4.077527387392285, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.018122343943965717, \"Confirmed\": 225.0, \"Deaths\": 0.0, \"Recovered\": 1.0, \"Long\": 26.2746656, \"Lat\": 64.49884603, \"Region\": \"Europe\"}, {\"Country/Region\": \"France\", \"Confirmed/100k\": 6.687840449145809, \"Deaths/100k\": 0.13584675912327426, \"Recovered/100k\": 0.017913858345926282, \"Confirmed\": 4480.0, \"Deaths\": 91.0, \"Recovered\": 12.0, \"Long\": -2.76172945, \"Lat\": 42.17344011, \"Region\": \"Europe\"}, {\"Country/Region\": \"Germany\", \"Confirmed/100k\": 5.528897733624627, \"Deaths/100k\": 0.010852798168510723, \"Recovered/100k\": 0.055469857305721466, \"Confirmed\": 4585.0, \"Deaths\": 9.0, \"Recovered\": 46.0, \"Long\": 10.38578051, \"Lat\": 51.10698181, \"Region\": \"Europe\"}, {\"Country/Region\": \"Greece\", \"Confirmed/100k\": 2.1253454152384283, \"Deaths/100k\": 0.027965071253137214, \"Recovered/100k\": 0.07457352334169924, \"Confirmed\": 228.0, \"Deaths\": 3.0, \"Recovered\": 8.0, \"Long\": 22.95555794, \"Lat\": 39.07469623, \"Region\": \"Europe\"}, {\"Country/Region\": \"Iceland\", \"Confirmed/100k\": 44.1208912420031, \"Deaths/100k\": 0.0, \"Recovered/100k\": 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5.565544970444868, \"Deaths/100k\": 0.06964185573027988, \"Recovered/100k\": 0.011606975955046644, \"Confirmed\": 959.0, \"Deaths\": 12.0, \"Recovered\": 2.0, \"Long\": 5.28144793, \"Lat\": 52.1007899, \"Region\": \"Europe\"}, {\"Country/Region\": \"Norway\", \"Confirmed/100k\": 20.510558609767997, \"Deaths/100k\": 0.056451078742480724, \"Recovered/100k\": 0.018817026247493568, \"Confirmed\": 1090.0, \"Deaths\": 3.0, \"Recovered\": 1.0, \"Long\": 15.34834656, \"Lat\": 68.75015572, \"Region\": \"Europe\"}, {\"Country/Region\": \"Philippines\", \"Confirmed/100k\": 0.10407688667814162, \"Deaths/100k\": 0.007501036877703902, \"Recovered/100k\": 0.0018752592194259754, \"Confirmed\": 111.0, \"Deaths\": 8.0, \"Recovered\": 2.0, \"Long\": 122.88393253, \"Lat\": 11.77536778, \"Region\": \"Asia\"}, {\"Country/Region\": \"Poland\", \"Confirmed/100k\": 0.2712057343529827, \"Deaths/100k\": 0.007899196146203378, \"Recovered/100k\": 0.0, \"Confirmed\": 103.0, \"Deaths\": 3.0, \"Recovered\": 0.0, 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\"Confirmed/100k\": 9.437135274607376, \"Deaths/100k\": 0.019640239905530446, \"Recovered/100k\": 0.009820119952765223, \"Confirmed\": 961.0, \"Deaths\": 2.0, \"Recovered\": 1.0, \"Long\": 16.74558049, \"Lat\": 62.77966519, \"Region\": \"Europe\"}, {\"Country/Region\": \"Switzerland\", \"Confirmed/100k\": 15.957178869407455, \"Deaths/100k\": 0.15264409514517804, \"Recovered/100k\": 0.04696741389082401, \"Confirmed\": 1359.0, \"Deaths\": 13.0, \"Recovered\": 4.0, \"Long\": 8.20867471, \"Lat\": 46.79785878, \"Region\": \"Europe\"}, {\"Country/Region\": \"US\", \"Confirmed/100k\": 0.8335181673369116, \"Deaths/100k\": 0.01650531024429528, \"Recovered/100k\": 0.0036678467209545055, \"Confirmed\": 2727.0, \"Deaths\": 54.0, \"Recovered\": 12.0, \"Long\": -112.4616737, \"Lat\": 45.6795472, \"Region\": \"Americas\"}, {\"Country/Region\": \"United Kingdom\", \"Confirmed/100k\": 1.719081584498703, \"Deaths/100k\": 0.031584176093152026, \"Recovered/100k\": 0.028576159322375637, \"Confirmed\": 1143.0, \"Deaths\": 21.0, \"Recovered\": 19.0, \"Long\": -2.86563164, \"Lat\": 54.12387156, \"Region\": \"Europe\"}]}}, {\"mode\": \"vega-lite\"});\n",
- "</script>"
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- "text/plain": [
- "alt.LayerChart(...)"
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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/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>"
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- "text/plain": [
- "<IPython.core.display.HTML object>"
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- "metadata": {},
- "output_type": "display_data"
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+ "outputs": [],
"source": [
"bars = alt.Chart(map_df).mark_bar().encode(\n",
" x='Confirmed/100k:Q',\n",
@@ -429,24 +154,11 @@
},
{
"cell_type": "code",
- "execution_count": 124,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
- "latest_confirmed_ser = rates_frames_map['confirmed'].iloc[:,-1]\n",
- "countries_over_1 = latest_confirmed_ser[latest_confirmed_ser >= 2].reset_index()['Country/Region']\n",
- "\n",
- "confirmed_rate_df = rates_frames_map['confirmed']\n",
- "confirmed_rate_df = confirmed_rate_df.loc[\n",
- " confirmed_rate_df.index.isin(countries_over_1) &\n",
- " confirmed_rate_df.index.isin(countries_over_thresh)]\n",
- "confirmed_rate_df = confirmed_rate_df.join(\n",
- " geodata_df[['Longitude', 'Latitude', 'region_un']]).set_index(\n",
- " ['Longitude', 'Latitude', 'region_un'], append=True)\n",
- "confirmed_rate_df = confirmed_rate_df.stack().reset_index()\n",
- "confirmed_rate_df = confirmed_rate_df.rename(\n",
- " {'region_un': 'Geo Region', 'level_4': 'Date', 0: 'Confirmed/100k'}, axis=1)\n",
- "\n",
+ "confirmed_rate_df = helper.growth_df(rates_frames_map, geodata_df, 'confirmed', countries_over_thresh)\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",
@@ -455,69 +167,9 @@
},
{
"cell_type": "code",
- "execution_count": 141,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
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- " \"vega-embed\": \"https://cdn.jsdelivr.net/npm//vega-embed@6?noext\",\n",
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- "\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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- " .catch(showError)\n",
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\"Geo Region\": \"Europe\", \"Date\": \"2020-03-06T00:00:00\", \"Confirmed/100k\": 0.6216770654401016}, {\"Country/Region\": \"Austria\", \"Longitude\": 14.1264761, \"Latitude\": 47.58549439, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-07T00:00:00\", \"Confirmed/100k\": 0.8929543303594186}, {\"Country/Region\": \"Austria\", \"Longitude\": 14.1264761, \"Latitude\": 47.58549439, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-08T00:00:00\", \"Confirmed/100k\": 1.1755348146503741}, {\"Country/Region\": \"Austria\", \"Longitude\": 14.1264761, \"Latitude\": 47.58549439, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-09T00:00:00\", \"Confirmed/100k\": 1.4807217376846056}, {\"Country/Region\": \"Austria\", \"Longitude\": 14.1264761, \"Latitude\": 47.58549439, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-10T00:00:00\", \"Confirmed/100k\": 2.057185925638154}, {\"Country/Region\": \"Austria\", \"Longitude\": 14.1264761, \"Latitude\": 47.58549439, \"Geo Region\": \"Europe\", \"Date\": 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\"Europe\", \"Date\": \"2020-02-16T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-17T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-18T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-19T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-20T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-21T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-22T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-23T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-24T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-25T00:00:00\", \"Confirmed/100k\": 0.011741853472706005}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-26T00:00:00\", \"Confirmed/100k\": 0.011741853472706005}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-27T00:00:00\", \"Confirmed/100k\": 0.09393482778164802}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-28T00:00:00\", \"Confirmed/100k\": 0.09393482778164802}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-29T00:00:00\", \"Confirmed/100k\": 0.21135336250870806}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-01T00:00:00\", \"Confirmed/100k\": 0.3170300437630621}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-02T00:00:00\", \"Confirmed/100k\": 0.4931578458536522}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-03T00:00:00\", \"Confirmed/100k\": 0.6575437944715362}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-04T00:00:00\", \"Confirmed/100k\": 1.0567668125435403}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-05T00:00:00\", \"Confirmed/100k\": 1.3385712958884843}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-06T00:00:00\", \"Confirmed/100k\": 2.5127566431590846}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-07T00:00:00\", \"Confirmed/100k\": 3.1468167306852086}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-08T00:00:00\", \"Confirmed/100k\": 3.957004620301923}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-09T00:00:00\", \"Confirmed/100k\": 4.391453198792045}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-10T00:00:00\", \"Confirmed/100k\": 5.7652500550986465}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-11T00:00:00\", \"Confirmed/100k\": 7.655688464204314}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-12T00:00:00\", \"Confirmed/100k\": 7.655688464204314}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-13T00:00:00\", \"Confirmed/100k\": 13.373971105412135}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-14T00:00:00\", \"Confirmed/100k\": 15.957178869407455}]}}, {\"mode\": \"vega-lite\"});\n",
- "</script>"
- ],
- "text/plain": [
- "alt.Chart(...)"
- ]
- },
- "execution_count": 141,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "outputs": [],
"source": [
"base = alt.Chart(confirmed_rate_df).properties(width=300, height=200, title=\"Countries with 2 or more cases per 100k\")\n",
"line = base.mark_line().encode(\n",
@@ -529,13 +181,6 @@
")\n",
"line"
]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": []
}
],
"metadata": {
diff --git a/requirements.txt b/requirements.txt
index bf54e26b..8e7719e0 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -15,6 +15,7 @@ Click==7.0
colorama==0.4.3
conda==4.7.12
conda-package-handling==1.6.0
+-e src/covid-19/covid_19_dashboard
cryptography==2.8
decorator==4.4.1
defusedxml==0.6.0
diff --git a/src/covid-19/covid_19_dashboard/.editorconfig b/src/covid-19/covid_19_dashboard/.editorconfig
new file mode 100644
index 00000000..d4a2c440
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/.editorconfig
@@ -0,0 +1,21 @@
+# http://editorconfig.org
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+insert_final_newline = true
+charset = utf-8
+end_of_line = lf
+
+[*.bat]
+indent_style = tab
+end_of_line = crlf
+
+[LICENSE]
+insert_final_newline = false
+
+[Makefile]
+indent_style = tab
diff --git a/src/covid-19/covid_19_dashboard/.github/ISSUE_TEMPLATE.md b/src/covid-19/covid_19_dashboard/.github/ISSUE_TEMPLATE.md
new file mode 100644
index 00000000..127e9a18
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/.github/ISSUE_TEMPLATE.md
@@ -0,0 +1,15 @@
+* COVID-19 Dashboard version:
+* Python version:
+* Operating System:
+
+### Description
+
+Describe what you were trying to get done.
+Tell us what happened, what went wrong, and what you expected to happen.
+
+### What I Did
+
+```
+Paste the command(s) you ran and the output.
+If there was a crash, please include the traceback here.
+```
diff --git a/src/covid-19/covid_19_dashboard/.gitignore b/src/covid-19/covid_19_dashboard/.gitignore
new file mode 100644
index 00000000..43091aa9
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/.gitignore
@@ -0,0 +1,105 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+# Usually these files are written by a python script from a template
+# before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# IDE settings
+.vscode/
\ No newline at end of file
diff --git a/src/covid-19/covid_19_dashboard/.travis.yml b/src/covid-19/covid_19_dashboard/.travis.yml
new file mode 100644
index 00000000..a51bcd5a
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/.travis.yml
@@ -0,0 +1,16 @@
+# Config file for automatic testing at travis-ci.com
+
+language: python
+python:
+ - 3.8
+ - 3.7
+ - 3.6
+ - 3.5
+
+# Command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
+install: pip install -U tox-travis
+
+# Command to run tests, e.g. python setup.py test
+script: tox
+
+
diff --git a/src/covid-19/covid_19_dashboard/CONTRIBUTING.rst b/src/covid-19/covid_19_dashboard/CONTRIBUTING.rst
new file mode 100644
index 00000000..d6e62ccc
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/CONTRIBUTING.rst
@@ -0,0 +1,128 @@
+.. highlight:: shell
+
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/ciyer/covid_19_dashboard/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
+wanted" is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+COVID-19 Dashboard could always use more documentation, whether as part of the
+official COVID-19 Dashboard docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/ciyer/covid_19_dashboard/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+ are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `covid_19_dashboard` for local development.
+
+1. Fork the `covid_19_dashboard` repo on GitHub.
+2. Clone your fork locally::
+
+ $ git clone git@github.com:your_name_here/covid_19_dashboard.git
+
+3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+
+ $ mkvirtualenv covid_19_dashboard
+ $ cd covid_19_dashboard/
+ $ python setup.py develop
+
+4. Create a branch for local development::
+
+ $ git checkout -b name-of-your-bugfix-or-feature
+
+ Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass flake8 and the
+ tests, including testing other Python versions with tox::
+
+ $ flake8 covid_19_dashboard tests
+ $ python setup.py test or pytest
+ $ tox
+
+ To get flake8 and tox, just pip install them into your virtualenv.
+
+6. Commit your changes and push your branch to GitHub::
+
+ $ git add .
+ $ git commit -m "Your detailed description of your changes."
+ $ git push origin name-of-your-bugfix-or-feature
+
+7. Submit a pull request through the GitHub website.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put
+ your new functionality into a function with a docstring, and add the
+ feature to the list in README.rst.
+3. The pull request should work for Python 3.5, 3.6, 3.7 and 3.8, and for PyPy. Check
+ https://travis-ci.com/ciyer/covid_19_dashboard/pull_requests
+ and make sure that the tests pass for all supported Python versions.
+
+Tips
+----
+
+To run a subset of tests::
+
+
+ $ python -m unittest tests.test_covid_19_dashboard
+
+Deploying
+---------
+
+A reminder for the maintainers on how to deploy.
+Make sure all your changes are committed (including an entry in HISTORY.rst).
+Then run::
+
+$ bump2version patch # possible: major / minor / patch
+$ git push
+$ git push --tags
+
+Travis will then deploy to PyPI if tests pass.
diff --git a/src/covid-19/covid_19_dashboard/HISTORY.rst b/src/covid-19/covid_19_dashboard/HISTORY.rst
new file mode 100644
index 00000000..5462ac16
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/HISTORY.rst
@@ -0,0 +1,8 @@
+=======
+History
+=======
+
+0.1.0 (2020-03-15)
+------------------
+
+* First release on PyPI.
diff --git a/src/covid-19/covid_19_dashboard/LICENSE b/src/covid-19/covid_19_dashboard/LICENSE
new file mode 100644
index 00000000..7db34eda
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/LICENSE
@@ -0,0 +1,16 @@
+Apache Software License 2.0
+
+Copyright (c) 2020, Chandrasekhar Ramakrishnan
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
diff --git a/src/covid-19/covid_19_dashboard/MANIFEST.in b/src/covid-19/covid_19_dashboard/MANIFEST.in
new file mode 100644
index 00000000..292d6dd9
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/MANIFEST.in
@@ -0,0 +1,10 @@
+include CONTRIBUTING.rst
+include HISTORY.rst
+include LICENSE
+include README.rst
+
+recursive-include tests *
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif
diff --git a/src/covid-19/covid_19_dashboard/Makefile b/src/covid-19/covid_19_dashboard/Makefile
new file mode 100644
index 00000000..924161a6
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/Makefile
@@ -0,0 +1,85 @@
+.PHONY: clean clean-test clean-pyc clean-build docs help
+.DEFAULT_GOAL := help
+
+define BROWSER_PYSCRIPT
+import os, webbrowser, sys
+
+from urllib.request import pathname2url
+
+webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
+endef
+export BROWSER_PYSCRIPT
+
+define PRINT_HELP_PYSCRIPT
+import re, sys
+
+for line in sys.stdin:
+ match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
+ if match:
+ target, help = match.groups()
+ print("%-20s %s" % (target, help))
+endef
+export PRINT_HELP_PYSCRIPT
+
+BROWSER := python -c "$$BROWSER_PYSCRIPT"
+
+help:
+ @python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
+
+clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
+
+clean-build: ## remove build artifacts
+ rm -fr build/
+ rm -fr dist/
+ rm -fr .eggs/
+ find . -name '*.egg-info' -exec rm -fr {} +
+ find . -name '*.egg' -exec rm -f {} +
+
+clean-pyc: ## remove Python file artifacts
+ find . -name '*.pyc' -exec rm -f {} +
+ find . -name '*.pyo' -exec rm -f {} +
+ find . -name '*~' -exec rm -f {} +
+ find . -name '__pycache__' -exec rm -fr {} +
+
+clean-test: ## remove test and coverage artifacts
+ rm -fr .tox/
+ rm -f .coverage
+ rm -fr htmlcov/
+ rm -fr .pytest_cache
+
+lint: ## check style with flake8
+ flake8 covid_19_dashboard tests
+
+test: ## run tests quickly with the default Python
+ python setup.py test
+
+test-all: ## run tests on every Python version with tox
+ tox
+
+coverage: ## check code coverage quickly with the default Python
+ coverage run --source covid_19_dashboard setup.py test
+ coverage report -m
+ coverage html
+ $(BROWSER) htmlcov/index.html
+
+docs: ## generate Sphinx HTML documentation, including API docs
+ rm -f docs/covid_19_dashboard.rst
+ rm -f docs/modules.rst
+ sphinx-apidoc -o docs/ covid_19_dashboard
+ $(MAKE) -C docs clean
+ $(MAKE) -C docs html
+ $(BROWSER) docs/_build/html/index.html
+
+servedocs: docs ## compile the docs watching for changes
+ watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
+
+release: dist ## package and upload a release
+ twine upload dist/*
+
+dist: clean ## builds source and wheel package
+ python setup.py sdist
+ python setup.py bdist_wheel
+ ls -l dist
+
+install: clean ## install the package to the active Python's site-packages
+ python setup.py install
diff --git a/src/covid-19/covid_19_dashboard/README.rst b/src/covid-19/covid_19_dashboard/README.rst
new file mode 100644
index 00000000..c3bb6b16
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/README.rst
@@ -0,0 +1,37 @@
+==================
+COVID-19 Dashboard
+==================
+
+
+.. image:: https://img.shields.io/pypi/v/covid_19_dashboard.svg
+ :target: https://pypi.python.org/pypi/covid_19_dashboard
+
+.. image:: https://img.shields.io/travis/ciyer/covid_19_dashboard.svg
+ :target: https://travis-ci.com/ciyer/covid_19_dashboard
+
+.. image:: https://readthedocs.org/projects/covid-19-dashboard/badge/?version=latest
+ :target: https://covid-19-dashboard.readthedocs.io/en/latest/?badge=latest
+ :alt: Documentation Status
+
+
+
+
+Helper functions for plotting covid-19 data
+
+
+* Free software: Apache Software License 2.0
+* Documentation: https://covid-19-dashboard.readthedocs.io.
+
+
+Features
+--------
+
+* TODO
+
+Credits
+-------
+
+This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
+
+.. _Cookiecutter: https://github.com/audreyr/cookiecutter
+.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
diff --git a/src/covid-19/covid_19_dashboard/covid_19_dashboard/__init__.py b/src/covid-19/covid_19_dashboard/covid_19_dashboard/__init__.py
new file mode 100644
index 00000000..b0b17a30
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/covid_19_dashboard/__init__.py
@@ -0,0 +1,7 @@
+"""Top-level package for COVID-19 Dashboard."""
+
+__author__ = """Chandrasekhar Ramakrishnan"""
+__email__ = 'cramakri@ethz.ch'
+__version__ = '0.1.0'
+
+from .helper import *
\ No newline at end of file
diff --git a/src/covid-19/covid_19_dashboard/covid_19_dashboard/helper.py b/src/covid-19/covid_19_dashboard/covid_19_dashboard/helper.py
new file mode 100644
index 00000000..6b62468e
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/covid_19_dashboard/helper.py
@@ -0,0 +1,130 @@
+"""Main module.
+Helper functions for the dashboard"""
+
+import altair as alt
+from vega_datasets import data
+import pandas as pd
+import os
+
+
+def read_jhu_covid_df(ts_folder, name):
+ filename = os.path.join(ts_folder, f"time_series_19-covid-{name}.csv")
+ df = pd.read_csv(filename)
+ df = df.set_index(['Province/State', 'Country/Region', 'Lat', 'Long'])
+ df.columns = pd.to_datetime(df.columns)
+ return df
+
+
+def read_jhu_frames_map(ts_folder):
+
+ jhu_frames_map = {
+ "confirmed": read_jhu_covid_df(ts_folder, "Confirmed"),
+ "deaths": read_jhu_covid_df(ts_folder, "Deaths"),
+ "recovered": read_jhu_covid_df(ts_folder, "Recovered")
+ }
+ return jhu_frames_map
+
+
+def read_rates_covid_df(rates_folder, name):
+ filename = os.path.join(rates_folder, f"ts_rates_19-covid-{name}.csv")
+ df = pd.read_csv(filename).drop("Unnamed: 0", axis=1)
+ df = df.set_index(['Country/Region'])
+ df.columns = pd.to_datetime(df.columns)
+ return df
+
+
+def read_rates_frames_map(rates_folder):
+ rates_frames_map = {
+ "confirmed": read_rates_covid_df(rates_folder, "confirmed"),
+ "deaths": read_rates_covid_df(rates_folder, "deaths"),
+ "recovered": read_rates_covid_df(rates_folder, "recovered")
+ }
+ return rates_frames_map
+
+
+def read_geodata(geodata_path):
+ geodata_df = pd.read_csv(geodata_path)
+ geodata_df = geodata_df.drop('Unnamed: 0', axis=1)
+ geodata_df = geodata_df.rename({'name_jhu':'Country/Region'}, axis=1)
+ geodata_df = geodata_df.set_index('Country/Region')
+ return geodata_df
+
+
+def latest_jhu_country_ser(jhu_frames_map, name):
+ return jhu_frames_map[name].iloc[:,-1].groupby(level='Country/Region').sum()
+
+
+def countries_with_number_of_cases(jhu_frames_map, name, count):
+ case_count_ser = latest_jhu_country_ser(jhu_frames_map, 'confirmed')
+ countries_over_thresh = case_count_ser[case_count_ser > count - 1].index
+ return countries_over_thresh
+
+
+def latest_rates_ser(rates_frames_map, name):
+ return rates_frames_map[name].iloc[:,-1]
+
+
+def compute_map_df(rates_frames_map, jhu_frames_map, geodata_df, countries_over_thresh):
+ map_df = pd.concat([
+ latest_rates_ser(rates_frames_map, 'confirmed'),
+ latest_rates_ser(rates_frames_map, 'deaths'),
+ latest_rates_ser(rates_frames_map, 'recovered')], axis=1)
+ nominal_df = pd.concat([
+ latest_jhu_country_ser(jhu_frames_map, 'confirmed'),
+ latest_jhu_country_ser(jhu_frames_map, 'deaths'),
+ latest_jhu_country_ser(jhu_frames_map, 'recovered')], axis=1)
+ map_df = pd.concat([map_df, nominal_df, geodata_df[['Longitude', 'Latitude']]], axis=1)
+ # Restrict to countries with 100 or more cases
+ map_df = map_df.loc[countries_over_thresh].dropna()
+ map_df = map_df.reset_index()
+ map_df.columns = ['Country/Region',
+ 'Confirmed/100k', 'Deaths/100k', 'Recovered/100k',
+ 'Confirmed', 'Deaths', 'Recovered',
+ 'Long', 'Lat']
+ return map_df
+
+
+def map_of_variable(map_df, variable, title):
+ # Data generators for the background
+ sphere = alt.sphere()
+ graticule = alt.graticule()
+
+ # Source of land data
+ source = alt.topo_feature(data.world_110m.url, 'countries')
+
+ # Layering and configuring the components
+ p = alt.layer(
+ alt.Chart(sphere).mark_geoshape(fill='#cae6ef'),
+ alt.Chart(graticule).mark_geoshape(stroke='white', strokeWidth=0.5),
+ alt.Chart(source).mark_geoshape(fill='#dddddd', stroke='#aaaaaa'),
+ alt.Chart(map_df).mark_circle(opacity=0.6).encode(
+ longitude='Long:Q',
+ latitude='Lat:Q',
+ size=alt.Size(f'{variable}:Q', title="Cases"),
+ color=alt.value('steelblue'),
+ tooltip=["Country/Region:N",
+ "Confirmed:Q", "Deaths:Q", "Recovered:Q",
+ "Confirmed/100k:Q", "Deaths/100k:Q", "Recovered/100k:Q"]
+ )
+ ).project(
+ 'naturalEarth1'
+ ).properties(width=600, height=400, title=f"{title} cases per 100k inhabitants"
+ ).configure_view(stroke=None)
+ return p
+
+
+def growth_df(rates_frames_map, geodata_df, name, countries_over_thresh):
+ latest_confirmed_ser = rates_frames_map['confirmed'].iloc[:,-1]
+ countries_over_1 = latest_confirmed_ser[latest_confirmed_ser >= 2].reset_index()['Country/Region']
+
+ confirmed_rate_df = rates_frames_map['confirmed']
+ confirmed_rate_df = confirmed_rate_df.loc[
+ confirmed_rate_df.index.isin(countries_over_1) &
+ confirmed_rate_df.index.isin(countries_over_thresh)]
+ confirmed_rate_df = confirmed_rate_df.join(
+ geodata_df[['Longitude', 'Latitude', 'region_un']]).set_index(
+ ['Longitude', 'Latitude', 'region_un'], append=True)
+ confirmed_rate_df = confirmed_rate_df.stack().reset_index()
+ confirmed_rate_df = confirmed_rate_df.rename(
+ {'region_un': 'Geo Region', 'level_4': 'Date', 0: 'Confirmed/100k'}, axis=1)
+ return confirmed_rate_df
diff --git a/src/covid-19/covid_19_dashboard/docs/Makefile b/src/covid-19/covid_19_dashboard/docs/Makefile
new file mode 100644
index 00000000..ba46b860
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS =
+SPHINXBUILD = python -msphinx
+SPHINXPROJ = covid_19_dashboard
+SOURCEDIR = .
+BUILDDIR = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+ @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/src/covid-19/covid_19_dashboard/docs/conf.py b/src/covid-19/covid_19_dashboard/docs/conf.py
new file mode 100755
index 00000000..c51f68fb
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/docs/conf.py
@@ -0,0 +1,162 @@
+#!/usr/bin/env python
+#
+# covid_19_dashboard documentation build configuration file, created by
+# sphinx-quickstart on Fri Jun 9 13:47:02 2017.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# If extensions (or modules to document with autodoc) are in another
+# directory, add these directories to sys.path here. If the directory is
+# relative to the documentation root, use os.path.abspath to make it
+# absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('..'))
+
+import covid_19_dashboard
+
+# -- General configuration ---------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = 'COVID-19 Dashboard'
+copyright = "2020, Chandrasekhar Ramakrishnan"
+author = "Chandrasekhar Ramakrishnan"
+
+# The version info for the project you're documenting, acts as replacement
+# for |version| and |release|, also used in various other places throughout
+# the built documents.
+#
+# The short X.Y version.
+version = covid_19_dashboard.__version__
+# The full version, including alpha/beta/rc tags.
+release = covid_19_dashboard.__version__
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output -------------------------------------------
+
+# The theme to use for HTML and HTML Help pages. See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a
+# theme further. For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+
+# -- Options for HTMLHelp output ---------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'covid_19_dashboarddoc'
+
+
+# -- Options for LaTeX output ------------------------------------------
+
+latex_elements = {
+ # The paper size ('letterpaper' or 'a4paper').
+ #
+ # 'papersize': 'letterpaper',
+
+ # The font size ('10pt', '11pt' or '12pt').
+ #
+ # 'pointsize': '10pt',
+
+ # Additional stuff for the LaTeX preamble.
+ #
+ # 'preamble': '',
+
+ # Latex figure (float) alignment
+ #
+ # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass
+# [howto, manual, or own class]).
+latex_documents = [
+ (master_doc, 'covid_19_dashboard.tex',
+ 'COVID-19 Dashboard Documentation',
+ 'Chandrasekhar Ramakrishnan', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+ (master_doc, 'covid_19_dashboard',
+ 'COVID-19 Dashboard Documentation',
+ [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+# dir menu entry, description, category)
+texinfo_documents = [
+ (master_doc, 'covid_19_dashboard',
+ 'COVID-19 Dashboard Documentation',
+ author,
+ 'covid_19_dashboard',
+ 'One line description of project.',
+ 'Miscellaneous'),
+]
+
+
+
diff --git a/src/covid-19/covid_19_dashboard/docs/contributing.rst b/src/covid-19/covid_19_dashboard/docs/contributing.rst
new file mode 100644
index 00000000..e582053e
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/docs/contributing.rst
@@ -0,0 +1 @@
+.. include:: ../CONTRIBUTING.rst
diff --git a/src/covid-19/covid_19_dashboard/docs/history.rst b/src/covid-19/covid_19_dashboard/docs/history.rst
new file mode 100644
index 00000000..25064996
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/docs/history.rst
@@ -0,0 +1 @@
+.. include:: ../HISTORY.rst
diff --git a/src/covid-19/covid_19_dashboard/docs/index.rst b/src/covid-19/covid_19_dashboard/docs/index.rst
new file mode 100644
index 00000000..4f3a7d4d
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/docs/index.rst
@@ -0,0 +1,19 @@
+Welcome to COVID-19 Dashboard's documentation!
+======================================
+
+.. toctree::
+ :maxdepth: 2
+ :caption: Contents:
+
+ readme
+ installation
+ usage
+ modules
+ contributing
+ history
+
+Indices and tables
+==================
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/src/covid-19/covid_19_dashboard/docs/installation.rst b/src/covid-19/covid_19_dashboard/docs/installation.rst
new file mode 100644
index 00000000..4378653f
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/docs/installation.rst
@@ -0,0 +1,51 @@
+.. highlight:: shell
+
+============
+Installation
+============
+
+
+Stable release
+--------------
+
+To install COVID-19 Dashboard, run this command in your terminal:
+
+.. code-block:: console
+
+ $ pip install covid_19_dashboard
+
+This is the preferred method to install COVID-19 Dashboard, as it will always install the most recent stable release.
+
+If you don't have `pip`_ installed, this `Python installation guide`_ can guide
+you through the process.
+
+.. _pip: https://pip.pypa.io
+.. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/
+
+
+From sources
+------------
+
+The sources for COVID-19 Dashboard can be downloaded from the `Github repo`_.
+
+You can either clone the public repository:
+
+.. code-block:: console
+
+ $ git clone git://github.com/ciyer/covid_19_dashboard
+
+Or download the `tarball`_:
+
+.. code-block:: console
+
+ $ curl -OJL https://github.com/ciyer/covid_19_dashboard/tarball/master
+
+Once you have a copy of the source, you can install it with:
+
+.. code-block:: console
+
+ $ python setup.py install
+
+
+.. _Github repo: https://github.com/ciyer/covid_19_dashboard
+.. _tarball: https://github.com/ciyer/covid_19_dashboard/tarball/master
diff --git a/src/covid-19/covid_19_dashboard/docs/make.bat b/src/covid-19/covid_19_dashboard/docs/make.bat
new file mode 100644
index 00000000..c18343e9
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/docs/make.bat
@@ -0,0 +1,36 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+ set SPHINXBUILD=python -msphinx
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+set SPHINXPROJ=covid_19_dashboard
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+ echo.
+ echo.The Sphinx module was not found. Make sure you have Sphinx installed,
+ echo.then set the SPHINXBUILD environment variable to point to the full
+ echo.path of the 'sphinx-build' executable. Alternatively you may add the
+ echo.Sphinx directory to PATH.
+ echo.
+ echo.If you don't have Sphinx installed, grab it from
+ echo.http://sphinx-doc.org/
+ exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd
diff --git a/src/covid-19/covid_19_dashboard/docs/readme.rst b/src/covid-19/covid_19_dashboard/docs/readme.rst
new file mode 100644
index 00000000..72a33558
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/docs/readme.rst
@@ -0,0 +1 @@
+.. include:: ../README.rst
diff --git a/src/covid-19/covid_19_dashboard/docs/usage.rst b/src/covid-19/covid_19_dashboard/docs/usage.rst
new file mode 100644
index 00000000..e459b07b
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/docs/usage.rst
@@ -0,0 +1,7 @@
+=====
+Usage
+=====
+
+To use COVID-19 Dashboard in a project::
+
+ import covid_19_dashboard
diff --git a/src/covid-19/covid_19_dashboard/requirements_dev.txt b/src/covid-19/covid_19_dashboard/requirements_dev.txt
new file mode 100644
index 00000000..c54c8cea
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/requirements_dev.txt
@@ -0,0 +1,10 @@
+pip==19.2.3
+bump2version==0.5.11
+wheel==0.33.6
+watchdog==0.9.0
+flake8==3.7.8
+tox==3.14.0
+coverage==4.5.4
+Sphinx==1.8.5
+twine==1.14.0
+
diff --git a/src/covid-19/covid_19_dashboard/setup.cfg b/src/covid-19/covid_19_dashboard/setup.cfg
new file mode 100644
index 00000000..33a68f1a
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/setup.cfg
@@ -0,0 +1,22 @@
+[bumpversion]
+current_version = 0.1.0
+commit = True
+tag = True
+
+[bumpversion:file:setup.py]
+search = version='{current_version}'
+replace = version='{new_version}'
+
+[bumpversion:file:covid_19_dashboard/__init__.py]
+search = __version__ = '{current_version}'
+replace = __version__ = '{new_version}'
+
+[bdist_wheel]
+universal = 1
+
+[flake8]
+exclude = docs
+
+[aliases]
+# Define setup.py command aliases here
+
diff --git a/src/covid-19/covid_19_dashboard/setup.py b/src/covid-19/covid_19_dashboard/setup.py
new file mode 100644
index 00000000..d045ce8e
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/setup.py
@@ -0,0 +1,48 @@
+#!/usr/bin/env python
+
+"""The setup script."""
+
+from setuptools import setup, find_packages
+
+with open('README.rst') as readme_file:
+ readme = readme_file.read()
+
+with open('HISTORY.rst') as history_file:
+ history = history_file.read()
+
+requirements = [ ]
+
+setup_requirements = [ ]
+
+test_requirements = [ ]
+
+setup(
+ author="Chandrasekhar Ramakrishnan",
+ author_email='cramakri@ethz.ch',
+ python_requires='>=3.5',
+ classifiers=[
+ 'Development Status :: 2 - Pre-Alpha',
+ 'Intended Audience :: Developers',
+ 'License :: OSI Approved :: Apache Software License',
+ 'Natural Language :: English',
+ 'Programming Language :: Python :: 3',
+ 'Programming Language :: Python :: 3.5',
+ 'Programming Language :: Python :: 3.6',
+ 'Programming Language :: Python :: 3.7',
+ 'Programming Language :: Python :: 3.8',
+ ],
+ description="Helper functions for plotting covid-19 data",
+ install_requires=requirements,
+ license="Apache Software License 2.0",
+ long_description=readme + '\n\n' + history,
+ include_package_data=True,
+ keywords='covid_19_dashboard',
+ name='covid_19_dashboard',
+ packages=find_packages(include=['covid_19_dashboard', 'covid_19_dashboard.*']),
+ setup_requires=setup_requirements,
+ test_suite='tests',
+ tests_require=test_requirements,
+ url='https://github.com/ciyer/covid_19_dashboard',
+ version='0.1.0',
+ zip_safe=False,
+)
diff --git a/src/covid-19/covid_19_dashboard/tests/__init__.py b/src/covid-19/covid_19_dashboard/tests/__init__.py
new file mode 100644
index 00000000..710f25a5
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/tests/__init__.py
@@ -0,0 +1 @@
+"""Unit test package for covid_19_dashboard."""
diff --git a/src/covid-19/covid_19_dashboard/tests/test_covid_19_dashboard.py b/src/covid-19/covid_19_dashboard/tests/test_covid_19_dashboard.py
new file mode 100644
index 00000000..2bb0a85f
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/tests/test_covid_19_dashboard.py
@@ -0,0 +1,21 @@
+#!/usr/bin/env python
+
+"""Tests for `covid_19_dashboard` package."""
+
+
+import unittest
+
+from covid_19_dashboard import covid_19_dashboard
+
+
+class TestCovid_19_dashboard(unittest.TestCase):
+ """Tests for `covid_19_dashboard` package."""
+
+ def setUp(self):
+ """Set up test fixtures, if any."""
+
+ def tearDown(self):
+ """Tear down test fixtures, if any."""
+
+ def test_000_something(self):
+ """Test something."""
diff --git a/src/covid-19/covid_19_dashboard/tox.ini b/src/covid-19/covid_19_dashboard/tox.ini
new file mode 100644
index 00000000..0a00bcd9
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/tox.ini
@@ -0,0 +1,20 @@
+[tox]
+envlist = py35, py36, py37, py38, flake8
+
+[travis]
+python =
+ 3.8: py38
+ 3.7: py37
+ 3.6: py36
+ 3.5: py35
+
+[testenv:flake8]
+basepython = python
+deps = flake8
+commands = flake8 covid_19_dashboard tests
+
+[testenv]
+setenv =
+ PYTHONPATH = {toxinidir}
+
+commands = python setup.py test
--
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