In malaria, individuals are often infected with different parasite strains, with the complexity of infection (COI) giving the number of genetically different parasite strains in an individual. Changes in the mean COI in a population have been shown to be informative of changes in transmission intensity with a number of probabilistic likelihood and Bayesian models now developed to estimate COI. However, rapid, direct measures based on heterozygosity or FwS have not been directly related to the COI. This package features two rapid, direct measures for characterizing polyclonal infections.

# Install most recent released version
devtools::install_github("bailey-lab/[email protected]")

# Install development version
devtools::install_github("bailey-lab/coiaf")

In order to run real data, please refer to the Articles drop-down menu. Several articles detail how the algorithm works, how data is simulated to test the algorithm, and, importantly, how to run real data. A short example of running real data is included and outlines the necessary data structure and the commands to run.