{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Geographically Weighted Regression (Part I): COVID 19 Incidence\n",
"\n",
"Author: Naomi W. Lazarus, PhD
\n",
"Date Created: 6-14-21\n",
"\n",
"This notebook provides the code for running a Geographically Weighted Regression (GWR) using COVID-19 incidence rates as the dependent variable and independent variables representing age and underlying conditions. It is an exploratory analysis of spatial relationships between COVID-19, age demographics, and comorbidities. It is not recommended for predictive purposes."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Notebook Outline\n",
"\n",
"- [Introduction](#Intro)\n",
" - [Install MGWR package](#Install)\n",
" - [Load required packages](#Load)\n",
"- [Load and preview data for incidence rates for peak period 1](#Peak1)\n",
" - [Preprocess data for GWR](#Data1)\n",
" - [Review GWR Results](#Results1)\n",
"- [Load and preview data for incidence rates for peak period 2](#Peak2)\n",
" - [Preprocess data for GWR](#Data2)\n",
" - [Review GWR Results](#Results2)\n",
"- [References](#Ref)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"\n",
"# Introduction\n",
"\n",
"The notebooks consists of two sections. The first uses covid-19 incidence rates for peak period 1 (03/01/20 - 04/30/20). The second uses covid-19 incidence rates for peak period 2 (06/01/20 - 07/31/20). The following links provide information on file descriptions and metadata. \n",
"\n",
"[Link to Metadata](Data_Files1/Metadata.txt)
\n",
"[Link to file descriptions](Data_Files1/Files.txt)\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"\n",
"## Install MGWR package"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"try:\n",
" from mgwr.gwr import GWR\n",
"except:\n",
" print('Installing MGWR')\n",
" ! pip install -U mgwr\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"\n",
"## Load required packages"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"import numpy as np\n",
"import pandas as pd\n",
"import libpysal as ps\n",
"from spreg import OLS\n",
"from mgwr.gwr import GWR, MGWR\n",
"from mgwr.sel_bw import Sel_BW\n",
"from mgwr.utils import compare_surfaces, truncate_colormap\n",
"import geopandas as gp\n",
"import matplotlib.pyplot as plt\n",
"import matplotlib as mpl"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"\n",
"# Load and preview data for incidence rates for peak period 1"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"covid_IR1 = gp.read_file('/home/jovyan/shared_data/data/geospatialfellows21/lazarus_data/Data_Files1/Layer_IR1_1.shp')"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
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1 | \n", "31 | \n", "109 | \n", "00835876 | \n", "31109 | \n", "Lancaster | \n", "Lancaster County | \n", "06 | \n", "H1 | \n", "G4020 | \n", "339 | \n", "... | \n", "186.9 | \n", "29.9 | \n", "2.752805 | \n", "191498.450302 | \n", "2.181031e+09 | \n", "-57758.726637 | \n", "198290.895484 | \n", "POLYGON ((-76484.353 198568.818, -76478.478 19... | \n", "0.323487 | \n", "0.005572 | \n", "
2 | \n", "31 | \n", "129 | \n", "00835886 | \n", "31129 | \n", "Nuckolls | \n", "Nuckolls County | \n", "06 | \n", "H1 | \n", "G4020 | \n", "None | \n", "... | \n", "548.3 | \n", "35.6 | \n", "1.984221 | \n", "154088.963652 | \n", "1.483452e+09 | \n", "-173426.738663 | \n", "132548.110644 | \n", "POLYGON ((-192849.850 123355.389, -192849.816 ... | \n", "0.314053 | \n", "-0.643062 | \n", "
3 | \n", "46 | \n", "099 | \n", "01265772 | \n", "46099 | \n", "Minnehaha | \n", "Minnehaha County | \n", "06 | \n", "H1 | \n", "G4020 | \n", "None | \n", "... | \n", "229.2 | \n", "31.1 | \n", "2.614508 | \n", "186372.852811 | \n", "2.103144e+09 | \n", "-63679.933739 | \n", "519393.038636 | \n", "POLYGON ((-71439.032 538818.414, -71405.569 53... | \n", "0.269650 | \n", "-0.392223 | \n", "
4 | \n", "48 | \n", "327 | \n", "01383949 | \n", "48327 | \n", "Menard | \n", "Menard County | \n", "06 | \n", "H1 | \n", "G4020 | \n", "None | \n", "... | \n", "342.1 | \n", "29.1 | \n", "2.874112 | \n", "204909.652555 | \n", "2.346750e+09 | \n", "-366739.340990 | \n", "-892066.944835 | \n", "POLYGON ((-365946.769 -870192.658, -365650.326... | \n", "0.414429 | \n", "1.072694 | \n", "
5 rows × 41 columns
\n", "