Additional file 1: of Measuring windows of selection for anti-malarial drug treatments

Includes data that support and expand some of the interpretations and conclusions drawn in the main text, but whose inclusion would detract from the main argument

MOESM1 of Markov chain Monte Carlo and expectation maximization approaches for estimation of haplotype frequencies for multiply infected human blood samples

Additional file 1. Data that support and expand some of the interpretations and conclusions drawn in the main text, but whose inclusion would detract from the main argument

Effect of spatial heterogeneity (pooled data from 80 simulated locations) on estimates of initial allele frequency, dominance and selection parameters.

<p>The value of the selection coefficient was held constant at 0.1, 0.3, 0.6, 0.8 or 1 in all locations and in every generation, hence there are five rows of results corresponding to each of the 5 values of the selection coefficient. Dominance (<i>h</i>∼∪(0,1)) varied between simulated locations, but was constant over time within each location. The true value is the mean parameter value over all locations. The Pearson correlation coefficient (r) is between estimated and true values. TV is the percentage of the true values that are included in the 95% confidence interval of the estimate. [ ] is the mean width of the 95% confidence interval in all runs.</p

Effect of spatial heterogeneity on estimates of initial allele frequency, dominance and selection parameters.

<p>The value of the dominance coefficient was held constant at 0, 0.25, 0.5, 0.75 or 1 in all locations and in every generation, hence there are five rows of results corresponding to each of the 5 values of the dominance coefficient. The value of the selection coefficient (<i>s</i>∼<i>N</i>(0.15, 0.025)) varied between locations, but was held constant over time in each location. The true value is the mean parameter value over all locations. The Pearson correlation coefficient (r) is between estimated and true values. TV is the percentage of the true values that are included in the 95% confidence interval of the estimate. [ ] is the mean width of the 95% confidence interval in all runs.</p

The typical change in insecticide concentration in the field over time.

<p>As concentration decays with time after deployment there is a differential survival of genotypes. In period A the RR genotype will survive while the RS and SS dies: this makes the R allele recessive in this period. In period B both RR and RS survive making the R allele dominant in this period. In period C all genotypes can survive so no selection occurs. These are windows of selection, adapted from <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001387#pntd.0001387-Hastings2" target="_blank">[37]</a>.</p

Details of 100 idealized simulated datasets.

<p>The simulated datasets were used to check the precision and accuracy of the ML procedure.</p><p>*r correlation coefficient between original value and estimate, TV percentage of true values in the estimates 95% confidence interval and [ ] mean range value of the confidence interval.</p

Simulated evolution of resistance allele frequency over 120 generations under two different scenarios of dominance relationship and analysing the full dataset or subsets of data.

<p>Specifications in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001387#pntd-0001387-t002" target="_blank">Table 2</a>.</p

Effect of temporal heterogeneity on estimates of initial allele frequency, dominance and selection coefficients parameters.

<p>Three different scenarios were simulated: (A) dominance and selection are different in every generation, (B) selection coefficient was held constant in all generations but dominance was allowed to vary, (C) dominance was held constant in all generations while the selection coefficient was allowed to vary. The Pearson correlation coefficient (r) between estimate and true value is shown. TV refers to the percentage of the true values that are included in the 95% confidence interval of the estimate. [ ] is the mean range of the 95% confidence interval in all runs.</p

Specifications of datasets of Figure 2.

<p>Sampled generations and true parameter values and ML parameter estimates with respective 95% confidence intervals.</p

A tiny target deployed near the lakeshore for control of <i>G</i>. <i>f</i>. <i>fuscipes</i> on Big Chamaunga island, Kenya.

<p>A tiny target deployed near the lakeshore for control of <i>G</i>. <i>f</i>. <i>fuscipes</i> on Big Chamaunga island, Kenya.</p