coiaf: Directly estimating complexity of infection with allele frequencies
Fig 3
Comparison between THE REAL McCOIL and coiaf.
The COI estimation using (A) the Variant Method and (B) the Frequency Method is compared against the THE REAL McCOIL. (C) The distribution of differences between our estimation and THE REAL McCOIL’s estimation is shown. This difference is computed by subtracting the THE REAL McCOIL’s median estimation of the COI from our estimated value of the COI. The high density observed above 0 for the Frequency Method occurs because the Frequency Method is undefined for a COI of 1. Consequently, for samples that THE REAL McCOIL estimates as having a COI equal to 2, the distribution of our estimates of the COI using the Frequency Method is skewed greater than 2 (B), in contrast to the Variant Method, which exhibits lower skewness (A).