Reliability of the multiplicity of infection (MOI) estimations for only one combination of parameters (i.e. run) per transmission intensity (i.e. run 12, 36, and 60 for the low-, moderate-, and high transmission intensities, respectively).

For each category, the horizontal central solid line represents the median, the diamond represents the mean, the box represents the interquartile range (IQR) from the 25th to 75th centiles, the whiskers indicate the most extreme data point which is no more than 1.5 times the interquartile range from the box, and the dots show the outliers, i.e. the points beyond the whiskers. The upper, middle, and lower row panels correspond to simulations under low-, moderate-, and high-transmission settings, respectively (S1 and S2 Tables). A) Accuracy of MOI estimates, defined as the difference between estimated and true MOI per host. While null values highlight accurate MOI estimates (indicated by a dashed black horizontal line), the positive and negative values highlight over- and under-estimation, respectively. Estimates with the neutral SNP-based approach (THE REAL McCOIL) are indicated in green, and those with the var gene-based approach (varcoding) are indicated in blue. The dark and light green or blue colors indicate respectively MOI estimations made without and with a measurement model (Fig 2). The column panels show differences for specific true MOI values. B) Population distribution of the estimated and true MOI per host from the simulated “true” values and those estimated with the methods indicated by the colors similar to panel A. (EPS)