Table 1.
The observational model for categorical method.
Fig 1.
True vs. estimated values of COI (A) and allele frequencies (B) using COIL and THE REAL McCOIL.
Each blue dot represents a sample. The black bar and the grey box show the median and 25% to 75% quantile. THE REAL McCOIL estimated allele frequencies and COI better than COIL, especially when the average COI was high and the majority of infections were polygenomic.
Fig 2.
Estimates of COI in Nagongera, Walukuba, and Kihihi.
(A) Estimates of COI by COIL, THE REAL McCOIL, and msp2. For THE REAL McCOIL, the point estimates of COI shown are medians from the posterior distributions. The COI estimated by THE REAL McCOIL in Nagongera and Walukuba were similar, and much higher than that in Kihihi (median COI = 5 [Nagongera], 4.5 [Walukuba], and 1 [Kihihi]; permutation test, p-values = 0.158 [Nagongera vs. Walukuba], 0.002 [Nagongera vs. Kihihi], 0.0006 [Walukuba vs. Kihihi]). Allele counts > 5 in msp2 typing were grouped into a single category due to difficulties in accurately distinguishing artifacts from true alleles at high complexities of infection. The dashed red lines represent the medians of COI in three regions. (B) The spatial distribution of estimated COI by THE REAL McCOIL in three regions. Small random noise was added to the location of samples in the map. COI of samples collected from the West of Walukuba was higher than those from the East of Walukuba (medians = 5 [West] and 3 [East], p-value = 0.027).
Fig 3.
(A) Estimated COI by THE REAL McCOIL was negatively associated with FWS. (B) FWS in Kihihi was higher than Nagongera and Walukuba. The FWS values shown were calculated using population allele frequencies estimated from categorical method of THE REAL McCOIL.