jeanpaulrsoucy / getddd

Get WHO Defined Daily Dose

About me

Hello! My name is Jean-Paul R. Soucy and I am a PhD candidate in infectious disease epidemiology at the Dalla Lana School of Public Health at the University of Toronto. My research interests focus on the use of emerging data sources in infectious disease surveillance.

Connect with me on Twitter. Find my personal website at jprs.me and my writing at Data Gripes. Code related to my blog can be found in the data-gripes repository.

My repositories

Table of contents

• COVID-19 Canada Open Data Working Group
• Python & R packages
• Reproducible research
• Presentations & workshops
• Miscellaneous

Software packages are highlighted with code text.

COVID-19 Canada Open Data Working Group

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COVID-19 datasets

• Covid19Canada: The original COVID-19 Canada Open Data Working Group dataset
• CovidTimelineCanada: The Timeline of COVID-19 in Canada, a definitive COVID-19 dataset for Canada
• Covid19CanadaArchive: The Canadian COVID-19 Data Archive
• Covid19CanadaBot, Covid19CanadaETL, Covid19CanadaDataProcess, Covid19CanadaData: Automated COVID-19 data collection pipeline

Other CCODWG projects

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• Covid19CanadaArchive-data-explorer: Data explorer for the Canadian COVID-19 Data Archive
• CovidTimelineCanada-js-dashboard: A simple JS dashboard for the Timeline of COVID-19 in Canada Dataset
• Covid19CanadaDashboard: The original COVID-19 Canada Open Data Working Group dashboard
• Covid19CanadaAPI: Python-based API for the COVID-19 Canada Open Data Working Group dataset
• WhatHappenedCovid19InCanada: Landing page for the What Happened? COVID-19 in Canada project
• CovidDataStandard
• CovidStoriesCanada
• FAIR COVID-19 Data for 🇨🇦

Python & R packages

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In addition to the COVID-19 data automation pipeline described above, I have also created the following R and Python packages:

• archivist: Python-based digital archive tool currently powering the Canadian COVID-19 Data Archive
• getDDD: Download defined daily dose (DDD) information for selected ATC codes from the website of the WHO Collaborating Centre for Drug Statistics Methodology

Reproducible research

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Wherever possible, I aim to publish reproducible research with open data:

• covid-19-mobility: Public transit mobility as a leading indicator of COVID-19 transmission in 40 cities during the first wave of the pandemic
• covid-19-antibiotic: Antibiotic prescribing in patients with COVID-19: A rapid review and meta-analysis
• ccodwg-scientific-data: A sub-national real-time epidemiological and vaccination database for the COVID-19 pandemic in Canada
• covid-19-coinfection-metaregression: Predictors and Microbiology of Co-Infection in Patients with COVID-19: Living Rapid Review Update and Meta-Regression
• california-counties-suicide-and-temperature: The Effect of Average Temperature on Suicide Rates in Five Urban California Counties, 1999–⁠2019: An Ecological Time Series Analysis
• covid-19-patients-amr-meta-analysis: Antimicrobial resistance in patients with COVID-19: a systematic review and meta-analysis
• covid-19-amr-meta-analysis: Antimicrobial resistance in patients with COVID-19: a systematic review and meta-analysis
• covid-19-mobility-responsiveness: Characterizing responsiveness to the COVID-19 pandemic in the United States and Canada using mobility data

Presentations & workshops

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• cssc-2021-r-shiny-workshop: What makes R Shiny so shiny? A step-by-step introduction to interactive dashboards in R (2021)
• dlsph-student-conf-2022-web-scraping-workshop: Web scraping for public health (2022)

Miscellaneous

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COVID-19 data

• canada-covid-vaccine-coverage
• ices-vaccine-coverage-by-fsa-time-series
• on-pharmacy-covid-vaccines
• covid-random-charts
• covid-19-cargill

Other

• canada-mortality-rates-by-age
• west-nile-canada
• lyme-usa-1993-2009
• r-approx-1

Gists

Find my GitHub gists here.

getddd's Issues

Add support for combined product DDDs

Add function that looks for ATC codes in the combined product DDD table (https://www.whocc.no/ddd/list_of_ddds_combined_products/). Since these data are given in a different format, some special processing will have to be done (e.g. interpreting the dosage form column).

Progress:

• Added partial supporting by reporting when ATC codes are in the combined product table.

Future:

• Interpret fields in the combined product table (e.g. convert dosage_form -> route)
• Extract ATC level info for combined products during initial search to limit number of queries
• After entries are processed, report entries that are not unique (excluding brand name)

Notes may be truncated

For ATC code "J01XX05", the notes "hippurate" and "mandelate" are truncated to "hippura" and "mandela".

Add some basic sanity checks to inputs

All ATC codes are 7 characters long; everything else supplied to the getDDD() function should be thrown out. The function could also check whether inputs are formatted like ATC codes (e.g. letter-integer-integer-letter-letter-integer-integer).