{ "cells": [ { "cell_type": "markdown", "id": "e8abbdd5", "metadata": {}, "source": [ "# Example Visualizations using CyberGIS-Vis" ] }, { "cell_type": "markdown", "id": "66bde9ed", "metadata": {}, "source": [ "#### Documentations and Demos about CyberGIS-Vis are available at: https://github.com/su-gis/CyberGIS-Vis" ] }, { "cell_type": "markdown", "id": "f785cd5e-96f8-4e27-a38e-1175c0a08d93", "metadata": {}, "source": [ "## Adaptive Choropleth Mapper with Multiple Line Chart (MLC): Temporal Patterns of Covid-19 Crude Rate and Death Rate in US Counties" ] }, { "cell_type": "markdown", "id": "c7da3cb3-793c-4da9-b295-3edd7842fcc9", "metadata": {}, "source": [ "## Setup environment" ] }, { "cell_type": "code", "execution_count": 1, "id": "f2fea90f-ace0-49a7-ba55-832f941eb6c4", "metadata": {}, "outputs": [], "source": [ "import pandas as pd\n", "import geopandas as gpd\n", "from Adaptive_Choropleth_Mapper import Adaptive_Choropleth_Mapper_viz, Adaptive_Choropleth_Mapper_log" ] }, { "cell_type": "markdown", "id": "efe245d9-5079-4a31-b131-86415f77e723", "metadata": {}, "source": [ "### Set input Data" ] }, { "cell_type": "markdown", "id": "e18f631a-5f9c-4178-a8c5-d367a5d345fd", "metadata": {}, "source": [ "1. Load U.S. counties from the Shapefile. Note: New York is an exception, represented by New York City with the city ID 777777, instead of county names and IDs.\n", "- Read the Shapefile \"County_NY_TIMES.shp\" into a GeoDataFrame\n", "- The Shapefile is located in the \"shp/US/\" directory\n", "- The 'geoid' column is explicitly set to be read as a string (str)" ] }, { "cell_type": "code", "execution_count": 2, "id": "2c3b778c-7391-4288-b198-097f7059b763", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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geoidnameShape_LengShape_Areageometry
010001Kent,DE2.0296820.215240POLYGON ((-75.74776 39.14334, -75.75600 39.246...
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210005Sussex,DE2.3690840.320841POLYGON ((-75.70157 38.56074, -75.70744 38.635...
31001Autauga,AL1.9949480.150242POLYGON ((-86.41312 32.70739, -86.41279 32.625...
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..................
32129007Middlesex,CT1.8781720.122471POLYGON ((-72.75218 41.57889, -72.75294 41.592...
32139009New Haven,CT2.6298680.240237POLYGON ((-73.31047 41.46881, -73.32091 41.477...
32149011New London,CT2.3902770.215441POLYGON ((-72.46673 41.58390, -72.41723 41.590...
32159013Tolland,CT1.8120810.117074POLYGON ((-72.13572 42.03025, -72.10217 42.028...
32169015Windham,CT1.7546120.146376POLYGON ((-71.78970 41.72456, -71.78725 41.656...
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3217 rows × 5 columns

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" ], "text/plain": [ " geoid name Shape_Leng Shape_Area \\\n", "0 10001 Kent,DE 2.029682 0.215240 \n", "1 10003 New Castle,DE 1.798779 0.134081 \n", "2 10005 Sussex,DE 2.369084 0.320841 \n", "3 1001 Autauga,AL 1.994948 0.150242 \n", "4 1003 Baldwin,AL 3.977560 0.494110 \n", "... ... ... ... ... \n", "3212 9007 Middlesex,CT 1.878172 0.122471 \n", "3213 9009 New Haven,CT 2.629868 0.240237 \n", "3214 9011 New London,CT 2.390277 0.215441 \n", "3215 9013 Tolland,CT 1.812081 0.117074 \n", "3216 9015 Windham,CT 1.754612 0.146376 \n", "\n", " geometry \n", "0 POLYGON ((-75.74776 39.14334, -75.75600 39.246... \n", "1 POLYGON ((-75.78860 39.72220, -75.77379 39.722... \n", "2 POLYGON ((-75.70157 38.56074, -75.70744 38.635... \n", "3 POLYGON ((-86.41312 32.70739, -86.41279 32.625... \n", "4 POLYGON ((-87.59883 30.99745, -87.59650 30.987... \n", "... ... \n", "3212 POLYGON ((-72.75218 41.57889, -72.75294 41.592... \n", "3213 POLYGON ((-73.31047 41.46881, -73.32091 41.477... \n", "3214 POLYGON ((-72.46673 41.58390, -72.41723 41.590... \n", "3215 POLYGON ((-72.13572 42.03025, -72.10217 42.028... \n", "3216 POLYGON ((-71.78970 41.72456, -71.78725 41.656... \n", "\n", "[3217 rows x 5 columns]" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "shapefile_US = gpd.read_file(\"shp/US/County_NY_TIMES.shp\", dtype={'geoid': str})\n", "shapefile_US" ] }, { "cell_type": "markdown", "id": "65768b48-5965-496b-a7bd-ec5ed2a6d7af", "metadata": {}, "source": [ "2. Load the attribute data that will be used for visualization. Data Source: \"The New York Times. (2021). Coronavirus (Covid-19) Data in the United States. Retrieved [08/01/2024], from https://github.com/nytimes/covid-19-data.\"\n", "- Read the CSV file \"Covid_Rate_US_2020_2021_weekly.csv\" into a DataFrame\n", "- The CSV file is located in the \"attributes/\" directory\n", "- The 'geoid' column is explicitly set to be read as a string (str)" ] }, { "cell_type": "code", "execution_count": 3, "id": "e37bce9e-9ba3-4b3c-b37b-35b36dbf7112", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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geoidperiodconfirmed_cases_totaldeath_totalcasesdeathpopconfirmed_rate_totaldeath_rate_tatalconfirmed_ratedeath_rate
0250212020-03-02101013176.340.00000076.340.000000
1170312020-03-027010371721.880.0000000.270.000000
260952020-03-0224010806802.970.0000000.120.000000
360752020-03-026000173763.450.0000000.000.000000
4120572020-03-022010139614.330.0000007.160.000000
....................................
276123421092021-11-2220504432930355657660.291214.848144261.530.000000
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276128 rows × 11 columns

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" ], "text/plain": [ " geoid period confirmed_cases_total death_total cases death \\\n", "0 25021 2020-03-02 1 0 1 0 \n", "1 17031 2020-03-02 7 0 1 0 \n", "2 6095 2020-03-02 24 0 1 0 \n", "3 6075 2020-03-02 6 0 0 0 \n", "4 12057 2020-03-02 2 0 1 0 \n", "... ... ... ... ... ... ... \n", "276123 42109 2021-11-22 20504 432 93 0 \n", "276124 42107 2021-11-22 84114 1951 491 8 \n", "276125 27139 2021-11-22 97191 694 853 7 \n", "276126 42121 2021-11-22 29499 625 310 7 \n", "276127 9015 2021-11-22 56217 891 206 1 \n", "\n", " pop confirmed_rate_total death_rate_tatal confirmed_rate \\\n", "0 131 76.34 0.000000 76.34 \n", "1 37172 1.88 0.000000 0.27 \n", "2 80680 2.97 0.000000 0.12 \n", "3 17376 3.45 0.000000 0.00 \n", "4 1396 14.33 0.000000 7.16 \n", "... ... ... ... ... \n", "276123 3556 57660.29 1214.848144 261.53 \n", "276124 36624 22966.91 532.710791 134.07 \n", "276125 112464 8641.97 61.708636 75.85 \n", "276126 1988 148385.31 3143.863179 1559.36 \n", "276127 81092 6932.50 109.875203 25.40 \n", "\n", " death_rate \n", "0 0.000000 \n", "1 0.000000 \n", "2 0.000000 \n", "3 0.000000 \n", "4 0.000000 \n", "... ... \n", "276123 0.000000 \n", "276124 2.180000 \n", "276125 0.622421 \n", "276126 35.210000 \n", "276127 0.120000 \n", "\n", "[276128 rows x 11 columns]" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "Covid_Rate_US_2020_2021_weekly = pd.read_csv(\"attributes/Covid_Rate_US_2020_2021_weekly.csv\", dtype={'geoid': str} )\n", "Covid_Rate_US_2020_2021_weekly" ] }, { "cell_type": "markdown", "id": "992254a5-165f-4b4a-bf25-1e7f5c57177b", "metadata": {}, "source": [ "### Configure the parameters to visualize your COVID-19 datasets. " ] }, { "cell_type": "markdown", "id": "94788292-d771-4943-920d-8ec60d382ad8", "metadata": { "jp-MarkdownHeadingCollapsed": true, "tags": [] }, "source": [ "#### Input Parameters for Visualizing Adaptive Choropleth Maps.\n", "| Parameter | Required | Description |\n", "|--------------------------------|:--------:|--------------------------------------------------------------------------------------------------------------------------------------------------|\n", "| **title** | ✓ | Enter the title to display at the top of your result visualization. |\n", "| **Subject** | | Enter the text to display at the top of your chart. |\n", "| **filename_suffix** | ✓ | Specify the name of the folder where your result files will be saved. |\n", "| **inputCSV** | ✓ | Specify the attributes from your input data. |\n", "| **shapefile** | ✓ | Provide the shapefile that includes the geometry of your study area. |\n", "| **periods** | ✓ | Enter \"All\" to visualize all dates from the 'period' column of your input data. To visualize specific periods, provide the desired values from the 'period' column as an array (e.g., `[2020, 2021, 2023]`). Ensure these values match the entries in your data. |\n", "| **variables** | ✓ | Enter the names of the columns in your input data to include in the visualization. |\n", "| **NumOfMaps** | ✓ | Specify the number of maps to display in your result visualization. |\n", "| **SortLayers** | | Choose between `'compare'` or `'temporal'` mode: |\n", "| | | - **Compare Mode**: Compare variables at a specific point in time. |\n", "| | | - **Temporal Mode**: Display spatiotemporal patterns of the same variable across multiple maps. |\n", "| **InitialLayers** | | Enter the variables to display by default on your maps. |\n", "| **Initial_map_center** | | Enter the longitude and latitude of the center of your study area in decimal degrees. If left blank, the map will automatically center based on your data. |\n", "| **Initial_map_zoom_level**| | Enter a number between 2 and 15 for the zoom level. If left blank, the maps will automatically adjust the zoom level. |\n", "| **Map_width** | | Specify the width of the maps. If left blank, the default is 500px. |\n", "| **Map_height** | | Specify the height of the maps. If left blank, the default is 500px. |\n", "\n", "#### Input parameters for visualizing charts.\n", "| Parameter | Required | Description |\n", "|--------------------------------|:--------:|--------------------------------------------------------------------------------------------------------------------------------------------------|\n", "| **Top10_Chart** | | Enter `True` or `False`. Set to `True` to display a bar chart representing the top and bottom values within the right map. If `False`, the chart will not be displayed. If left blank, `False` is the default. |\n", "| **Multiple_Line_Chart** | | Enter `True` or `False`. Set to `True` to display a Multiple Line Chart. If `False`, it will not be displayed. If left blank, `False` is the default. |\n", "| **Comparision_Chart** | | Enter `True` or `False`. Set to `True` to display a Comparision Line Chart. If `False`, it will not be displayed. If left blank, `False` is the default. |\n", "| **Stacked_Chart** | | Enter `True` or `False`. Set to `True` to display a Stacked Chart. If `False`, it will not be displayed. If left blank, `False` is the default. |\n", "| **Correlogram** | | Enter `True` or `False`. Set to `True` to display a Correlogram. If `False`, it will not be displayed. If left blank, `False` is the default. |\n", "| **Scatter_Plot** | | Enter `True` or `False`. Set to `True` to display a Scatter Chart. If `False`, it will not be displayed. If left blank, `False` is the default. |\n", "| **Parallel_Coordinates_Plot** | | Enter `True` or `False`. Set to `True` to display a Parallel Coordinates Plot. If `False`, it will not be displayed. If left blank, `False` is the default. |\n", "\n", "#### Input parameters for visualizing 'Multiple Line Chart'.\n", "| Parameter | Required | Description |\n", "|--------------------------------|:--------:|--------------------------------------------------------------------------------------------------------------------------------------------------|\n", "| **titlesOfMLC** || Enter a title for each line chart to be displayed at the top of the chart in the Multiple Line Chart. If left blank, a line chart will be created for each variable in your input attribute file.|\n", "| **NumOfMLC** | | Specify the number of line charts to include in the Multiple Line Chart. If left blank, the number of charts will default to the number of variables entered in the 'Variables' parameter above. |\n", "| **InitialVariableMLC** ||Select the variables to be displayed on the line chart. If left blank, the variables in your input attribute file will be visualized in order.|\n", "| **DefaultRegion_MLC** || Enter the 'id' from your attribute table to specify the default region displayed in the Multiple Line Chart. If left blank, the first region listed in your attribute table will be used. |\n", "| **HighlightMLC** ||Define the highlighted ranges for the x-axis values (periods) by specifying the start and end periods for the range you emphasize. |\n", "\n", "#### Input parameters for visualizing 'Comparison Line Chart'.\n", "| Parameter | Required | Description |\n", "|--------------------------------|:--------:|--------------------------------------------------------------------------------------------------------------------------------------------------|\n", "| **NumOfCLC** | | Specify the number of line charts to include in the Comparision Line Chart. If left blank, the number of charts will default to the number of variables entered in the 'Variables' parameter above. |\n", "| **InitialVariableCLC** ||Select the variables to be displayed on the line chart. If left blank, the variables in your input attribute file will be visualized in order.|\n", "| **DefaultRegion_CLC** | | Enter the 'id' of two regions to display the temporal patterns of the selected variable in the Comparison Line Chart. If left blank, the first two regions in your attribute table will be used. |\n", "| **HighlightCLC** ||Define the highlighted ranges for the x-axis values (periods) by specifying the start and end periods for the range you emphasize. |\n" ] }, { "cell_type": "markdown", "id": "0b70ddc9-6188-4e33-9d58-ceab6d67aaa3", "metadata": {}, "source": [ "

\n", "### Set the parameters to create visualizations using Multiple Linked Charts (MLC)." ] }, { "cell_type": "markdown", "id": "7eb80694-2898-49b7-b72b-9f1e37d4403a", "metadata": {}, "source": [ "The interface will include two choropleth maps, a chart displaying the top or bottom values of your selected variable, such as COVID-19 confirmed rates, within the geographic regions of your map, and multiple linked charts (MLC). The MLC feature allows users to click on any county to explore spatiotemporal patterns of selected variables, such as COVID-19 confirmed or death rates, across multiple time series charts.\n", "\n", "     Your result visualization would be similar to the image below.
\n", "     " ] }, { "cell_type": "code", "execution_count": 4, "id": "269543bc-acf3-4ccb-bc8d-9413ce120a37", "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/cvmfs/cybergis.illinois.edu/software/conda/cybergisx/python3-0.9.0/lib/python3.8/site-packages/pandas/core/dtypes/cast.py:1990: ShapelyDeprecationWarning: __len__ for multi-part geometries is deprecated and will be removed in Shapely 2.0. Check the length of the `geoms` property instead to get the number of parts of a multi-part geometry.\n", " result[:] = values\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "output directory : ACM_COVID_MLC_US_2020_2021\n", "To see your visualization, click the URL below (or locate the files):\n", "https://cybergisx.cigi.illinois.edu/user/suhan2/view/CyberGIS-Vis_SIGSPATIAL2024_20240828/Quantitative_Data_Vis/ACM_COVID_MLC_US_2020_2021/index.html\n", "To access all visualizations that you have created, click the URL below (or locate the files):\n", "https://cybergisx.cigi.illinois.edu/user/suhan2/view/CyberGIS-Vis_SIGSPATIAL2024_20240828/Quantitative_Data_Vis//ACM_log.html\n", "Advanced options are available in \n", "https://cybergisx.cigi.illinois.edu/user/suhan2/edit/CyberGIS-Vis_SIGSPATIAL2024_20240828/Quantitative_Data_Vis/ACM_COVID_MLC_US_2020_2021/data/CONFIG_COVID_MLC_US_2020_2021.js\n" ] } ], "source": [ "param_MLC_COVID_US_2020_2021 = {\n", " 'title': \"Spatiotemporal Dynamics of COVID-19 Cases and Deaths in U.S. Counties\",\n", " 'Subject': \"Temporal Patterns of COVID-19 Risk Factors\",\n", " 'filename_suffix': \"COVID_MLC\", # max 30 character \n", " 'inputCSV': Covid_Rate_US_2020_2021_weekly, \n", " 'shapefile': shapefile_US, \n", " 'periods': \"All\",\n", " 'variables': [ \n", " \"confirmed_rate\", \n", " \"death_rate\",\n", " \"confirmed_rate_total\",\n", " \"death_rate_tatal\"\n", " ],\n", " 'NumOfMaps':2,\n", " 'SortLayers': \"temporal\", \n", " 'InitialLayers':[\"2020-04-06_confirmed_rate\" , \"2020-07-20_confirmed_rate\"],\n", " 'Initial_map_center':[38, -97],\n", " 'Initial_map_zoom_level':4, \n", " 'Map_width':\"650px\",\n", " 'Map_height':\"450px\", \n", " 'Top10_Chart': True, \n", " 'Multiple_Line_Chart': True,\n", " 'NumOfMLC':4,\n", " 'titlesOfMLC':[\"1. Confirmed Rate (Confirmed Cases per 10k population)\", \"2. Death Rate (Deaths per 10k population)\", \"3. Cumulative Confirmed Rate\", \"4. Cumulative Death Rate\"],\n", " 'DefaultRegion_MLC':\"12086\" \n", "}\n", "Adaptive_Choropleth_Mapper_viz(param_MLC_COVID_US_2020_2021)\n", "Adaptive_Choropleth_Mapper_log(param_MLC_COVID_US_2020_2021)" ] }, { "cell_type": "markdown", "id": "f5134aca-cf82-4835-9b2b-8a97cf4257be", "metadata": {}, "source": [ "

\n", "### Set the parameters to create visualizations using Comparison Line Chart (CLC)." ] }, { "cell_type": "markdown", "id": "8db91fe1-d554-4a2c-8892-89e34412c435", "metadata": { "tags": [] }, "source": [ "Configure the parameters to visualize your COVID-19 datasets using the Comparison Line Chart (CLC). The interface will include two choropleth maps, a chart displaying the top or bottom values of your selected variable, such as COVID-19 confirmed rates, within the geographic regions of your map, and the Comparison Line Chart (CLC). The CLC feature allows users to click on any county on the two choropleth maps to compare spatiotemporal patterns of selected variables, such as COVID-19 confirmed or death rates, in a single interactive line chart.\n", "\n", "     Your result visualization would be similar to the image below.
\n", "     " ] }, { "cell_type": "code", "execution_count": 5, "id": "3ab4f457-b995-43a0-acc1-ce2feba5eaf9", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "output directory : ACM_COVID_CLC_US_2020_2021\n", "To see your visualization, click the URL below (or locate the files):\n", "https://cybergisx.cigi.illinois.edu/user/suhan2/view/CyberGIS-Vis_SIGSPATIAL2024_20240828/Quantitative_Data_Vis/ACM_COVID_CLC_US_2020_2021/index.html\n", "To access all visualizations that you have created, click the URL below (or locate the files):\n", "https://cybergisx.cigi.illinois.edu/user/suhan2/view/CyberGIS-Vis_SIGSPATIAL2024_20240828/Quantitative_Data_Vis//ACM_log.html\n", "Advanced options are available in \n", "https://cybergisx.cigi.illinois.edu/user/suhan2/edit/CyberGIS-Vis_SIGSPATIAL2024_20240828/Quantitative_Data_Vis/ACM_COVID_CLC_US_2020_2021/data/CONFIG_COVID_CLC_US_2020_2021.js\n" ] } ], "source": [ "param_CLC_COVID = {\n", " 'title': \"Comparison of Temporal Patterns of Covid-19 Confirmed Rate between US Counties\",\n", " 'Subject': \"Temporal Patterns of COVID-19 Cases per 10,000 Population in Two Selected Regions\",\n", " 'filename_suffix': \"COVID_CLC\", \n", " 'inputCSV': Covid_Rate_US_2020_2021_weekly, \n", " 'shapefile': shapefile_US, \n", " 'periods': \"All\",\n", " 'variables': [ \n", " \"confirmed_rate\", \n", " ],\n", " 'NumOfMaps':2,\n", " 'SortLayers': \"temporal\", \n", " 'InitialLayers':[\"2020-04-06_confirmed_rate\" , \"2020-07-20_confirmed_rate\"],\n", " 'Initial_map_center':[38, -97],\n", " 'Initial_map_zoom_level':4, \n", " 'Map_width':\"650px\",\n", " 'Map_height':\"450px\", \n", " 'Top10_Chart': True, \n", " 'Comparision_Chart': True,\n", " 'DefaultRegion_CLC': [\"777777\", \"12086\"] \n", "}\n", "Adaptive_Choropleth_Mapper_viz(param_CLC_COVID)\n", "Adaptive_Choropleth_Mapper_log(param_CLC_COVID) " ] } ], "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": "3.8.12" } }, "nbformat": 4, "nbformat_minor": 5 }