{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "data": { "text/markdown": [ "[Execute this notebook with Binder](https://mybinder.org/v2/gh/oscovida/binder/master?filepath=ipynb/tutorial-overview-plot_reproduction_number.ipynb)" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "%config InlineBackend.figure_formats = ['svg']\n", "import oscovida as ov\n", "import matplotlib.pyplot as plt\n", "from matplotlib.dates import DateFormatter, MONDAY, WeekdayLocator, DayLocator\n", "\n", "ov.display_binder_link(\"tutorial-overview-plot_reproduction_number.ipynb\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Reproduction number\n", "\n", "The forth and the fifth graphs returned by the `overview` function \n", "(see the [overview](tutorial-overview-graphs.nbdata.html)\n", "and the explanation of the [observables](tutorial-observables.nbdata.html))\n", "show the R-value and the growth factor for COVID cases and deaths respectively. Here we show how it is created internally.\n", "\n", "(Find more on reproduction number [here](r-value.html).)\n", "\n", "As earlier, we retrieve cases and deaths data, create an empty graph and populate the graph with the number calculated by a function `plot_reproduction_number`.\n", "\n", "This function has the following parameters:\n", "* `ax` — an axis object;\n", "* `series` — the data source;\n", "* `labels` — a pair of strings: region label and identifier of cases or deaths;\n", "* `color_g` and `color_R` — two colors, here we use the scheme `CN` where `N` is a number digit, but one may use [any colormap](https://matplotlib.org/tutorials/colors/colormaps.html)." ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "image/svg+xml": [ "\n", "\n", "\n", "\n" ], "text/plain": [ "

" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "fig, ax = plt.subplots(); # create an empty graph\n", "country = \"US\"\n", "region = \"California\"\n", "\n", "cases, deaths = ov.get_country_data(country, region) # get actual data\n", "\n", "# pass the data to the plotting function\n", "ov.plot_reproduction_number(ax=ax, series=cases, labels=(\"USA: California\",\"cases\"), color_g=\"C0\", color_R=\"C4\");\n", "ax.set_title(\"COVID Cases: R-value and Growth Factor\");\n", "\n", "# nicer X-axis formatting: put a tick every Monday\n", "ax.get_xaxis().set_major_locator(DayLocator(bymonthday=(1))) \n", "ax.get_xaxis().set_major_formatter(DateFormatter('%d %b'))\n", "\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Other tutorials\n", "\n", "You can find [more tutorials here](tag-tutorial.html)." ] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.7.7" } }, "nbformat": 4, "nbformat_minor": 4 }