Howell County, Missouri, COVID-19 data and (unofficial) estimates

Overview

COVID-19 in Howell County, Missouri

This repository contains the daily data files used to generate my COVID-19 dashboard for Howell County, Missouri, as well as the Hugo source files needed to generate the page, and the Python source files for processing and updating the daily data files.

How it works

  1. Daily data is entered into the relevant file in the daily-data directory.
  2. Python scripts process the daily data into files for the dashboard.
  3. Hugo uses these data files and template files to generate HTML.
  4. The generated HTML is deployed to AWS.

Notable updates

  • October 25, 2020: Launched the dashboard site at https://covid.jonblatho.com/.
  • October 26, 2020: Added a table with all daily data.
  • October 27, 2020: The total cases chart was changed from a single line for total cases in the county to a stacked area chart with data by town.
  • November 8, 2020: Added vertical markers on the total cases chart to show dates of significant events.
  • November 9, 2020: Changed the positivity rate metric from the 7-day positivity rate to the 14-day positivity rate.
  • November 24, 2020: Added a column in the table to show the discrepancy between HCHD and DHSS reported case totals for a given date.
  • December 8, 2020: Date markers on the dashboard chart can now be toggled on and off.
  • December 9, 2020: Added charts for new cases, active cases, and positivity rate.
  • December 18, 2020: Moved the All Data table to its own page and added Dark Mode support.
  • January 5, 2021: Added a categorical risk level to characterize the status of COVID-19 in the county.
  • January 21, 2021: Added historical risk levels to the All Data table.
  • January 31, 2021: Open-sourced Python processing script.
  • February 10, 2021: Automated nightly updates at 11 PM and 12 AM CST.
  • March 25, 2021: Made site responsive to improve legibility on mobile devices.
  • July 4, 2021: Added two vaccination charts to the homepage.
  • July 9, 2021: Redesigned the chart and dashboard section of the homepage with a new full-width layout.
  • August 1, 2021: Redesigned the Active Cases by Town section as a map with estimates available for all Howell County towns.
  • August 10, 2021: Adds a customized calculation of the CDC Level of Community Transmission parameter including antigen tests, which are anomalously common in Howell County.
  • August 12, 2021: Redesigned and expanded All Data table with support for new cases by town for all towns, vaccination data, and a new CDC Level of Community Transmission column.
  • September 13, 2021: Migrated the site from GitHub Pages to AWS using S3 and CloudFront.
  • October 3, 2021: Added an automation to pull in state DHSS data daily.
  • October 6, 2021: Monthly case tables were split up by year in an accordion format, with the current year expanded and past year(s) collapsed by default.
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Comments
  • switch to DHSS testing data

    switch to DHSS testing data

    HCHD's testing numbers are bordering on unreasonable, possibly because they might have switched back to reporting "number of individuals tested" rather than "number of tests conducted." To counteract this, it is probably time to switch to DHSS testing data. Case data would be unimpacted and still come from the HCHD dashboard.

    ~DHSS reports PCR and antigen tests separately, and this is likely a useful differentiation given that the CDC seemingly only counts PCR tests (looking toward adding Level of Community Transmission data). However, this is a breaking change because currently test counts are recorded in the daily data files as the sum reported by HCHD on their Facebook page on most weekdays.~

    Testing data would still be updated manually in the morning update, but instead it would come from data downloaded from DHSS. ~The new testing data format in the daily data files would be as follows:~

    ~..."tests": { "pcr": 0, "antigen": 0 }, ...~

    ~where instead of the cumulative sum for each, only the single-day PCR and antigen tests are included (since we can calculate the sum as needed). It may still prove necessary to add in antigen tests for the Level of Community Transmission in a minor break from the CDC methodology, but given the prevalence of antigen testing in Howell County that may hold more benefits than drawbacks.~

    enhancement data 
    opened by jonblatho 1
Releases(6.19.1)
  • 6.19.1(Jan 3, 2022)

    • Fixed an issue where archive-dhss-data.py would fail to upload due to the calendar year switch from 2021 to 2022. (The script was attempting to read a key on items that didn't exist.)
    • Updated the Anaconda environment to use Python 3.10 and associated dependencies.
    Source code(tar.gz)
    Source code(zip)
  • 6.19.0(Oct 22, 2021)

    • Refreshed footer design with a two-column layout.
    • Separated page titles from content.
    • Added page titles to <title> tag except on the homepage.
    • Revised privacy policy wording.
    Source code(tar.gz)
    Source code(zip)
  • 6.18.1(Oct 21, 2021)

  • 6.18.0(Oct 21, 2021)

    • Refreshed, more compact categorical risk level design on the homepage.
    • The wording of the "Considerable" Community Transmission level was changed to "Substantial."
    • The chart on the homepage was made less tall to reflect the updated sidebar design.
    Source code(tar.gz)
    Source code(zip)
  • 6.17.1(Oct 13, 2021)

  • 6.17.0(Oct 7, 2021)

    • Redesigned header.
    • Replaced the chart selection dropdown menu and events toggle button with Bootstrap-based equivalents.
    • New case charts by month are now split by year, with past year(s) collapsed by default.
    • Now using CDN-hosted Chart.js and chartjs-plugin-annotation in place of self-hosted equivalents.
    • Improved colors for headings in dark mode.
    Source code(tar.gz)
    Source code(zip)
  • 6.16.0(Oct 4, 2021)

    • New: Added a script (download-dhss-data.py) to automatically pull in DHSS data daily, using headless Chrome.
    • New: Added an automation to run in the early morning hours to pull in DHSS data automatically.
    • Fixed: By default, archive-dhss-data.py will no longer overwrite an existing object in S3. There’s a new --force/-f flag to force an upload anyway, if needed.
    • Fixed: add-source-url.py will no longer add a URL if it is already present.
    • Removed: Generated data files — assets/chart-data.json and data/* — have been removed from Git. The auto-update automation has been updated to reflect this change.
    Source code(tar.gz)
    Source code(zip)
  • 6.15.2(Oct 4, 2021)

  • 6.15.1(Sep 20, 2021)

  • 6.15.0(Sep 18, 2021)

    • New: Data from March 2020 has been added. While the first COVID-19 case in Howell County was confirmed on April 1, 2020, the state has testing data dating back to March 10, 2020. The absence of this data throws off some calculations near the beginning of the dataset, so it has been added while keeping the start of the publicly available dataset at April 1, 2020.
      • Updated processing scripts and unit tests to account for the March 2020 data.
    • New: archive-dhss-data.py has gained a -d (or --date) flag to set the date to which the DHSS data corresponds and should be added in the daily data files.
    • New: add-source-url.py's --date flag may now also be provided with the abbreviated flag -d.
    • Fixed: archive-dhss-data.py will now only delete original files after a confirmed successful upload.
    Source code(tar.gz)
    Source code(zip)
  • 6.14.2(Sep 16, 2021)

  • 6.14.1(Sep 16, 2021)

    • Fixed an issue that caused the autoupdate workflow to run more updates than it needed to.
    • Fixed an issue that would not allow the autoupdate workflow to create an issue upon a failed attempt to archive the HCHD dashboard to the Wayback Machine.
    Source code(tar.gz)
    Source code(zip)
  • 6.14.0(Sep 16, 2021)

  • 6.13.1(Sep 13, 2021)

    The generated site is now placed in the public/ directory instead of docs/, and the .gitignore file has been updated to include the generated site directory.

    Source code(tar.gz)
    Source code(zip)
  • 6.13.0(Sep 13, 2021)

    • Made necessary configuration changes to deploy the site to AWS S3 and CloudFront.
    • The docs/ directory has been removed because it is no longer necessary, since its sole purpose was to host the site on GitHub Pages.
    • CSS is now loaded asynchronously via JavaScript to improve page load times.
    Source code(tar.gz)
    Source code(zip)
  • 6.12.0(Sep 13, 2021)

  • 6.11.0(Sep 10, 2021)

    This one’s all about helping to automate the manual daily maintenance tasks to keep the site updated.

    • New: Updated the script for adding an archive URL (add-archive-url.py) to the daily data files to use the utilities module, use the ArgumentParser module, and be date-agnostic, only defaulting to the latest date. Renamed the script to add-source-url.py.
      • Fixed: The above script no longer always overwrites the sources key in daily data files; instead, it either creates or appends to a list depending on whether a list already exists there.
      • Fixed: Updated GitHub Actions workflows to use add-source-url.py.
    • New: Added a script (add-dhss-data.py) to add all DHSS data in a single command if the four files exist under expected names and are in the same directory.
    • New: Added a script (archive-dhss-data.py) to archive and upload DHSS data files (under the same conditions as add-dhss-data.py) to Amazon S3, then optionally delete the original data files if successful.
    • New: add-vaccine-data.py now attempts to guess the data type (total doses, or initiated/completed vaccinations) based on the file name provided, if the argument is not explicitly given. The type argument is no longer required and has been renamed to --type.
    • New: add-vaccine-data.py and add-test-data.py now have a --quiet flag to only print to stdout for errors. A similar argument was added to utilities.save_json.
    Source code(tar.gz)
    Source code(zip)
  • 6.10.0(Aug 29, 2021)

    • Introduces a script for self-hosted web analytics.
    • Introduces a privacy policy, linked in the footer, explaining exactly what user data is collected and by whom.
    Source code(tar.gz)
    Source code(zip)
  • 6.9.0(Aug 13, 2021)

    • All Data:
      • Total cases by town have been added to the table for all towns.
      • New cases by town have been removed; now, only the county total is displayed.
      • Added vaccination data showing the number of doses administered and cumulative number of residents who have initiated or completed vaccination.
      • Added the Community Transmission level.
      • Risk Level and Community Transmission columns use a redesigned categorical indicator for improved legibility.
    • Added a slim border to the categorical indicators for Risk Level and Community Transmission on the homepage to improve legibility.
    • Completed the migration of the site to a full-width layout.
    Source code(tar.gz)
    Source code(zip)
  • 6.8.0(Aug 11, 2021)

    • Adds support for the CDC Level of Community Transmission calculated with both PCR and antigen tests.
    • Adds a note on the FAQ page explaining the inclusion of antigen tests.
    Source code(tar.gz)
    Source code(zip)
  • 6.7.0(Aug 11, 2021)

  • 6.6.0(Aug 5, 2021)

    • Active hospitalizations have been added to the Active Cases chart.
    • Reduced the size of the chart data JSON file fetched by the browser when loading the charts by about 25%.
    Source code(tar.gz)
    Source code(zip)
  • 6.5.0(Aug 1, 2021)

    • The Active Cases by Town section has been redesigned as a county map with full support for dark mode and screen readers.
    • The Active Cases by Town and New Cases sections have been placed alongside each other on larger displays to use the full width of the display.
    Source code(tar.gz)
    Source code(zip)
  • 6.4.0(Jul 29, 2021)

  • 6.3.0(Jul 26, 2021)

    • A new Risk Level chart has been added to view the color-coded Risk Level over time.
    • The Notes page has been reformatted and renamed to Frequently Asked Questions.
    • Corrected a missing Dark Mode color.
    Source code(tar.gz)
    Source code(zip)
  • 6.2.0(Jul 9, 2021)

    • The chart and dashboard area on the homepage has been redesigned with a new layout to take advantage of the full width of the viewport.
    • A meter displaying the percentage of Howell County residents who are fully vaccinated and have initiated vaccination has been added.
    • Total cases and deaths have been placed into the new sidebar to emphasize these counts.
    • Because it usually tracks very closely with the active cases dashboard item, the "New Cases in the Past Week" dashboard item has been removed and replaced with the above total case change indicator.
    • The risk level area has been redesigned for simplicity and clarity.
    Source code(tar.gz)
    Source code(zip)
  • 6.1.2(Jul 6, 2021)

  • 6.1.1(Jul 5, 2021)

    Fixed

    • Corrected the behavior of the processing and auto-update scripts to correctly handle new unavailable vaccine data, as it must be input manually the following day.
    Source code(tar.gz)
    Source code(zip)
  • 6.1.0(Jul 4, 2021)

    New

    • Vaccination data has been added to the daily data files. Total doses, individuals having initiated vaccination, and fully vaccinated individuals are the variables tracked at this time. (#31)
    • Added charts to the homepage for Vaccine Doses (by day and 7-day average) and Vaccinated Individuals (initiated and completed). (#34)

    Changed

    • The homepage now defaults to the New Cases chart.
    • Date markers are now disabled by default on the chart for all devices (previously, they were disabled by default only on mobile).
    • The background color for date markers has been made darker.
    • The "Date Markers" button has been changed to "Events."
    • The font size for buttons above the chart has been made slightly smaller.
    • The Time Machine navigation bar no longer appears on the homepage.
    Source code(tar.gz)
    Source code(zip)
  • 6.0.0(Jul 3, 2021)

    New

    • Processing and automation scripts have been completely refactored to be more modular for improved reliability.

    Fixed

    • Corrects a layout issue with the redesigned Time Machine navigation.
    Source code(tar.gz)
    Source code(zip)
Owner
Jonathan Thornton
Jonathan Thornton
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