{
"nbformat": 4,
"nbformat_minor": 0,
"metadata": {
"accelerator": "GPU",
"colab": {
"name": "Israel_changing_point.ipynb",
"provenance": [],
"collapsed_sections": [],
"toc_visible": true
},
"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": "3.6.10"
}
},
"cells": [
{
"cell_type": "markdown",
"metadata": {
"id": "kqXl71t9suiG"
},
"source": [
"# Estimating the Date of COVID-19 Changes\n",
"\n",
"https://nbviewer.jupyter.org/github/jramkiss/jramkiss.github.io/blob/master/_posts/notebooks/covid19-changes.ipynb "
]
},
{
"cell_type": "code",
"metadata": {
"id": "gFnvD8OysuiI",
"colab": {
"base_uri": "https://localhost:8080/"
},
"outputId": "bcece40f-0a99-4836-a32e-0f29e21a3eec"
},
"source": [
"import pandas as pd\n",
"import numpy as np\n",
"\n",
"import seaborn as sns; sns.set()\n",
"import matplotlib.pyplot as plt\n",
"import matplotlib.dates as mdates\n",
"\n",
"\n",
"from sklearn.linear_model import LinearRegression\n",
"\n",
"from scipy import stats\n",
"import statsmodels.api as sm\n",
"import pylab\n",
"\n",
"# from google.colab import files\n",
"# from io import StringIO\n",
"# uploaded = files.upload()\n",
"\n",
"url = 'https://raw.githubusercontent.com/assemzh/ProbProg-COVID-19/master/israel.csv'\n",
"data = pd.read_csv(url)\n",
"\n",
"data.Date = pd.to_datetime(data.Date)\n",
"\n",
"# for fancy python printing\n",
"from IPython.display import Markdown, display\n",
"def printmd(string):\n",
" display(Markdown(string))\n",
" \n",
"import warnings\n",
"warnings.filterwarnings('ignore')\n",
"\n",
"import matplotlib as mpl\n",
"mpl.rcParams['figure.dpi'] = 250"
],
"execution_count": null,
"outputs": [
{
"output_type": "stream",
"text": [
"/usr/local/lib/python3.7/dist-packages/statsmodels/tools/_testing.py:19: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead.\n",
" import pandas.util.testing as tm\n"
],
"name": "stderr"
}
]
},
{
"cell_type": "code",
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/",
"height": 204
},
"id": "kvgkeTE9yls9",
"outputId": "8d179fc1-4c45-44eb-d3d6-266625b6fb53"
},
"source": [
"\n",
"data.tail()"
],
"execution_count": null,
"outputs": [
{
"output_type": "execute_result",
"data": {
"text/html": [
"\n",
"\n",
"
\n",
" \n",
" \n",
" | \n",
" Date | \n",
" Country/Region | \n",
" Province_State | \n",
" Confirmed | \n",
" Deaths | \n",
" Recovered | \n",
" Active | \n",
" New cases | \n",
" New deaths | \n",
" New recovered | \n",
"
\n",
" \n",
" \n",
" \n",
" | 396 | \n",
" 2021-04-22 | \n",
" Israel | \n",
" NaN | \n",
" 837807.0 | \n",
" 6346.0 | \n",
" 829424.0 | \n",
" 2037.0 | \n",
" 85.0 | \n",
" 0.0 | \n",
" 272.0 | \n",
"
\n",
" \n",
" | 397 | \n",
" 2021-04-23 | \n",
" Israel | \n",
" NaN | \n",
" 837892.0 | \n",
" 6346.0 | \n",
" 829696.0 | \n",
" 1850.0 | \n",
" 82.0 | \n",
" 4.0 | \n",
" 115.0 | \n",
"
\n",
" \n",
" | 398 | \n",
" 2021-04-24 | \n",
" Israel | \n",
" NaN | \n",
" 837974.0 | \n",
" 6350.0 | \n",
" 829811.0 | \n",
" 1813.0 | \n",
" 50.0 | \n",
" 2.0 | \n",
" 172.0 | \n",
"
\n",
" \n",
" | 399 | \n",
" 2021-04-25 | \n",
" Israel | \n",
" NaN | \n",
" 838024.0 | \n",
" 6352.0 | \n",
" 829983.0 | \n",
" 1689.0 | \n",
" 83.0 | \n",
" 1.0 | \n",
" 105.0 | \n",
"
\n",
" \n",
" | 400 | \n",
" 2021-04-26 | \n",
" Israel | \n",
" NaN | \n",
" 838107.0 | \n",
" 6353.0 | \n",
" 830088.0 | \n",
" 1666.0 | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
"
\n",
" \n",
"
\n",
"
"
]
},
"metadata": {
"tags": []
}
}
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "nn_ZriL0P8Di"
},
"source": [
""
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "DnUbQCQXP_eZ"
},
"source": [
"https://www.dw.com/en/israels-clever-coronavirus-vaccination-strategy/a-56586888#:~:text=To%20date%2C%20Israel%20has%20administered,40%25%20of%20the%20country's%20population."
]
},
{
"cell_type": "code",
"metadata": {
"id": "UR0BM7TysujG"
},
"source": [
"cad_start = \"2020-12-01\" # 13 confirmed cases\n",
"cad = cad[cad.date >= cad_start].reset_index(drop = True)\n",
"cad[\"days_since_start\"] = np.arange(cad.shape[0]) + 1"
],
"execution_count": null,
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {
"id": "loi3CtjSsuoz"
},
"source": [
"## Data for Regression"
]
},
{
"cell_type": "code",
"metadata": {
"id": "Os_M7r4Tsuo4"
},
"source": [
"# variable for data to easily swap it out:\n",
"country_ = \"Israel\"\n",
"reg_data = cad.copy()"
],
"execution_count": null,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/",
"height": 204
},
"id": "3RjDFEbA91X-",
"outputId": "1c99ed59-922f-4b3b-9954-383c39bbeef9"
},
"source": [
"reg_data.head()"
],
"execution_count": null,
"outputs": [
{
"output_type": "execute_result",
"data": {
"text/html": [
"\n",
"\n",
"
\n",
" \n",
" \n",
" | \n",
" country | \n",
" date | \n",
" confirmed | \n",
" deaths | \n",
" recovered | \n",
" daily_confirmed | \n",
" days_since_start | \n",
"
\n",
" \n",
" \n",
" \n",
" | 0 | \n",
" Israel | \n",
" 2020-12-01 | \n",
" 338389.0 | \n",
" 2882.0 | \n",
" 324396.0 | \n",
" 1198.0 | \n",
" 1 | \n",
"
\n",
" \n",
" | 1 | \n",
" Israel | \n",
" 2020-12-02 | \n",
" 339968.0 | \n",
" 2886.0 | \n",
" 325255.0 | \n",
" 1579.0 | \n",
" 2 | \n",
"
\n",
" \n",
" | 2 | \n",
" Israel | \n",
" 2020-12-03 | \n",
" 341406.0 | \n",
" 2895.0 | \n",
" 326706.0 | \n",
" 1438.0 | \n",
" 3 | \n",
"
\n",
" \n",
" | 3 | \n",
" Israel | \n",
" 2020-12-04 | \n",
" 342101.0 | \n",
" 2896.0 | \n",
" 327162.0 | \n",
" 695.0 | \n",
" 4 | \n",
"
\n",
" \n",
" | 4 | \n",
" Israel | \n",
" 2020-12-05 | \n",
" 343826.0 | \n",
" 2909.0 | \n",
" 327749.0 | \n",
" 1725.0 | \n",
" 5 | \n",
"
\n",
" \n",
"
\n",
"