covid-19-outbreak-paths
Projects to explore detailed outbreak paths. Mostly dataviz using Power BI
Australia - Outbreaks by Area
For NSW & VIC, analyses PCR and RAT reported cases down to LGA level, with derived metrics like Reff and Cases per 100K. Data is published weekly on Fridays.
For QLD, analyses RAT reported cases and tests down to LGA level, with added derived metrics like % Positive and Tests per 100K. Data is published on Wednesdays.
If you are dissappointed by the data provided by your state or jurisdiction, please contact your elected representatives and let them know.
Charts of Metrics by Area - State, Region and Local Government Area (LGA)
State, Region and Local Government Area (LGA) are available as options for presentation.
Column and stacked column charts are available on adjacent pages.
Map by LGA
Bubble Chart of Cases per 100k population vs Reff by LGA
Charts of Metrics by Age Group
Column and stacked column charts are available on adjacent pages.
Many other report pages are available, just click on one of the links above, then use the page navigation control at bottom-centre: < 1 of 15 >. Clicking the centre of that control will show a menu of pages.
New South Wales by Area
This report will not be updated after April 2023. Refer to the Australia report above for the the latest info.
NSW - Map of Case and Test metrics by LGA
Victoria by Area
This report will not be updated after April 2023. Refer to the Australia report above for the the latest info.
VIC - Map of Case metrics by LGA
Victoria: August 2021
Preview animation: https://youtu.be/aRyP7bmoBoc
Queensland: July 2021
Preview animation: https://youtu.be/KLGz4zk6pbM
Victoria: July 2021
Preview animation: https://youtu.be/eNPYLosZhvI
South Australia: July 2021
Preview animation: https://youtu.be/kcwz9ZupVyU
New South Wales: June 2021
Preview animation: https://youtu.be/84jbzh94jJ0
Queensland: June 2021
Preview animation: YouTube: https://youtu.be/SMQNCCahJrg
Northern Territory: June 2021
Preview animation: https://youtu.be/iXiemDw6L4A
Victoria: May-June 2021
Preview animation: https://youtu.be/PTgq2XbJ83Q
Summary
The “Australia Outbreak” report has the following features:
- NSW Cases by location data loaded from dataset: Cases by location aggregated data
- NSW Case by Age data loaded from dataset: COVID-19 cases by notification date and age range
- NSW Postcodes with missing LHD & LGA data were translated manually by Ann McLean, the results are in this translation file.
- VIC Case by location data loaded from dataset: All PCR and RAT cases by Local Government Area
- VIC Cases by Age data loaded from dataset: All PCR and RAT cases by age group
- QLD Case by location data loaded from dataset: Queensland COVID-19 Case Line List - Location & Source of Infection
- QLD Case by age data loaded from dataset: Queensland COVID-19 Case Line List - Age Groups
- QLD Tests by location data loaded from dataset: Queensland COVID-19 Pathology Test Totals by Collection Day and SA2
- ABS Population by State-Territory and Age
- dynamic Reff, calculated using Professor Adrian Esterman’s method, detailed on this Twitter thread
Data sources for older reports
Case-level data on:
- Victoria outbreak during July 2021
- Queensland / Northern Territory outbreak during June 2021
- Victoria outbreak during May-June 2021
dbRaevn has manually constructed diagrams of the outbreak paths, based on information from daily press cases.
For the New South Wales June-July 2021 outbreak, manually constructed diagrams are not available after 7 July. So I have used the NSW COVID-19 cases by location dataset. Each day’s new cases are arbitrarily linked to prior cases in the same local health district.
This project turns that information into structured data and feeds it through an interactive dataviz solution, using Power BI with the Drill Down Graph PRO Custom Visual by ZoomCharts. The interactive features allow the audience to filter the dataset by date, cluster or variant.
For this project, the manual diagram info is converted into a structured data table (Excel). Each row represents a transmission link between cases. The codes used for each node on the manual diagram are used as Source and Target nodes to drive the diagram visual. Cases with an unknown source are loaded with the same code for Source and Target. The dataviz tool used requires unique codes for each node, so suffixes have been added where the manual diagram codes were not unique. Once the initial dataset is established, ongoing updates are relatively simple.
Another sheet in the Excel file provides the colours assigned to each node by date. The preferred colours scheme is a steady gradient of purple. The colour scheme used on the manual diagram is also presented on an alternate page, for those who prefer that scheme.
Several dataviz variations are presented on alternate pages - use the page navigation controls at the bottom to view them. They explore different layout options and colour schemes, and some alternative visuals. The Drill Down Graph PRO Custom Visual by ZoomCharts is the preferred visual, and the kind folks at ZoomCharts have supported this project.
Here’s how the animations are produced :
- screen capture using Windows 10 Game bar (Start-G)
- trim video using Windows 10 Photos app - aim for 1 second or less “paused” at the start and 2 at the end
- crop to focus on the animated part of the screen using https://www.freeconvert.com/crop-video. Save as mp4 (for twitter, youtube)
- convert to gif using https://ezgif.com/video-to-gif (for github)
THIS REPORT IS NOT HEALTH ADVICE - REFER TO YOUR LOCAL HEALTH AUTHORITY.
🤝 Support
Contributions, issues, feature requests and sponsorship are all welcome!
Give a ⭐️ if you like this project!