Contact Tracing Covid-19 cases: R Shiny App available for download

Hi community,

If you are using the DHIS2 Tracker metadata package for Covid-19 surveillance, you may be using the “Relationships” feature to link suspected cases with their contacts. As of v2.33 there are limited features for analytics based on tracker relationships data, making it difficult to trace all the possible links between confirmed Covid-19 cases, their contacts, and their “contacts of contacts”.

To address this gap and support contact tracing efforts, I’ve released a prototype R Shiny app around the Covid-19 metadata package. In short, it analyzes your system’s relationship data across “contact registration” and “case-based surveillance” programs, and displays these in interactive/customizable network diagrams.

How might network analysis be practically helpful for contact tracing?
Let’s say you’re at a district or hospital and are sorting through confirmed Covid cases for follow-up. Some have no contacts, some have many. You look at the Network Model tab and filter to your location. You see two confirmed cases connected to a larger cluster; scanning the data, you see they have a higher “centrality” score than others.

When searching for one of the confirmed cases in the Contact Tracer tab, you see that the case has a contact of a contact that is a suspected case, with many recorded contacts, and whose symptoms started just days after the confirmed case. In all this case is less than 5 degrees removed from 11 contacts/cases. So you might want to start by calling the connections of this confirmed ID.

The contact tracer tab also helpfully lists the ID’s of all of the contacts connected to a single individual case. You can select any of these ID’s and it will take you directly to the tracker dashboard. This can potentially support follow-up workflows if you have the correct level of access, as with the current set of DHIS2 features you have to go to each index case’s tracker dashboard separately; here you can switch between them quite quickly by choosing a different root node ID.

How might this app support Covid-19 data analysis?
At a higher level, you can explore all relationships as an interactive network diagram, and see what types of cases (positive, suspected, contacts) are most commonly related. For example, in the Analysis tab, you can see the average number of contacts and suspected cases that are related to cases whose symptoms started in the last month. You can also download these data for use in other analysis software.

A generic network modeling app within DHIS2 should be available in the coming months, but this might be a useful tool in the short-term.


Disclaimer: this app has been tested on demo instances with 6000+ TEI, but not production systems. Please share your feedback on Github or below.


Thanks, @brian, for sharing this exciting piece of work! If available, please could you also share a link to the hosted app. Thanks

Hi @INyabuto, the live demo of the app is hosted at this link : Covid Relationships Explorer Demo

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UPDATE: HISP Sri Lanka and HISP Oslo have developed a DHIS2 app to model the generic relationships between tracked entity instances.

Since this is a generic DHIS2 app, you do not need to host a separate R Shiny app, or use metadata from the Covid-19 metadata package, to visualize the relationship networks in your DHIS2 instance. Simply install the app into your DHIS2 system as described in Pamod’s post above.