{
 "cells": [
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# T1 - Getting Started "
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To install just type `pip install emodlib`.  If it worked, you should be able to call `import emodlib`.\n",
    "\n",
    "In this first tutorial, we'll introduce the basics of:\n",
    "\n",
    "- Setting parameters\n",
    "- Simulating an infected individual\n",
    "- Inspecting individual model state"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Defining simulation parameters"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": "First let's create a configuration instance with default malaria intra-host model parameters and look at them..."
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": "from emodlib.malaria import IntrahostComponent, create_config\n\nconfig = create_config()\nprint(config.yaml)"
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": "We can create a new configuration with modifications to arbitrary parameters (on top of existing defaults) by passing a dictionary to `create_config` function..."
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": "config2 = create_config({'Run_Number': 6789, 'susceptibility_params': {'Antibody_CSP_Decay_Days': 99}})\nprint(config2.yaml)"
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": "Each config instance is independent. Note that `config` above still has its original defaults (Run_Number=12345), while `config2` has our modified values. Creating a new config always starts from defaults..."
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": "config3 = create_config({'Run_Number': 99999})\nprint(f\"config.random_seed = {config.random_seed}\")\nprint(f\"config2.random_seed = {config2.random_seed}\")\nprint(f\"config3.random_seed = {config3.random_seed}\")"
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Simulating an infection in a naive host"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": "Now let's create a naive host using one of our configs..."
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": "ic = IntrahostComponent.create(config)"
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Let's subject our naive host to an infectious challenge..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "ic.challenge()"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now let's define a little helper function to print a descriptive line for the model state..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "def describe(c, t=None):\n",
    "    \"\"\" Helper function to print a description of the intra-host model state \"\"\"\n",
    "    s = 't=%d: ' % t if t is not None else ''\n",
    "    s += '(asexual, mature gametocyte, fever, infectiousness) = (%0.2f, %0.3f, %0.1f %0.2f)' % \\\n",
    "        (c.parasite_density, c.gametocyte_density, c.fever_temperature, c.infectiousness)\n",
    "    print(s)"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Let's do enough timestep updates to see the emergence of asexual-stage parasites from the liver, the onset of fever with high parasite density, and the progression of differentiated gametocytes to mature gametocytes..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "t=0: (asexual, mature gametocyte, fever, infectiousness) = (0.00, 0.000, 37.0 0.00)\n",
      "t=1: (asexual, mature gametocyte, fever, infectiousness) = (0.00, 0.000, 37.0 0.00)\n",
      "t=2: (asexual, mature gametocyte, fever, infectiousness) = (0.00, 0.000, 37.0 0.00)\n",
      "t=3: (asexual, mature gametocyte, fever, infectiousness) = (0.00, 0.000, 37.0 0.00)\n",
      "t=4: (asexual, mature gametocyte, fever, infectiousness) = (0.00, 0.000, 37.0 0.00)\n",
      "t=5: (asexual, mature gametocyte, fever, infectiousness) = (0.00, 0.000, 37.0 0.00)\n",
      "t=6: (asexual, mature gametocyte, fever, infectiousness) = (0.00, 0.000, 37.0 0.00)\n",
      "t=7: (asexual, mature gametocyte, fever, infectiousness) = (0.00, 0.000, 37.0 0.00)\n",
      "t=8: (asexual, mature gametocyte, fever, infectiousness) = (0.05, 0.000, 37.0 0.00)\n",
      "t=9: (asexual, mature gametocyte, fever, infectiousness) = (0.05, 0.000, 37.0 0.00)\n",
      "t=10: (asexual, mature gametocyte, fever, infectiousness) = (0.71, 0.000, 37.0 0.00)\n",
      "t=11: (asexual, mature gametocyte, fever, infectiousness) = (0.71, 0.000, 37.0 0.00)\n",
      "t=12: (asexual, mature gametocyte, fever, infectiousness) = (10.61, 0.000, 37.0 0.00)\n",
      "t=13: (asexual, mature gametocyte, fever, infectiousness) = (10.61, 0.000, 37.0 0.00)\n",
      "t=14: (asexual, mature gametocyte, fever, infectiousness) = (158.18, 0.000, 37.0 0.00)\n",
      "t=15: (asexual, mature gametocyte, fever, infectiousness) = (158.18, 0.000, 37.1 0.00)\n",
      "t=16: (asexual, mature gametocyte, fever, infectiousness) = (2359.20, 0.000, 37.1 0.00)\n",
      "t=17: (asexual, mature gametocyte, fever, infectiousness) = (2359.20, 0.000, 38.1 0.00)\n",
      "t=18: (asexual, mature gametocyte, fever, infectiousness) = (35184.98, 0.000, 38.1 0.00)\n",
      "t=19: (asexual, mature gametocyte, fever, infectiousness) = (6473.13, 0.000, 43.2 0.00)\n",
      "t=20: (asexual, mature gametocyte, fever, infectiousness) = (17369.77, 0.002, 41.9 0.00)\n",
      "t=21: (asexual, mature gametocyte, fever, infectiousness) = (2538.02, 0.002, 44.6 0.00)\n",
      "t=22: (asexual, mature gametocyte, fever, infectiousness) = (12189.47, 0.031, 37.0 0.00)\n",
      "t=23: (asexual, mature gametocyte, fever, infectiousness) = (2932.88, 0.023, 37.6 0.00)\n",
      "t=24: (asexual, mature gametocyte, fever, infectiousness) = (9026.20, 0.462, 37.0 0.00)\n",
      "t=25: (asexual, mature gametocyte, fever, infectiousness) = (1683.18, 0.350, 37.7 0.00)\n",
      "t=26: (asexual, mature gametocyte, fever, infectiousness) = (4068.65, 6.887, 37.0 0.03)\n",
      "t=27: (asexual, mature gametocyte, fever, infectiousness) = (574.03, 5.221, 37.4 0.00)\n",
      "t=28: (asexual, mature gametocyte, fever, infectiousness) = (1090.37, 102.722, 37.0 0.34)\n",
      "t=29: (asexual, mature gametocyte, fever, infectiousness) = (131.97, 77.868, 37.1 0.09)\n"
     ]
    }
   ],
   "source": [
    "for t in range(30):\n",
    "    ic.update(dt=1)\n",
    "    describe(ic, t)"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "And finally treat the individual and see their infections are now gone...\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(asexual, mature gametocyte, fever, infectiousness) = (0.00, 0.000, 37.1 0.00)\n"
     ]
    }
   ],
   "source": [
    "ic.treat()\n",
    "describe(ic)"
   ]
  }
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