poisson_class.ipynb

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   "source": [
    "import datetime\n",
    "import numpy as np\n",
    "from scipy.stats import poisson\n"
   ]
  },
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   "execution_count": 2,
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   "source": [
    "#testing\n",
    "import random\n",
    "from bokeh.plotting import figure\n",
    "from bokeh.io import show\n",
    "from bokeh.io import output_notebook\n"
   ]
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   "execution_count": 3,
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   "source": [
    "def get_poisson_for_day(date, cases, loc = 2):\n",
    "    \"\"\"\n",
    "    Calculate when the infections occurred for a single day\n",
    "    \"\"\"\n",
    "    final = []\n",
    "    for i in range(14):\n",
    "        p = poisson.pmf(i, 5, loc = loc)\n",
    "        final.append((date, p * cases))\n",
    "        date -= datetime.timedelta(days = 1)\n",
    "    return final\n",
    "\n",
    "def test_get_poisson_for_day():\n",
    "    date = datetime.datetime(2020,9,1)\n",
    "    num_infected = 100\n",
    "    data = get_poisson_for_day(date, num_infected)\n",
    "    assert len(data) == 14\n",
    "    assert abs(sum([x[1] for x in data]) - num_infected) < 1\n",
    "test_get_poisson_for_day()"
   ]
  },
  {
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   "execution_count": 4,
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   "outputs": [],
   "source": [
    "def get_poisson_for_all_days(dates, cases):\n",
    "    temp_dict = {}\n",
    "    for i in range(len(cases)):\n",
    "        p_data =  get_poisson_for_day(dates[i], cases[i])\n",
    "        data = {}\n",
    "        for i in p_data:\n",
    "            data[i[0]] = i[1]\n",
    "        for key in data.keys():\n",
    "            if not temp_dict.get(key):\n",
    "                temp_dict[key] = data[key]\n",
    "            else:\n",
    "                temp_dict[key] += data[key]\n",
    "    final = []\n",
    "    for key in sorted(temp_dict.keys()):\n",
    "        final.append((key, temp_dict[key]))\n",
    "    return final\n",
    "\n",
    "def test_get_poisson_for_all_days():\n",
    "    dates = [datetime.datetime(2020,9,1), datetime.datetime(2020,9,2)]\n",
    "    cases = [100, 200]\n",
    "    data = get_poisson_for_all_days(dates, cases)\n",
    "    assert data[0][0] == datetime.datetime(2020, 8, 19)\n",
    "    assert data[-1][0] == datetime.datetime(2020, 9, 2)\n",
    "    assert abs(sum([x[1] for x in data]) - sum(cases)) < 2\n",
    "test_get_poisson_for_all_days()    "
   ]
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Possible fixes:\\n\"+\n     \"</p>\\n\"+\n     \"<ul>\\n\"+\n     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n     \"</ul>\\n\"+\n     \"<code>\\n\"+\n     \"from bokeh.resources import INLINE\\n\"+\n     \"output_notebook(resources=INLINE)\\n\"+\n     \"</code>\\n\"+\n     \"</div>\"}};\n\n  function display_loaded() {\n    var el = document.getElementById(\"1205\");\n    if (el != null) {\n      el.textContent = \"BokehJS is loading...\";\n    }\n    if (root.Bokeh !== undefined) {\n      if (el != null) {\n        el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n      }\n    } else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(display_loaded, 100)\n    }\n  }\n\n\n  function run_callbacks() {\n    try {\n      root._bokeh_onload_callbacks.forEach(function(callback) {\n        if (callback != null)\n          callback();\n      });\n    } finally {\n      delete root._bokeh_onload_callbacks\n    }\n    console.debug(\"Bokeh: all callbacks have finished\");\n  }\n\n  function load_libs(css_urls, js_urls, callback) {\n    if (css_urls == null) css_urls = [];\n    if (js_urls == null) js_urls = [];\n\n    root._bokeh_onload_callbacks.push(callback);\n    if (root._bokeh_is_loading > 0) {\n      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n      return null;\n    }\n    if (js_urls == null || js_urls.length === 0) {\n      run_callbacks();\n      return null;\n    }\n    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n    root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n    function on_load() {\n      root._bokeh_is_loading--;\n      if (root._bokeh_is_loading === 0) {\n        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n        run_callbacks()\n      }\n    }\n\n    function on_error() {\n      console.error(\"failed to load \" + url);\n    }\n\n    for (var i = 0; i < css_urls.length; i++) {\n      var url = css_urls[i];\n      const element = document.createElement(\"link\");\n      element.onload = on_load;\n      element.onerror = on_error;\n      element.rel = \"stylesheet\";\n      element.type = \"text/css\";\n      element.href = url;\n      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n      document.body.appendChild(element);\n    }\n\n    const hashes = {\"https://cdn.bokeh.org/bokeh/release/bokeh-2.0.2.min.js\": \"ufR9RFnRs6lniiaFvtJziE0YeidtAgBRH6ux2oUItHw5WTvE1zuk9uzhUU/FJXDp\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.0.2.min.js\": \"8QM/PGWBT+IssZuRcDcjzwIh1mkOmJSoNMmyYDZbCfXJg3Ap1lEvdVgFuSAwhb/J\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.0.2.min.js\": \"Jm8cH3Rg0P6UeZhVY5cLy1WzKajUT9KImCY+76hEqrcJt59/d8GPvFHjCkYgnSIn\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-2.0.2.min.js\": \"Ozhzj+SI7ywm74aOI/UajcWz+C0NjsPunEVyVIrxzYkB+jA+2tUw8x5xJCbVtK5I\"};\n\n    for (var i = 0; i < js_urls.length; i++) {\n      var url = js_urls[i];\n      var element = document.createElement('script');\n      element.onload = on_load;\n      element.onerror = on_error;\n      element.async = false;\n      element.src = url;\n      if (url in hashes) {\n        element.crossOrigin = \"anonymous\";\n        element.integrity = \"sha384-\" + hashes[url];\n      }\n      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n      document.head.appendChild(element);\n    }\n  };\n\n  function inject_raw_css(css) {\n    const element = document.createElement(\"style\");\n    element.appendChild(document.createTextNode(css));\n    document.body.appendChild(element);\n  }\n\n  \n  var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.0.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.0.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.0.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-2.0.2.min.js\"];\n  var css_urls = [];\n  \n\n  var inline_js = [\n    function(Bokeh) {\n      Bokeh.set_log_level(\"info\");\n    },\n    function(Bokeh) {\n    \n    \n    }\n  ];\n\n  function run_inline_js() {\n    \n    if (root.Bokeh !== undefined || force === true) {\n      \n    for (var i = 0; i < inline_js.length; i++) {\n      inline_js[i].call(root, root.Bokeh);\n    }\n    if (force === true) {\n        display_loaded();\n      }} else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(run_inline_js, 100);\n    } else if (!root._bokeh_failed_load) {\n      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n      root._bokeh_failed_load = true;\n    } else if (force !== true) {\n      var cell = $(document.getElementById(\"1205\")).parents('.cell').data().cell;\n      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n    }\n\n  }\n\n  if (root._bokeh_is_loading === 0) {\n    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n    run_inline_js();\n  } else {\n    load_libs(css_urls, js_urls, function() {\n      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n      run_inline_js();\n    });\n  }\n}(window));"
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "output_notebook()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "# not used\n",
    "def get_new_dates(last_date):\n",
    "    raise NotImplementedError('')\n",
    "\n",
    "    final = []\n",
    "    for i in range(1,14):\n",
    "        final.append(last_date + datetime.timedelta(days = i))\n",
    "    return final"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "#not used\n",
    "def get_pred_slope(x, conf_i):\n",
    "        \"\"\"\n",
    "        calculate slope and intercepts for confidence intervals\n",
    "        \"\"\"\n",
    "        raise NotImplementedError('')\n",
    "\n",
    "        sl_upper = (conf_i[-1][1]  - conf_i[0][0])/(x[-1] - x[0])\n",
    "        sl_lower = (conf_i[-1][0] - conf_i[0][1])/(x[-1] -x[0])\n",
    "        return sl_lower, sl_upper\n",
    "\n",
    "#not used\n",
    "def get_projected_cases(dates, cases):\n",
    "    raise NotImplementedError('')\n",
    "    assert len(dates) == len(cases)\n",
    "    x = range(len(dates[-14:]))\n",
    "    X = list(zip(*[x]))\n",
    "    xm = sm.add_constant(X)\n",
    "    model = sm.OLS(cases[-14:], xm) \n",
    "    result = model.fit()\n",
    "    predictions = result.get_prediction(xm)\n",
    "    print('p value is {p}'.format(p = result.pvalues[1]))\n",
    "    frame = predictions.summary_frame(alpha=0.05)\n",
    "    new_dates =  get_new_dates(last_date = dates[-1])\n",
    "    slope_low, slope_high = get_pred_slope(x, predictions.conf_int())\n",
    "    proj_upper = [frame.mean_ci_upper.tolist()[-1] + slope_high * x for x in range(len(new_dates))]\n",
    "    proj_lower = [frame.mean_ci_lower.tolist()[-1] + slope_low * x for x in range(len(new_dates))]\n",
    "    y_hat = [x * result.params[1] + cases[-1] for x in range(len(new_dates))]\n",
    "    return new_dates, y_hat, proj_lower, proj_upper\n",
    "\n",
    "#not used\n",
    "def test_get_projected_cases():\n",
    "    return\n",
    "    dates = [datetime.datetime(2020, 8, 1) + datetime.timedelta(days = x) for x in range(14)]\n",
    "    cases = [1.3 * x * 10 + random.gauss(40, 30) for x in range(14)]\n",
    "    n_dates, y_hat, lower, upper = get_projected_cases(dates, cases)\n",
    "    assert len(lower) == 13\n",
    "    assert len(lower) == len(upper)\n",
    "    assert len(lower) == len(n_dates)\n",
    "    assert len(y_hat) == len(lower)\n",
    "    p = figure(x_axis_type = 'datetime')\n",
    "    p.line(x = dates, y = cases)\n",
    "    p.line(x = n_dates, y = y_hat)\n",
    "    p.line(x = n_dates, y =  upper, color = 'red')\n",
    "    p.line(x =  n_dates, y = lower, color = 'green')\n",
    "\n",
    "\n",
    "    show(p)\n",
    "\n",
    "test_get_projected_cases()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "def make_poisson_data(dates, cases):\n",
    "    raise NotImplementedError('')\n",
    "\n",
    "    assert len(dates) == len(cases)\n",
    "    #n_dates, y_hat, lower, upper = get_projected_cases(dates, cases)\n",
    "    med = get_poisson_for_all_days(\n",
    "        dates, cases)\n",
    "    return med\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_test_dates():\n",
    "    return [   datetime.datetime(2020, 7, 30, 0, 0),\n",
    "    datetime.datetime(2020, 7, 31, 0, 0),\n",
    "    datetime.datetime(2020, 8, 1, 0, 0),\n",
    "    datetime.datetime(2020, 8, 2, 0, 0),\n",
    "    datetime.datetime(2020, 8, 3, 0, 0),\n",
    "    datetime.datetime(2020, 8, 4, 0, 0),\n",
    "    datetime.datetime(2020, 8, 5, 0, 0),\n",
    "    datetime.datetime(2020, 8, 6, 0, 0),\n",
    "    datetime.datetime(2020, 8, 7, 0, 0),\n",
    "    datetime.datetime(2020, 8, 8, 0, 0),\n",
    "    datetime.datetime(2020, 8, 9, 0, 0),\n",
    "    datetime.datetime(2020, 8, 10, 0, 0),\n",
    "    datetime.datetime(2020, 8, 11, 0, 0),\n",
    "    datetime.datetime(2020, 8, 12, 0, 0),\n",
    "    datetime.datetime(2020, 8, 13, 0, 0),\n",
    "    datetime.datetime(2020, 8, 14, 0, 0),\n",
    "    datetime.datetime(2020, 8, 15, 0, 0),\n",
    "    datetime.datetime(2020, 8, 16, 0, 0),\n",
    "    datetime.datetime(2020, 8, 17, 0, 0),\n",
    "    datetime.datetime(2020, 8, 18, 0, 0),\n",
    "    datetime.datetime(2020, 8, 19, 0, 0),\n",
    "    datetime.datetime(2020, 8, 20, 0, 0),\n",
    "    datetime.datetime(2020, 8, 21, 0, 0),\n",
    "    datetime.datetime(2020, 8, 22, 0, 0),\n",
    "    datetime.datetime(2020, 8, 23, 0, 0),\n",
    "    datetime.datetime(2020, 8, 24, 0, 0),\n",
    "    datetime.datetime(2020, 8, 25, 0, 0),\n",
    "    datetime.datetime(2020, 8, 26, 0, 0),\n",
    "    datetime.datetime(2020, 8, 27, 0, 0),\n",
    "    datetime.datetime(2020, 8, 28, 0, 0),\n",
    "    datetime.datetime(2020, 8, 29, 0, 0),\n",
    "    datetime.datetime(2020, 8, 30, 0, 0),\n",
    "    datetime.datetime(2020, 8, 31, 0, 0),\n",
    "    datetime.datetime(2020, 9, 1, 0, 0),\n",
    "    datetime.datetime(2020, 9, 2, 0, 0),\n",
    "    datetime.datetime(2020, 9, 3, 0, 0),\n",
    "    datetime.datetime(2020, 9, 4, 0, 0),\n",
    "    datetime.datetime(2020, 9, 5, 0, 0),\n",
    "    datetime.datetime(2020, 9, 6, 0, 0),\n",
    "    datetime.datetime(2020, 9, 7, 0, 0)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_test_cases():\n",
    "    return [160, 158, 202, 111, 124, 145, 167, 192, 134, 200, 129, \n",
    "            148, 81, 149, 225, 136, 174, 129, 181, 165, 141, 183, 105, 152, 108, \n",
    "            146, 53, 172, 128, 184, 119, 74, 111, 46, 108, 96, 158, 92, 99, 56]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_lin_vals(cases):\n",
    "    x = range(len(cases))\n",
    "    X = list(zip(*[x]))\n",
    "    xm = sm.add_constant(X)\n",
    "    model = sm.OLS(cases, xm) \n",
    "    result = model.fit()\n",
    "    predictions = result.get_prediction(xm)\n",
    "    print(result.pvalues[1])\n",
    "\n",
    "    pass"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "    <div class=\"bk-root\">\n",
       "        <a href=\"https://bokeh.org\" target=\"_blank\" class=\"bk-logo bk-logo-small bk-logo-notebook\"></a>\n",
       "        <span id=\"1002\">Loading BokehJS ...</span>\n",
       "    </div>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/javascript": [
       "\n",
       "(function(root) {\n",
       "  function now() {\n",
       "    return new Date();\n",
       "  }\n",
       "\n",
       "  var force = true;\n",
       "\n",
       "  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n",
       "    root._bokeh_onload_callbacks = [];\n",
       "    root._bokeh_is_loading = undefined;\n",
       "  }\n",
       "\n",
       "  var JS_MIME_TYPE = 'application/javascript';\n",
       "  var HTML_MIME_TYPE = 'text/html';\n",
       "  var EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n",
       "  var CLASS_NAME = 'output_bokeh rendered_html';\n",
       "\n",
       "  /**\n",
       "   * Render data to the DOM node\n",
       "   */\n",
       "  function render(props, node) {\n",
       "    var script = document.createElement(\"script\");\n",
       "    node.appendChild(script);\n",
       "  }\n",
       "\n",
       "  /**\n",
       "   * Handle when an output is cleared or removed\n",
       "   */\n",
       "  function handleClearOutput(event, handle) {\n",
       "    var cell = handle.cell;\n",
       "\n",
       "    var id = cell.output_area._bokeh_element_id;\n",
       "    var server_id = cell.output_area._bokeh_server_id;\n",
       "    // Clean up Bokeh references\n",
       "    if (id != null && id in Bokeh.index) {\n",
       "      Bokeh.index[id].model.document.clear();\n",
       "      delete Bokeh.index[id];\n",
       "    }\n",
       "\n",
       "    if (server_id !== undefined) {\n",
       "      // Clean up Bokeh references\n",
       "      var cmd = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n",
       "      cell.notebook.kernel.execute(cmd, {\n",
       "        iopub: {\n",
       "          output: function(msg) {\n",
       "            var id = msg.content.text.trim();\n",
       "            if (id in Bokeh.index) {\n",
       "              Bokeh.index[id].model.document.clear();\n",
       "              delete Bokeh.index[id];\n",
       "            }\n",
       "          }\n",
       "        }\n",
       "      });\n",
       "      // Destroy server and session\n",
       "      var cmd = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n",
       "      cell.notebook.kernel.execute(cmd);\n",
       "    }\n",
       "  }\n",
       "\n",
       "  /**\n",
       "   * Handle when a new output is added\n",
       "   */\n",
       "  function handleAddOutput(event, handle) {\n",
       "    var output_area = handle.output_area;\n",
       "    var output = handle.output;\n",
       "\n",
       "    // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n",
       "    if ((output.output_type != \"display_data\") || (!output.data.hasOwnProperty(EXEC_MIME_TYPE))) {\n",
       "      return\n",
       "    }\n",
       "\n",
       "    var toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n",
       "\n",
       "    if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n",
       "      toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n",
       "      // store reference to embed id on output_area\n",
       "      output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n",
       "    }\n",
       "    if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n",
       "      var bk_div = document.createElement(\"div\");\n",
       "      bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n",
       "      var script_attrs = bk_div.children[0].attributes;\n",
       "      for (var i = 0; i < script_attrs.length; i++) {\n",
       "        toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n",
       "        toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n",
       "      }\n",
       "      // store reference to server id on output_area\n",
       "      output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n",
       "    }\n",
       "  }\n",
       "\n",
       "  function register_renderer(events, OutputArea) {\n",
       "\n",
       "    function append_mime(data, metadata, element) {\n",
       "      // create a DOM node to render to\n",
       "      var toinsert = this.create_output_subarea(\n",
       "        metadata,\n",
       "        CLASS_NAME,\n",
       "        EXEC_MIME_TYPE\n",
       "      );\n",
       "      this.keyboard_manager.register_events(toinsert);\n",
       "      // Render to node\n",
       "      var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n",
       "      render(props, toinsert[toinsert.length - 1]);\n",
       "      element.append(toinsert);\n",
       "      return toinsert\n",
       "    }\n",
       "\n",
       "    /* Handle when an output is cleared or removed */\n",
       "    events.on('clear_output.CodeCell', handleClearOutput);\n",
       "    events.on('delete.Cell', handleClearOutput);\n",
       "\n",
       "    /* Handle when a new output is added */\n",
       "    events.on('output_added.OutputArea', handleAddOutput);\n",
       "\n",
       "    /**\n",
       "     * Register the mime type and append_mime function with output_area\n",
       "     */\n",
       "    OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n",
       "      /* Is output safe? */\n",
       "      safe: true,\n",
       "      /* Index of renderer in `output_area.display_order` */\n",
       "      index: 0\n",
       "    });\n",
       "  }\n",
       "\n",
       "  // register the mime type if in Jupyter Notebook environment and previously unregistered\n",
       "  if (root.Jupyter !== undefined) {\n",
       "    var events = require('base/js/events');\n",
       "    var OutputArea = require('notebook/js/outputarea').OutputArea;\n",
       "\n",
       "    if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n",
       "      register_renderer(events, OutputArea);\n",
       "    }\n",
       "  }\n",
       "\n",
       "  \n",
       "  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n",
       "    root._bokeh_timeout = Date.now() + 5000;\n",
       "    root._bokeh_failed_load = false;\n",
       "  }\n",
       "\n",
       "  var NB_LOAD_WARNING = {'data': {'text/html':\n",
       "     \"<div style='background-color: #fdd'>\\n\"+\n",
       "     \"<p>\\n\"+\n",
       "     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n",
       "     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n",
       "     \"</p>\\n\"+\n",
       "     \"<ul>\\n\"+\n",
       "     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n",
       "     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n",
       "     \"</ul>\\n\"+\n",
       "     \"<code>\\n\"+\n",
       "     \"from bokeh.resources import INLINE\\n\"+\n",
       "     \"output_notebook(resources=INLINE)\\n\"+\n",
       "     \"</code>\\n\"+\n",
       "     \"</div>\"}};\n",
       "\n",
       "  function display_loaded() {\n",
       "    var el = document.getElementById(\"1002\");\n",
       "    if (el != null) {\n",
       "      el.textContent = \"BokehJS is loading...\";\n",
       "    }\n",
       "    if (root.Bokeh !== undefined) {\n",
       "      if (el != null) {\n",
       "        el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n",
       "      }\n",
       "    } else if (Date.now() < root._bokeh_timeout) {\n",
       "      setTimeout(display_loaded, 100)\n",
       "    }\n",
       "  }\n",
       "\n",
       "\n",
       "  function run_callbacks() {\n",
       "    try {\n",
       "      root._bokeh_onload_callbacks.forEach(function(callback) {\n",
       "        if (callback != null)\n",
       "          callback();\n",
       "      });\n",
       "    } finally {\n",
       "      delete root._bokeh_onload_callbacks\n",
       "    }\n",
       "    console.debug(\"Bokeh: all callbacks have finished\");\n",
       "  }\n",
       "\n",
       "  function load_libs(css_urls, js_urls, callback) {\n",
       "    if (css_urls == null) css_urls = [];\n",
       "    if (js_urls == null) js_urls = [];\n",
       "\n",
       "    root._bokeh_onload_callbacks.push(callback);\n",
       "    if (root._bokeh_is_loading > 0) {\n",
       "      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n",
       "      return null;\n",
       "    }\n",
       "    if (js_urls == null || js_urls.length === 0) {\n",
       "      run_callbacks();\n",
       "      return null;\n",
       "    }\n",
       "    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n",
       "    root._bokeh_is_loading = css_urls.length + js_urls.length;\n",
       "\n",
       "    function on_load() {\n",
       "      root._bokeh_is_loading--;\n",
       "      if (root._bokeh_is_loading === 0) {\n",
       "        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n",
       "        run_callbacks()\n",
       "      }\n",
       "    }\n",
       "\n",
       "    function on_error() {\n",
       "      console.error(\"failed to load \" + url);\n",
       "    }\n",
       "\n",
       "    for (var i = 0; i < css_urls.length; i++) {\n",
       "      var url = css_urls[i];\n",
       "      const element = document.createElement(\"link\");\n",
       "      element.onload = on_load;\n",
       "      element.onerror = on_error;\n",
       "      element.rel = \"stylesheet\";\n",
       "      element.type = \"text/css\";\n",
       "      element.href = url;\n",
       "      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n",
       "      document.body.appendChild(element);\n",
       "    }\n",
       "\n",
       "    const hashes = {\"https://cdn.bokeh.org/bokeh/release/bokeh-2.0.2.min.js\": \"ufR9RFnRs6lniiaFvtJziE0YeidtAgBRH6ux2oUItHw5WTvE1zuk9uzhUU/FJXDp\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.0.2.min.js\": \"8QM/PGWBT+IssZuRcDcjzwIh1mkOmJSoNMmyYDZbCfXJg3Ap1lEvdVgFuSAwhb/J\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.0.2.min.js\": \"Jm8cH3Rg0P6UeZhVY5cLy1WzKajUT9KImCY+76hEqrcJt59/d8GPvFHjCkYgnSIn\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-2.0.2.min.js\": \"Ozhzj+SI7ywm74aOI/UajcWz+C0NjsPunEVyVIrxzYkB+jA+2tUw8x5xJCbVtK5I\"};\n",
       "\n",
       "    for (var i = 0; i < js_urls.length; i++) {\n",
       "      var url = js_urls[i];\n",
       "      var element = document.createElement('script');\n",
       "      element.onload = on_load;\n",
       "      element.onerror = on_error;\n",
       "      element.async = false;\n",
       "      element.src = url;\n",
       "      if (url in hashes) {\n",
       "        element.crossOrigin = \"anonymous\";\n",
       "        element.integrity = \"sha384-\" + hashes[url];\n",
       "      }\n",
       "      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n",
       "      document.head.appendChild(element);\n",
       "    }\n",
       "  };\n",
       "\n",
       "  function inject_raw_css(css) {\n",
       "    const element = document.createElement(\"style\");\n",
       "    element.appendChild(document.createTextNode(css));\n",
       "    document.body.appendChild(element);\n",
       "  }\n",
       "\n",
       "  \n",
       "  var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.0.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.0.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.0.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-2.0.2.min.js\"];\n",
       "  var css_urls = [];\n",
       "  \n",
       "\n",
       "  var inline_js = [\n",
       "    function(Bokeh) {\n",
       "      Bokeh.set_log_level(\"info\");\n",
       "    },\n",
       "    function(Bokeh) {\n",
       "    \n",
       "    \n",
       "    }\n",
       "  ];\n",
       "\n",
       "  function run_inline_js() {\n",
       "    \n",
       "    if (root.Bokeh !== undefined || force === true) {\n",
       "      \n",
       "    for (var i = 0; i < inline_js.length; i++) {\n",
       "      inline_js[i].call(root, root.Bokeh);\n",
       "    }\n",
       "    if (force === true) {\n",
       "        display_loaded();\n",
       "      }} else if (Date.now() < root._bokeh_timeout) {\n",
       "      setTimeout(run_inline_js, 100);\n",
       "    } else if (!root._bokeh_failed_load) {\n",
       "      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n",
       "      root._bokeh_failed_load = true;\n",
       "    } else if (force !== true) {\n",
       "      var cell = $(document.getElementById(\"1002\")).parents('.cell').data().cell;\n",
       "      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n",
       "    }\n",
       "\n",
       "  }\n",
       "\n",
       "  if (root._bokeh_is_loading === 0) {\n",
       "    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
       "    run_inline_js();\n",
       "  } else {\n",
       "    load_libs(css_urls, js_urls, function() {\n",
       "      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n",
       "      run_inline_js();\n",
       "    });\n",
       "  }\n",
       "}(window));"
      ],
      "application/vnd.bokehjs_load.v0+json": "\n(function(root) {\n  function now() {\n    return new Date();\n  }\n\n  var force = true;\n\n  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n    root._bokeh_onload_callbacks = [];\n    root._bokeh_is_loading = undefined;\n  }\n\n  \n\n  \n  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n    root._bokeh_timeout = Date.now() + 5000;\n    root._bokeh_failed_load = false;\n  }\n\n  var NB_LOAD_WARNING = {'data': {'text/html':\n     \"<div style='background-color: #fdd'>\\n\"+\n     \"<p>\\n\"+\n     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n     \"</p>\\n\"+\n     \"<ul>\\n\"+\n     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n     \"</ul>\\n\"+\n     \"<code>\\n\"+\n     \"from bokeh.resources import INLINE\\n\"+\n     \"output_notebook(resources=INLINE)\\n\"+\n     \"</code>\\n\"+\n     \"</div>\"}};\n\n  function display_loaded() {\n    var el = document.getElementById(\"1002\");\n    if (el != null) {\n      el.textContent = \"BokehJS is loading...\";\n    }\n    if (root.Bokeh !== undefined) {\n      if (el != null) {\n        el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n      }\n    } else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(display_loaded, 100)\n    }\n  }\n\n\n  function run_callbacks() {\n    try {\n      root._bokeh_onload_callbacks.forEach(function(callback) {\n        if (callback != null)\n          callback();\n      });\n    } finally {\n      delete root._bokeh_onload_callbacks\n    }\n    console.debug(\"Bokeh: all callbacks have finished\");\n  }\n\n  function load_libs(css_urls, js_urls, callback) {\n    if (css_urls == null) css_urls = [];\n    if (js_urls == null) js_urls = [];\n\n    root._bokeh_onload_callbacks.push(callback);\n    if (root._bokeh_is_loading > 0) {\n      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n      return null;\n    }\n    if (js_urls == null || js_urls.length === 0) {\n      run_callbacks();\n      return null;\n    }\n    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n    root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n    function on_load() {\n      root._bokeh_is_loading--;\n      if (root._bokeh_is_loading === 0) {\n        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n        run_callbacks()\n      }\n    }\n\n    function on_error() {\n      console.error(\"failed to load \" + url);\n    }\n\n    for (var i = 0; i < css_urls.length; i++) {\n      var url = css_urls[i];\n      const element = document.createElement(\"link\");\n      element.onload = on_load;\n      element.onerror = on_error;\n      element.rel = \"stylesheet\";\n      element.type = \"text/css\";\n      element.href = url;\n      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n      document.body.appendChild(element);\n    }\n\n    const hashes = {\"https://cdn.bokeh.org/bokeh/release/bokeh-2.0.2.min.js\": \"ufR9RFnRs6lniiaFvtJziE0YeidtAgBRH6ux2oUItHw5WTvE1zuk9uzhUU/FJXDp\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.0.2.min.js\": \"8QM/PGWBT+IssZuRcDcjzwIh1mkOmJSoNMmyYDZbCfXJg3Ap1lEvdVgFuSAwhb/J\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.0.2.min.js\": \"Jm8cH3Rg0P6UeZhVY5cLy1WzKajUT9KImCY+76hEqrcJt59/d8GPvFHjCkYgnSIn\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-2.0.2.min.js\": \"Ozhzj+SI7ywm74aOI/UajcWz+C0NjsPunEVyVIrxzYkB+jA+2tUw8x5xJCbVtK5I\"};\n\n    for (var i = 0; i < js_urls.length; i++) {\n      var url = js_urls[i];\n      var element = document.createElement('script');\n      element.onload = on_load;\n      element.onerror = on_error;\n      element.async = false;\n      element.src = url;\n      if (url in hashes) {\n        element.crossOrigin = \"anonymous\";\n        element.integrity = \"sha384-\" + hashes[url];\n      }\n      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n      document.head.appendChild(element);\n    }\n  };\n\n  function inject_raw_css(css) {\n    const element = document.createElement(\"style\");\n    element.appendChild(document.createTextNode(css));\n    document.body.appendChild(element);\n  }\n\n  \n  var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.0.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.0.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.0.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-2.0.2.min.js\"];\n  var css_urls = [];\n  \n\n  var inline_js = [\n    function(Bokeh) {\n      Bokeh.set_log_level(\"info\");\n    },\n    function(Bokeh) {\n    \n    \n    }\n  ];\n\n  function run_inline_js() {\n    \n    if (root.Bokeh !== undefined || force === true) {\n      \n    for (var i = 0; i < inline_js.length; i++) {\n      inline_js[i].call(root, root.Bokeh);\n    }\n    if (force === true) {\n        display_loaded();\n      }} else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(run_inline_js, 100);\n    } else if (!root._bokeh_failed_load) {\n      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n      root._bokeh_failed_load = true;\n    } else if (force !== true) {\n      var cell = $(document.getElementById(\"1002\")).parents('.cell').data().cell;\n      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n    }\n\n  }\n\n  if (root._bokeh_is_loading === 0) {\n    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n    run_inline_js();\n  } else {\n    load_libs(css_urls, js_urls, function() {\n      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n      run_inline_js();\n    });\n  }\n}(window));"
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "\n",
       "\n",
       "\n",
       "\n",
       "\n",
       "\n",
       "  <div class=\"bk-root\" id=\"e61bb287-5db7-4b5a-9263-3ba073fe4251\" data-root-id=\"1003\"></div>\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/javascript": [
       "(function(root) {\n",
       "  function embed_document(root) {\n",
       "    \n",
       "  var docs_json = 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       "  var render_items = [{\"docid\":\"10c02b2b-5808-4f51-8f8d-d10e563f7668\",\"root_ids\":[\"1003\"],\"roots\":{\"1003\":\"e61bb287-5db7-4b5a-9263-3ba073fe4251\"}}];\n",
       "  root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n",
       "\n",
       "  }\n",
       "  if (root.Bokeh !== undefined) {\n",
       "    embed_document(root);\n",
       "  } else {\n",
       "    var attempts = 0;\n",
       "    var timer = setInterval(function(root) {\n",
       "      if (root.Bokeh !== undefined) {\n",
       "        clearInterval(timer);\n",
       "        embed_document(root);\n",
       "      } else {\n",
       "        attempts++;\n",
       "        if (attempts > 100) {\n",
       "          clearInterval(timer);\n",
       "          console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n",
       "        }\n",
       "      }\n",
       "    }, 10, root)\n",
       "  }\n",
       "})(window);"
      ],
      "application/vnd.bokehjs_exec.v0+json": ""
     },
     "metadata": {
      "application/vnd.bokehjs_exec.v0+json": {
       "id": "1003"
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "output_notebook()\n",
    "def test_all():\n",
    "    cases = get_test_cases()\n",
    "    dates = get_test_dates()\n",
    "    main = get_poisson_for_all_days(\n",
    "        dates, cases)[0:-14]\n",
    "    #get_lin_vals([x[1] for x in main][-7:])\n",
    "    \n",
    "    p = figure(x_axis_type = 'datetime')\n",
    "    p.line(x = dates, y = cases )\n",
    "    p.line(x = [x[0] for x in main], y = [x[1] for x in main], color ='red')\n",
    "    show(p)\n",
    "   \n",
    "    \n",
    "test_all()"
   ]
  }
 ],
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