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   "source": [
    "# T1 - Getting started\n",
    "\n",
    "Installing and getting started with Covasim is quite simple. \n",
    "\n",
    "To install, just type `pip install covasim`. If it worked, you should be able to import Covasim with `import covasim as cv`.\n",
    "\n",
    "The basic design philosophy of Covasim is: **common tasks should be simple**. For example:\n",
    "\n",
    "- Defining parameters\n",
    "- Running a simulation\n",
    "- Plotting results\n",
    "\n",
    "This tutorial walks you through how to do these things."
   ]
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   "source": [
    "<div class=\"alert alert-info\">\n",
    "    \n",
    "Click [here](https://mybinder.org/v2/gh/institutefordiseasemodeling/covasim/HEAD?urlpath=lab%2Ftree%2Fdocs%2Ftutorials%2Ftut_intro.ipynb) to open an interactive version of this notebook.\n",
    "    \n",
    "</div>"
   ]
  },
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   "metadata": {},
   "source": [
    "## Hello world\n",
    "\n",
    "To create, run, and plot a sim with default options is just:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import covasim as cv\n",
    "\n",
    "sim = cv.Sim()\n",
    "sim.run()\n",
    "fig = sim.plot()"
   ]
  },
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   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Defining parameters and running simulations\n",
    "\n",
    "Parameters are defined as a dictionary. The most common parameters to modify are the population size, the initial number of people infected, and the start and end dates of the simulation. We can define those as:"
   ]
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   "source": [
    "pars = dict(\n",
    "    pop_size = 50e3,\n",
    "    pop_infected = 100,\n",
    "    start_day = '2020-04-01',\n",
    "    end_day = '2020-06-01',\n",
    ")"
   ]
  },
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   "cell_type": "markdown",
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   "source": [
    "Running a simulation is pretty easy. In fact, running a sim with the parameters we defined above is just:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "sim = cv.Sim(pars)\n",
    "sim.run()"
   ]
  },
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   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This will generate a results dictionary `sim.results`. For example, the number of new infections per day is `sim.results['new_infections']`.\n",
    "\n",
    "Rather than creating a parameter dictionary, any valid parameter can also be passed to the sim directly. For example, exactly equivalent to the above is:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "sim = cv.Sim(pop_size=50e3, pop_infected=100, start_day='2020-04-01', end_day='2020-06-01')\n",
    "sim.run()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "You can mix and match too – pass in a parameter dictionary with default options, and then include other parameters as keywords (including overrides; keyword arguments take precedence). For example:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "sim = cv.Sim(pars, pop_infected=10) # Use parameters defined above, except start with 10 infected people\n",
    "sim.run()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Plotting results\n",
    "\n",
    "As you saw above, plotting the results of a simulation is rather easy too:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "fig = sim.plot()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Full usage example\n",
    "\n",
    "Many of the details of this example will be explained in later tutorials, but to give you a taste, here's an example of how you would run two simulations to determine the impact of a custom intervention aimed at protecting the elderly."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import covasim as cv\n",
    "\n",
    "# Custom intervention -- see Tutorial 5\n",
    "def protect_elderly(sim):\n",
    "    if sim.t == sim.day('2020-04-01'):\n",
    "        elderly = sim.people.age>70\n",
    "        sim.people.rel_sus[elderly] = 0.0\n",
    "\n",
    "pars = dict(\n",
    "    pop_type = 'hybrid', # Use a more realistic population model\n",
    "    location = 'japan', # Use population characteristics for Japan\n",
    "    pop_size = 50e3, # Have 50,000 people total in the population\n",
    "    pop_infected = 100, # Start with 100 infected people\n",
    "    n_days = 90, # Run the simulation for 90 days\n",
    "    verbose = 0, # Do not print any output\n",
    ")\n",
    "\n",
    "# Running with multisims -- see Tutorial 3\n",
    "s1 = cv.Sim(pars, label='Default')\n",
    "s2 = cv.Sim(pars, interventions=protect_elderly, label='Protect the elderly')\n",
    "msim = cv.MultiSim([s1, s2])\n",
    "msim.run()\n",
    "fig = msim.plot(['cum_deaths', 'cum_infections'])"
   ]
  }
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