{ "cells": [ { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "# T2 - Infectious Challenge Time Series" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": "import numpy as np\nimport pandas as pd\nimport matplotlib.pyplot as plt\n\nfrom emodlib.malaria import IntrahostComponent, create_config" }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": "duration = 300\n\nasexuals = np.zeros(duration)\ngametocytes = np.zeros(duration)\n\nconfig = create_config()\nic = IntrahostComponent.create(config)\nic.challenge()\n\nfor t in range(duration):\n ic.update(dt=1)\n asexuals[t] = ic.parasite_density\n gametocytes[t] = ic.gametocyte_density\n\ndf = pd.DataFrame({'days': range(duration),\n 'parasite_density': asexuals,\n 'gametocyte_density': gametocytes}).set_index('days')" }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
| \n", " | parasite_density | \n", "gametocyte_density | \n", "
|---|---|---|
| days | \n", "\n", " | \n", " |
| 0 | \n", "0.000000 | \n", "0.0 | \n", "
| 1 | \n", "0.000000 | \n", "0.0 | \n", "
| 2 | \n", "0.000000 | \n", "0.0 | \n", "
| 3 | \n", "0.000000 | \n", "0.0 | \n", "
| 4 | \n", "0.000000 | \n", "0.0 | \n", "
| 5 | \n", "0.000000 | \n", "0.0 | \n", "
| 6 | \n", "0.003000 | \n", "0.0 | \n", "
| 7 | \n", "0.003000 | \n", "0.0 | \n", "
| 8 | \n", "0.047676 | \n", "0.0 | \n", "
| 9 | \n", "0.047676 | \n", "0.0 | \n", "