To illustrate the connections between software outputs, we have chosen a few focal packages that capture some portion of the graph.

individual is an R package for specifying and simulating individual-based models. It is used in the department for individual-based malaria and covid models.

Naomi is a model for subnational HIV estimates. It is exposed to the web via an API and a web application, with more details available at https://reside-ic.github.io/projects/naomi/

The odin package is a “domain specific language”, hosted in R, for representing and compiling ordinary differential equations. Currently it is being used within the department for research on malaria, measles, HIV, flu and COVID.

orderly is a lightweight system for reproduducible reporting, in R. Composed of an R package, orderly and a web application, OrderlyWeb, orderly makes it straightforward to associate analyses with their inputs, version outputs and organise and distribute everything with a user-friendly front-end. It is widely used in the department.