COVID-19 dynamics plot

COVID-19.ipynb

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   "cell_type": "markdown",
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   "source": [
    "# COVID-19 Dynamics\n",
    "\n",
    "There are many visiualizations of the ongoing [COVID-19](https://en.wikipedia.org/wiki/Coronavirus_disease_2019) (or Corona) virus outbreak. As most are static, this one specifically aims to illustrate the dynamics of the COVID-19 virus infection using the official datasets available at https://github.com/CSSEGISandData/COVID-19. It builds on [Jupyter](https://jupyter.org) and [IPyLeaflet](https://github.com/jupyter-widgets/ipyleaflet) (and [Voilà](https://github.com/voila-dashboards/voila) and [MyBinder](https://mybinder.org), soon)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from functools import partial\n",
    "from math import pi\n",
    "\n",
    "from ipyleaflet import basemap_to_tiles, basemaps, CircleMarker, \\\n",
    "    FullScreenControl, LayersControl, LayerGroup, Map, Marker, \\\n",
    "    WidgetControl\n",
    "from ipywidgets import IntSlider, HBox, jslink, Layout, Output, Play\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "url = (\"https://raw.githubusercontent.com/CSSEGISandData/COVID-19/\"\n",
    "       \"master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Confirmed.csv\")\n",
    "df_confirmed = pd.read_csv(url)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# df_confirmed.describe()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# df_confirmed.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "day_cols = [col for col in df_confirmed.columns if col.count(\"/\") == 2]\n",
    "locations = list(zip(df_confirmed.Lat, df_confirmed.Long))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def radius_sphere(volume):\n",
    "    return (volume / pi / 4 * 3) ** (1/2.75)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def slider_changed(change, the_map=None, output=None, slider=None, group=None):\n",
    "    day = change['new']\n",
    "    values = df_confirmed[day_cols[day]]\n",
    "    if slider:\n",
    "        slider.description = day_cols[day]\n",
    "    if the_map:\n",
    "        circle_layers = list(l for l in group.layers if type(l) == CircleMarker)\n",
    "        if not circle_layers:\n",
    "            # if output:\n",
    "            #     with output:\n",
    "            #         print(f\"updating {day_cols[day]}\")\n",
    "            markers = []\n",
    "            for i, loc in enumerate(locations):\n",
    "                rad = int(radius_sphere(values[i]))\n",
    "                marker = CircleMarker(\n",
    "                    location=tuple(loc),\n",
    "                    radius=rad,\n",
    "                    color=\"red\" if rad > 0 else \"white\",\n",
    "                    opacity=rad > 0)\n",
    "                markers.append(marker)\n",
    "            group.layers = tuple(markers)\n",
    "        else:\n",
    "            for i, lay in enumerate(circle_layers):\n",
    "                rad = int(radius_sphere(values[i]))\n",
    "                lay.radius = rad\n",
    "                lay.color=\"red\" if rad > 0 else \"white\"\n",
    "                lay.opacity = rad > 0"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# output = Output()\n",
    "# display(output)\n",
    "\n",
    "m = Map(zoom=2, basemap=basemaps.CartoDB.Positron)\n",
    "\n",
    "m += FullScreenControl()\n",
    "\n",
    "# dark_matter_layer = basemap_to_tiles(basemaps.CartoDB.DarkMatter)\n",
    "# m.add_layer(dark_matter_layer)\n",
    "# nat_geo_world_layer = basemap_to_tiles(basemaps.Esri.NatGeoWorldMap)\n",
    "# m.add_layer(nat_geo_world_layer)\n",
    "layers_control = LayersControl(position='topright')\n",
    "m += layers_control\n",
    "\n",
    "confirmed_group = LayerGroup(layers=[], name=\"Confirmed\")\n",
    "m += confirmed_group\n",
    "\n",
    "play = Play(\n",
    "    value=0,\n",
    "    min=0,\n",
    "    max=len(day_cols)-1,\n",
    "    step=1,\n",
    "    interval=500,\n",
    "    # description=\"Press play\",\n",
    "    disabled=False\n",
    ")\n",
    "day_slider = IntSlider(\n",
    "    description='Day:',\n",
    "    layout=Layout(width=\"600px\"),\n",
    "    min=-1, max=len(day_cols)-1, value=-1)\n",
    "jslink((play, 'value'), (day_slider, 'value'))\n",
    "cb = partial(slider_changed,\n",
    "             the_map=m,\n",
    "             # output=output,\n",
    "             group=confirmed_group,\n",
    "             slider=day_slider)\n",
    "day_slider.observe(cb, names='value')\n",
    "widget_control1 = WidgetControl(\n",
    "    widget=HBox([play, day_slider]),\n",
    "    position='bottomleft',\n",
    "    layout=Layout(width=\"600px\"),\n",
    ")\n",
    "day_slider.value = 0\n",
    "day_slider.min = 0\n",
    "m.add_control(widget_control1)\n",
    "\n",
    "m"
   ]
  }
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