{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "## Windowed PCA and fluctuation intensity in COVID19 data" ] }, { "cell_type": "code", "execution_count": 99, "metadata": {}, "outputs": [], "source": [ "import pandas as pd\n", "import numpy as np\n", "import seaborn as sns\n", "import matplotlib.pyplot as plt\n", "from jmspack.utils import apply_scaling, JmsColors\n", "from jmspack.NLTSA import (fluctuation_intensity,\n", " distribution_uniformity,\n", " complexity_resonance,\n", " complexity_resonance_diagram,\n", " cumulative_complexity_peaks,\n", " cumulative_complexity_peaks_plot)\n", "from sklearn import decomposition\n", "from sklearn.linear_model import LinearRegression\n", "from scipy.stats import norm\n", "import time" ] }, { "cell_type": "code", "execution_count": 100, "metadata": {}, "outputs": [], "source": [ "start = time.time()" ] }, { "cell_type": "code", "execution_count": 101, "metadata": {}, "outputs": [], "source": [ "if \"jms_style_sheet\" in plt.style.available:\n", " plt.style.use(\"jms_style_sheet\")" ] }, { "cell_type": "code", "execution_count": 102, "metadata": {}, "outputs": [], "source": [ "country_choice=\"Netherlands\"\n", "filepath=f\"../shield-complexity/data/{country_choice}_worldsurvey_nonmissing_c_of_v_since_2021-06-08_to_2022-01-21.csv\"" ] }, { "cell_type": "code", "execution_count": 103, "metadata": {}, "outputs": [], "source": [ "df = pd.read_csv(filepath)" ] }, { "cell_type": "code", "execution_count": 104, "metadata": {}, "outputs": [], "source": [ "df[\"date\"] = pd.to_datetime(df[\"date\"]).dt.date" ] }, { "cell_type": "code", "execution_count": 105, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
| \n", " | date | \n", "pct_covid | \n", "pct_flu | \n", "percent_mc | \n", "percent_hf | \n", "percent_anos | \n", "pct_twodoses | \n", "pct_concerned_sideeffects | \n", "pct_community_cli | \n", "pct_activity_work_outside_home | \n", "... | \n", "pct_want_info_children_education | \n", "pct_want_info_economic_impact | \n", "pct_want_info_mental_health | \n", "pct_want_info_relationships | \n", "pct_want_info_employment | \n", "pct_want_info_none | \n", "pct_delayed_care_cost | \n", "pct_mask_work_outside_home_1d | \n", "pct_mask_shop_1d | \n", "pct_mask_spent_time_1d | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "2021-06-09 | \n", "14.535989 | \n", "13.195395 | \n", "0.770978 | \n", "3.346972 | \n", "6.422849 | \n", "1.337626 | \n", "1.292528 | \n", "4.387491 | \n", "1.258690 | \n", "... | \n", "5.271337 | \n", "4.509109 | \n", "3.382587 | \n", "3.528127 | \n", "4.871057 | \n", "1.119098 | \n", "3.155650 | \n", "1.074371 | \n", "0.432519 | \n", "3.148366 | \n", "
| 1 | \n", "2021-06-10 | \n", "14.773657 | \n", "14.773657 | \n", "0.715611 | \n", "3.498316 | \n", "7.144337 | \n", "1.267841 | \n", "1.550583 | \n", "4.649098 | \n", "1.376345 | \n", "... | \n", "4.687061 | \n", "3.669607 | \n", "3.150838 | \n", "3.858300 | \n", "5.208682 | \n", "1.071412 | \n", "3.435815 | \n", "1.034580 | \n", "0.358411 | \n", "3.208651 | \n", "
| 2 | \n", "2021-06-11 | \n", "18.572413 | \n", "18.203818 | \n", "0.649700 | \n", "3.456743 | \n", "9.709611 | \n", "1.245488 | \n", "1.449014 | \n", "4.170443 | \n", "1.320875 | \n", "... | \n", "5.485248 | \n", "3.985184 | \n", "3.796074 | \n", "3.540908 | \n", "4.152605 | \n", "1.011222 | \n", "3.139859 | \n", "0.967428 | \n", "0.346627 | \n", "2.720786 | \n", "
| 3 | \n", "2021-06-13 | \n", "17.418052 | \n", "17.418052 | \n", "0.703517 | \n", "3.761218 | \n", "10.277039 | \n", "1.348971 | \n", "1.526305 | \n", "5.509964 | \n", "1.503175 | \n", "... | \n", "5.254944 | \n", "3.342272 | \n", "3.168605 | \n", "3.342676 | \n", "4.585373 | \n", "1.245500 | \n", "3.266020 | \n", "1.129369 | \n", "0.294228 | \n", "3.224900 | \n", "
| 4 | \n", "2021-06-14 | \n", "20.332173 | \n", "17.400103 | \n", "0.716563 | \n", "3.497908 | \n", "7.931059 | \n", "1.214978 | \n", "1.482273 | \n", "5.389113 | \n", "1.490736 | \n", "... | \n", "5.430036 | \n", "3.805503 | \n", "3.120780 | \n", "3.441871 | \n", "4.359385 | \n", "1.047207 | \n", "3.108143 | \n", "0.911346 | \n", "0.471995 | \n", "3.524901 | \n", "
5 rows × 67 columns
\n", "| \n", " | windowed_PCA | \n", "
|---|---|
| date | \n", "\n", " |
| 2021-06-09 | \n", "35.991569 | \n", "
| 2021-06-10 | \n", "37.060099 | \n", "
| 2021-06-11 | \n", "38.635545 | \n", "
| 2021-06-13 | \n", "38.527492 | \n", "
| 2021-06-14 | \n", "38.777388 | \n", "