Making the DAEN information accessible.

Overview

AccessibleAdverseEventNotification

Making the DAEN information accessible.

The purpose of this repository is to make the information on Australian COVID-19 adverse events accessible. The Therapeutics Goods Administration (TGA) keeps a database of adverse reactions to medications including the COVID-19 vaccines. This Database of Adverse Event Notifications (DAEN) is available to the public via this awful web interface. The most recent two weeks is never available.

The DAEN website doesn't provide information in a format that might be useful for analysis. Instead you have to scrape the information by entering each individual day and collecting the results from two tables which might span multiple pages. I've already done that and the code is here (this code isn't great, but it is good enough to get the job done).

Please be aware that the numbers reported in DAEN are probably significantly less than the actual number of adverse events and deaths. As the DAEN website states:

Adverse event reports from consumers and health professionals to the TGA are voluntary, so there is under-reporting by these groups of adverse events related to therapeutic goods in Australia. This is the same around the world.

The scraped data is found in the data directory. These files are tab separated files which you can easily import in to a spreadsheet program. All of the files are only for COVID-19 vaccines.

  • DAEN_webscrape_simple.txt This file shows the date (twice for reasons that made sense at the time, but don't necessarily make sense anymore), the number of cases reported that day, the number of cases with a single suspected medicine for that day, and the number of deaths reported that day.
  • DAEN_webscrape_medsummary.txt This file gives a daily count of each adverse event category. Please note that if one patient had multiple adverse events, then each event would be counted in the appropriate category.
  • DAEN_webscrape_listofreports.txt This file provides the individual reports and includes sex and age (when recorded).

Figure 1 shows some of the basic information such as number of adverse events and deaths reported each day for the COVID-19 vaccines, myocarditis, pericarditis and the more general term cardiac disorder.

Figure 1 Figure 1.

Figure 2 shows a histogram of reported cases of myocarditis and pericarditis from the COVID-19 vaccine. Please note that the age group 10-19 is somewhat distorted as the age 10-11 should not receive the vaccine (although there are cases of 8 year olds getting the vaccine when that should not have occurred). This age group also has a significantly lower uptake than other age groups.

Figure 2 Figure 2.

Figures 3 and 4 plot the reports of myocarditis by age grouped by sex or manufacturer respectively. Figures 5 and 6 are the same for pericarditis. A '-' is used where an age was not given in the report.

Figure 3 Figure 3.

Figure 4 Figure 4.

Figure 5 Figure 5.

Figure 6 Figure 6.

Figure 7 shows how the histogram for myocarditis has progressed over time.

Figure 7
Figure 7.

Figure 8 shows the death rate of people in Australia who contracted COVID-19. Data taken from health.gov on 1/12/2021. Bottom graph is zoomed in to 1% to see what is happening with those under the age of 60.

Figure 8
Figure 8.

An implementation of the largeVis algorithm for visualizing large, high-dimensional datasets, for R

largeVis This is an implementation of the largeVis algorithm described in (https://arxiv.org/abs/1602.00370). It also incorporates: A very fast algori

336 May 25, 2022
Random dataframe and database table generator

Random database/dataframe generator Authored and maintained by Dr. Tirthajyoti Sarkar, Fremont, USA Introduction Often, beginners in SQL or data scien

Tirthajyoti Sarkar 249 Jan 08, 2023
Analysiscsv.py for extracting analysis and exporting as CSV

wcc_analysis Lichess page documentation: https://lichess.org/page/world-championships Each WCC has a study, studies are fetched using: https://lichess

32 Apr 25, 2022
.npy, .npz, .mtx converter.

npy-converter Matrix Data Converter. Expand matrix for multi-thread, multi-process Divid matrix for multi-thread, multi-process Support: .mtx, .npy, .

taka 1 Feb 07, 2022
PySpark bindings for H3, a hierarchical hexagonal geospatial indexing system

h3-pyspark: Uber's H3 Hexagonal Hierarchical Geospatial Indexing System in PySpark PySpark bindings for the H3 core library. For available functions,

Kevin Schaich 12 Dec 24, 2022
PipeChain is a utility library for creating functional pipelines.

PipeChain Motivation PipeChain is a utility library for creating functional pipelines. Let's start with a motivating example. We have a list of Austra

Michael Milton 2 Aug 07, 2022
Py-price-monitoring - A Python price monitor

A Python price monitor This project was focused on Brazil, so the monitoring is

Samuel 1 Jan 04, 2022
Tokyo 2020 Paralympics, Analytics

Tokyo 2020 Paralympics, Analytics Thanks for checking out my app! It was built entirely using matplotlib and Tokyo 2020 Paralympics data. This applica

Petro Ivaniuk 1 Nov 18, 2021
Pandas and Dask test helper methods with beautiful error messages.

beavis Pandas and Dask test helper methods with beautiful error messages. test helpers These test helper methods are meant to be used in test suites.

Matthew Powers 18 Nov 28, 2022
Lale is a Python library for semi-automated data science.

Lale is a Python library for semi-automated data science. Lale makes it easy to automatically select algorithms and tune hyperparameters of pipelines that are compatible with scikit-learn, in a type-

International Business Machines 293 Dec 29, 2022
Data analysis and visualisation projects from a range of individual projects and applications

Python-Data-Analysis-and-Visualisation-Projects Data analysis and visualisation projects from a range of individual projects and applications. Python

Tom Ritman-Meer 1 Jan 25, 2022
Amundsen is a metadata driven application for improving the productivity of data analysts, data scientists and engineers when interacting with data.

Amundsen is a metadata driven application for improving the productivity of data analysts, data scientists and engineers when interacting with data.

Amundsen 3.7k Jan 03, 2023
Bigdata Simulation Library Of Dream By Sandman Books

BIGDATA SIMULATION LIBRARY OF DREAM BY SANDMAN BOOKS ================= Solution Architecture Description In the realm of Dreaming, its ruler SANDMAN,

Maycon Cypriano 3 Jun 30, 2022
A Python package for the mathematical modeling of infectious diseases via compartmental models

A Python package for the mathematical modeling of infectious diseases via compartmental models. Originally designed for epidemiologists, epispot can be adapted for almost any type of modeling scenari

epispot 12 Dec 28, 2022
The micro-framework to create dataframes from functions.

The micro-framework to create dataframes from functions.

Stitch Fix Technology 762 Jan 07, 2023
A lightweight, hub-and-spoke dashboard for multi-account Data Science projects

A lightweight, hub-and-spoke dashboard for cross-account Data Science Projects Introduction Modern Data Science environments often involve many indepe

AWS Samples 3 Oct 30, 2021
An ETL framework + Monitoring UI/API (experimental project for learning purposes)

Fastlane An ETL framework for building pipelines, and Flask based web API/UI for monitoring pipelines. Project structure fastlane |- fastlane: (ETL fr

Dan Katz 2 Jan 06, 2022
Building house price data pipelines with Apache Beam and Spark on GCP

This project contains the process from building a web crawler to extract the raw data of house price to create ETL pipelines using Google Could Platform services.

1 Nov 22, 2021
Describing statistical models in Python using symbolic formulas

Patsy is a Python library for describing statistical models (especially linear models, or models that have a linear component) and building design mat

Python for Data 866 Dec 16, 2022
Statistical Rethinking course winter 2022

Statistical Rethinking (2022 Edition) Instructor: Richard McElreath Lectures: Uploaded Playlist and pre-recorded, two per week Discussion: Online, F

Richard McElreath 3.9k Dec 31, 2022