COVID19_Tracker.ipynb

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  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import scipy.optimize\n",
    "import pandas as pd\n",
    "import matplotlib.pyplot as plt\n",
    "%matplotlib inline\n",
    "%config InlineBackend.figure_format = 'svg'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Only works in a separate cell\n",
    "plt.rcParams['figure.figsize'] = [10, 6]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_data(csv_type='confirmed'):\n",
    "    # Pull data from Johns Hopkins https://github.com/CSSEGISandData/COVID-19\n",
    "    base_url= 'https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_'\n",
    "    url = base_url+csv_type+\"_global.csv\"\n",
    "    df = pd.read_csv(url)\n",
    "    del df['Lat']\n",
    "    del df['Long']\n",
    "    return df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "confirmed = get_data()\n",
    "deaths = get_data(csv_type='deaths')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "def logistic(t, L, t0, k):\n",
    "    return L/(1+np.exp(-k*(t-t0)))\n",
    "\n",
    "def fit_logistic(t, n):\n",
    "    sigma = np.sqrt(n)\n",
    "    popt, pcov = scipy.optimize.curve_fit(logistic, xdata=t, ydata=n, sigma=sigma, \n",
    "                                          p0=[10000., 25., 0.5],absolute_sigma=True)\n",
    "    return (popt, pcov)\n",
    "\n",
    "def print_fit(popt, pcov):\n",
    "#    print(popt)\n",
    "    print(popt[0], np.sqrt(pcov[0,0]))\n",
    "    print(popt[1], np.sqrt(pcov[1,1]))\n",
    "    print(popt[2], np.sqrt(pcov[2,2]))\n",
    "    \n",
    "#    print(\" Max: {:7d}+/-{:7d}\".format(int(popt[0]),int(np.sqrt(pcov[0,0])))+\n",
    "#          \" Delay: {:2d}+/-{:2d}\".format(int(popt[1]),int(np.sqrt(pcov[1,1])))+\n",
    "#          \" Slope: {:5.2f}+/-{:5.2f}\".format(popt[2]),np.sqrt(pcov[2,2]))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "def plot_df(df, start=10, \n",
    "            countries=['Italy','Spain','Germany','France',\n",
    "                        'US','United Kingdom','Canada','Korea, South','China']):\n",
    "\n",
    "    lastdate = df.columns[-1]\n",
    "\n",
    "    for country in countries:\n",
    "        df=df.append(df[df['Country/Region']==country][:].sum(axis=0), ignore_index=True)\n",
    "        last = df.tail(1).index[0]\n",
    "        df.loc[last,'Province/State']=''\n",
    "        df.loc[last,'Country/Region']=country\n",
    "        if str(start) == start:\n",
    "            pass\n",
    "        else:\n",
    "            n=0\n",
    "            ndates = len(df.columns[2:])\n",
    "            for date in df.columns[2:]:\n",
    "                #print(country, date, df.loc[last, date] )\n",
    "                if df.loc[last, date] > start:\n",
    "                    startidx = n\n",
    "                    break\n",
    "                n+=1\n",
    "            x = np.arange(ndates-n)\n",
    "            base_line, = plt.semilogy(x, df.iloc[last][n+2:], alpha=0.5)\n",
    "            plt.plot([ndates-n-1],[df.iloc[last][-1]],'o', color=base_line.get_color())\n",
    "            try:\n",
    "                (popt, pcov) = fit_logistic(x.astype(float), df.iloc[last][n+2:].values.astype(float))\n",
    "                x = np.arange(50)\n",
    "                print(\"{:15s}\".format(country),end=\"\")\n",
    "                print_fit(popt, pcov)\n",
    "                plt.plot(x, logistic(x, popt[0], popt[1], popt[2]),':', color=base_line.get_color())\n",
    "            except:\n",
    "                pass\n",
    "\n",
    "            plt.annotate(country, ((ndates-n-1+0.2),(df.iloc[last][-1])*1.10), \n",
    "                         xycoords='data', color=base_line.get_color(),\n",
    "                         clip_on=True)\n",
    "    \n",
    "#    left, right = plt.xlim()\n",
    "#    for rate in [1.33,1.25,1.20,1.15,1.10,1.05]:\n",
    "#        plt.semilogy([left, right],[start,start*(rate**(right-left))],\n",
    "#                     label=str('{:2d}'.format(int(round((rate-1)*100.,0))))+'% per day',ls=\":\",c='k',alpha=0.2)\n",
    "    plt.legend(loc='upper left')"
   ]
  },
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   "cell_type": "code",
   "execution_count": 7,
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     "name": "stdout",
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      "Italy          128163.65599491708 241.74707524419588\n",
      "28.79225618557589 0.026205625733019867\n",
      "0.1976794228964047 0.0003315639368999044\n",
      "Spain          137717.3304046669 357.74293382837226\n",
      "25.278859376935138 0.02628237253890293\n",
      "0.24849076587733554 0.0004639068082569177\n",
      "Germany        104491.25851959373 317.9629399311626\n",
      "26.078708707406236 0.03208958513575056\n",
      "0.23750778906556239 0.0005171132278548686\n",
      "France         107109.10472578452 681.4271397997996\n",
      "29.91871377828247 0.06498518112050423\n",
      "0.1952244353667135 0.0004964003686040002\n",
      "US             372680.6587050603 982.2244092999824\n",
      "27.580564893796865 0.020522539776450584\n",
      "0.2847071882231828 0.0003933878066957302\n",
      "United Kingdom 70321.19484398163 867.9502913524342\n",
      "28.249975591650852 0.10334038412627009\n",
      "0.2195639975587064 0.0008642751959758734\n",
      "Canada         18017.757148084576 283.21310031962366\n",
      "20.216228532810497 0.13126636541021586\n",
      "0.2521702015932875 0.0019163966301366958\n",
      "Korea, South   8967.457189503777 19.688652684313364\n",
      "11.516883565224035 0.03881231741082462\n",
      "0.31694955655164814 0.002133126866681484\n"
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     "text": [
      "No handles with labels found to put in legend.\n"
     ]
    },
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     "name": "stdout",
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     "text": [
      "China          80818.86893512562 43.10086939482576\n",
      "17.709996055577427 0.01381112801121295\n",
      "0.2423807325487284 0.00042555342133302024\n"
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   "source": [
    "plot_df(confirmed, start=100)\n",
    "plt.xlabel('Days since 100th confirmed case')\n",
    "plt.ylabel('Confirmed cases');"
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  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
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    "plot_df(deaths, start=10)\n",
    "plt.xlabel('Days since 10th death')\n",
    "plt.ylabel('Deaths');"
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