{
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[-1 -1 -1 -1 -1]\n"
     ]
    }
   ],
   "source": [
    "\n",
    "import numpy\n",
    "\n",
    "\n",
    "# Run the nanochip dispersal hidden markov model n times starting at state s\n",
    "def run_HMM(n,s):\n",
    "    \n",
    "    \n",
    "    symbols = []\n",
    "    \n",
    "    for i in range(n):\n",
    "        \n",
    "\n",
    "        # Emit the symbol\n",
    "        randomNum = numpy.random.uniform()\n",
    "        if s == 0:\n",
    "            \n",
    "            \n",
    "            symbol = -1\n",
    "            ### TODO:  select a symbol (0 or 1) to emit when the state is 0\n",
    "            \n",
    "            ###\n",
    "            symbols.append(symbol)\n",
    "            \n",
    "        elif s == 1:\n",
    "            \n",
    "            symbol = -1\n",
    "            ### TODO:  select a symbol (0 or 1) to emit when the state is 1\n",
    "            \n",
    "            ###\n",
    "            symbols.append(symbol)\n",
    "            \n",
    "            \n",
    "        # Choose the next state\n",
    "        randomNum = numpy.random.uniform()\n",
    "        if s == 0:\n",
    "            \n",
    "            newState = 0\n",
    "            ### TODO: select the next state when the current state is 0\n",
    "            \n",
    "            ###\n",
    "            s = newState\n",
    "        \n",
    "        elif s == 1:\n",
    "            \n",
    "            newState = 0\n",
    "            ### TODO: select the next state when the current state is 1\n",
    "            \n",
    "            ###\n",
    "            s = newState\n",
    "        \n",
    "\n",
    "    return numpy.array(symbols)\n",
    "    \n",
    "    \n",
    "\n",
    "print(run_HMM(5,0))\n",
    "\n",
    "\n",
    "#proportion_murky = numpy.mean(run_HMM(10000,0))\n",
    "#print(\"At equilibrium the water is murky with probability\", proportion_murky)\n",
    "\n",
    "\n",
    "\n",
    "def run_HMM_k_times(k,n,s):\n",
    "    \n",
    "    \n",
    "    simulations = numpy.zeros([k,n])\n",
    "    \n",
    "    ### TODO: call run_HMM k times and add each simulation to the rows of 'simulations'\n",
    "        \n",
    "    return simulations\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "    \n",
    "\n"
   ]
  }
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