r

Rcpp implementation of [hmmIBD](https://github.com/glipsnort/hmmIBD).

Individual based malaria transmission model for the study of P. falciparum pfhrp2 gene deletions

Infection composition estimation in R

Rcpp implementation of [THEREALMcCOIL](https://github.com/Greenhouse-Lab/THEREALMcCOIL).

Vaccination model of SARS-CoV-2 transmission.

Paper outbreak teaching practical

An R package to interact with DHS surveys

Compartmental model of SARS-CoV-2 transmission.

This is an overview of the squire package, which is a deterministic model of COVID-19 transmission. The squire model was developed as part of the Imperial College COVID-19 Response Team and has been key in a number of our COVID-19 projects and publications to date, including: This is a brief overview of the model, which is fully described at https://github.com/mrc-ide/squire Overview squire is a package enabling users to quickly and easily generate calibrated estimates of SARS-CoV-2 epidemic trajectories under different control scenarios.

An individual-based simulation model of malaria epidemiology and parasite genetics