{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "## Windowed PCA and fluctuation intensity in COVID19 data" ] }, { "cell_type": "code", "execution_count": 111, "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": 112, "metadata": {}, "outputs": [], "source": [ "start = time.time()" ] }, { "cell_type": "code", "execution_count": 113, "metadata": {}, "outputs": [], "source": [ "if \"jms_style_sheet\" in plt.style.available:\n", " plt.style.use(\"jms_style_sheet\")" ] }, { "cell_type": "code", "execution_count": 114, "metadata": {}, "outputs": [], "source": [ "# df = pd.read_csv(\"../shield-complexity/data/Finland_worldsurvey_nonmissing_since_2021-06-08_to_2022-01-20.csv\")\n", "df = pd.read_csv(\"../shield-complexity/data/Finland_worldsurvey_nonmissing_c_of_v_since_2021-06-08_to_2022-01-20.csv\")" ] }, { "cell_type": "code", "execution_count": 115, "metadata": {}, "outputs": [], "source": [ "df[\"date\"] = pd.to_datetime(df[\"date\"]).dt.date" ] }, { "cell_type": "code", "execution_count": 116, "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_community_cli | \n", "pct_activity_work_outside_home | \n", "pct_activity_shop | \n", "... | \n", "pct_want_info_covid_variants | \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_shop_1d | \n", "pct_mask_spent_time_1d | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "2021-06-09 | \n", "9.039486 | \n", "9.039486 | \n", "0.612679 | \n", "2.813836 | \n", "6.958875 | \n", "2.033529 | \n", "4.412780 | \n", "1.701158 | \n", "0.408198 | \n", "... | \n", "1.796540 | \n", "3.263608 | \n", "3.377915 | \n", "2.276444 | \n", "2.927897 | \n", "3.459269 | \n", "1.471821 | \n", "2.490908 | \n", "0.552925 | \n", "1.417980 | \n", "
| 1 | \n", "2021-06-10 | \n", "11.782998 | \n", "11.782998 | \n", "0.512932 | \n", "2.422617 | \n", "8.330548 | \n", "2.013005 | \n", "5.110684 | \n", "1.874262 | \n", "0.391850 | \n", "... | \n", "1.617688 | \n", "3.455750 | \n", "4.811816 | \n", "2.227195 | \n", "2.701875 | \n", "3.445995 | \n", "1.478371 | \n", "2.153090 | \n", "0.386451 | \n", "1.578405 | \n", "
| 2 | \n", "2021-06-11 | \n", "19.488523 | \n", "15.235526 | \n", "2.173259 | \n", "2.121825 | \n", "7.898911 | \n", "3.045827 | \n", "4.672163 | \n", "2.991276 | \n", "2.263277 | \n", "... | \n", "1.611505 | \n", "3.279128 | \n", "5.133363 | \n", "2.492608 | \n", "2.942794 | \n", "4.426361 | \n", "1.449034 | \n", "2.251560 | \n", "0.236805 | \n", "1.628893 | \n", "
| 3 | \n", "2021-06-12 | \n", "13.118015 | \n", "13.118015 | \n", "1.162009 | \n", "2.543860 | \n", "8.630301 | \n", "1.826629 | \n", "5.658765 | \n", "2.148999 | \n", "0.995366 | \n", "... | \n", "1.701548 | \n", "3.803658 | \n", "3.688413 | \n", "2.070748 | \n", "2.775816 | \n", "3.189387 | \n", "1.242110 | \n", "2.605254 | \n", "0.580646 | \n", "2.399832 | \n", "
| 4 | \n", "2021-06-13 | \n", "10.705081 | \n", "12.118662 | \n", "0.782932 | \n", "2.329260 | \n", "8.237337 | \n", "2.684727 | \n", "5.455478 | \n", "2.414263 | \n", "0.566504 | \n", "... | \n", "1.922228 | \n", "3.769134 | \n", "3.916612 | \n", "2.752952 | \n", "3.658005 | \n", "3.275252 | \n", "1.477509 | \n", "2.832298 | \n", "0.449128 | \n", "2.521729 | \n", "
5 rows × 64 columns
\n", "| \n", " | windowed_PCA | \n", "
|---|---|
| date | \n", "\n", " |
| 2021-06-09 | \n", "39.595692 | \n", "
| 2021-06-10 | \n", "37.623526 | \n", "
| 2021-06-11 | \n", "38.198733 | \n", "
| 2021-06-12 | \n", "38.344276 | \n", "
| 2021-06-13 | \n", "39.809786 | \n", "