Epiverse-TRACE Autumn 2023 showcase

pipeline demo

Carmen Tamayo

Karim Mané

Abdoelnaser Degoot

Bankole Ahadzie


November 30, 2023

This showcase is part of a regular cycle of online meetings to present tools for epidemiology.

Time Item Presenter
12:00 - 12:05


  • Intro to Epiverse-TRACE
  • Purpose of the session
  • Housekeeping
    • 15 min for PKGs,
    • 25 min for demo
    • 10 min for Q & A
  • Closing remarks
12:05 - 12:06 One line intro to Karim & readepi & cleanepi Carmen
12:06 - 12:22

readepi & cleanepi PKGs

  • Purpose (motivation for developing the PKGs, problem they are trying to address)
  • Features
12:22 - 12:23 One line intro to Degoot & demo pipeline Carmen
12:23 - 12:45 Pipeline demo: Degoot
  • overview
  • Acutal demo
12:46 - 12:58 Questions Attendees, all (Carmen moderates)
12:58 - 13:00 Closing remarks Carmen

readepi slides

cleanepi slides

pipeline demo

  • Coming soon

Questions & answers

Will {cleanepi} package have an option to create new columns and to perform other actions such as filtering and sorting data?

Some cleaning processes in the {cleanepi} package actually create new columns. {cleanepi} does data filtering but not data sorting, which can be done with other existing packages.

When will the {readepi} and {cleanepi} packages be available on CRAN?

These packages are still in development stage, and we intend to submit them to CRAN soon.

Does {cleanepi} has an option to show which IDs are been cleaned? This will help to inform the curators about which ID as wrong?

Yes, {cleanepi} reports any change to the end-user.

Will there be a package in epiverse for spatial analysis to visualize distribution of cases during epidemics?

Yes. We intend to create a package for visualization.

Have you thought about combining the epiverse packages into a single package (like tidyverse package for example) so the user won’t have to load the packages one by one?

Yes. In fact such package is already under development, see epiverse.

Can the epiverse be used to model severity or case fatality of outbreaks against counter factual to proof effectiveness of disease control interventions?

For this, we would say that Epiverse-TRACE packages such as {cfr} provide robust methods for computing unbiased and timely case fatality ratios. With such knowledge, it is up to the user to decide whether or not control measures are effective.

Is there any plan to account for genomic data?

Yes. We intend to create a package for reading and integrating genomic data with case data.


Go to the “Watch the recording” button on the event website to watch back this showcase.



BibTeX citation:
  author = {Tamayo, Carmen and Mané, Karim and Degoot, Abdoelnaser and
    Ahadzie, Bankole},
  title = {Epiverse-TRACE {Autumn} 2023 Showcase},
  date = {2023-11-30},
  url = {https://epiverse-trace.github.io/slides/showcase-november-2023},
  langid = {en}
For attribution, please cite this work as:
Tamayo, Carmen, Karim Mané, Abdoelnaser Degoot, and Bankole Ahadzie. 2023. “Epiverse-TRACE Autumn 2023 Showcase.” November 30, 2023. https://epiverse-trace.github.io/slides/showcase-november-2023.