Mathematica notebook containing model and analysis

Mathemetica Notebook with the model description and analysis to create the Figures presented in the manuscript

R Script for sensitivity analysis

R script for the sensitivity analysis as described in the manuscrip

Illustrations of partitioned phylogenies and MCMC proposals modifying them.

<p>Nodes in all cases are coloured by the partition element containing them. (A) An example partitioned phylogeny. Tips are labelled by the hosts that the isolates corresponding to them were taken from. Where more than one isolate is taken from a host <i>a</i>_<i>i</i>, <i>c</i>(<i>a</i>_<i>i</i>) is labelled; in all other cases <i>c</i>(<i>a</i>_<i>i</i>) is the single tip corresponding to an isolate taken from that host. Black diamonds designate nodes that are not ancestral under the partition. The hosts <i>a</i>₇ and <i>a</i>₈ are root-blocked by <i>a</i>₆ due to the position of <i>c</i>(<i>a</i>₆) (black cross). (B) The downward infection branch move. The move attempts to move the node <i>u</i> from the green partition element to the red (which already contains its parent <i>uP</i>). In i), the move is impossible because <i>u</i> is the MRCA node of the tips in the green element. In ii), it can be done with no further modifications required to obey the rules. In iii), the node <i>uC</i>₂, which is not ancestral under the initial partition, must also be moved to the red element so the result obeys the rules. (C) The upward infection branch move. The move attempts to move the node <i>vP</i> from the red partition element to the green (which already contains its child <i>v</i>). In i), the move is impossible because <i>vP</i> is ancestral under the partition and the host represented by the green element is root-blocked by the host represented by the red. In ii), it can be done with no further modifications required to obey the rules. In iii), the node <i>vS</i>, which is not ancestral under the initial partition, must also be moved to the green element, and in iv) the node <i>vG</i> must be because <i>vS</i> is ancestral. (D) The type A phylogeny moves. The exchange move exchanges the nodes <i>u</i> and <i>v</i>; the subtree slide and Wilson-Balding moves change the position of the node <i>u</i> and its parent <i>uP</i>. (E) The type B phylogeny moves. The exchange move exchanges the nodes <i>u</i> and <i>v</i>; the subtree slide move the node <i>w</i> and its parent <i>wP</i>, and the Wilson-Balding the node <i>v</i> and its parent <i>vP</i>. After the latter two moves the transplanted parent node is randomly assigned to one of two new partition elements with equal probability.</p

Accuracy of the reconstruction of the phylogeny. Each violin plot represents the density of a statistic calculated from the results of separate analyses of 25 simulated datasets; the clock model used to generate the dataset and the analysis method are indicated on the <i>y</i>-axis.

<p>(A) posterior median of mean bias in estimation of all pairwise TMRCAs. (B) posterior median of mean error in estimation of all pairwise TMRCAs. (C) Posterior median SPR distance from the true phylogeny.</p

The five possible transmission tree structures of a phylogenetic tree with three tips, depicted as partitions of the nodes of a phylogeny (above) and as directed graphs amongst the hosts A, B and C (below).

<p>The five possible transmission tree structures of a phylogenetic tree with three tips, depicted as partitions of the nodes of a phylogeny (above) and as directed graphs amongst the hosts A, B and C (below).</p

Accuracy of the reconstruction of the transmission tree.

<p>Each violin plot represents the density of a statistic calculated from the results of separate analyses of 25 simulated datasets; the clock model used to generate the dataset and the analysis method are indicated on the <i>y</i>-axis. (A) posterior median of mean bias in estimation of infection dates. (B) posterior median of mean error in estimation of infection dates. (C) Posterior median proportion of hosts whose infector is correctly identified. (D) Proportion of hosts whose infector is correctly identified in the maximum parent credibility (MPC) transmission tree.</p

Estimates of prevalence ratios (PR) weighted by age group for each of the morbidity markers assessed using different diagnostic tools and test for homogeneity of the probability of detecting morbidity in infected children.

<p>Comparisons between preschool-aged (1–5 years) versus primary school-aged (6–10 years) children. Prevalence ratios significantly higher than 1 are shown in bold.</p><p>^aTest statistic could not be computed.</p><p>Estimates of prevalence ratios (PR) weighted by age group for each of the morbidity markers assessed using different diagnostic tools and test for homogeneity of the probability of detecting morbidity in infected children.</p

Flowchart indicating number of children enrolled in the study and excluded from the final analysis.

<p>Flowchart indicating number of children enrolled in the study and excluded from the final analysis.</p

Multiple logistic regression odds ratios (OR) to investigate factors associated with the prevalence of morbidity assessed using different diagnostic tools.

<p>Significant effects (p<0.05) are shown in bold.</p><p>^aOR not adjusted for serological infection status;</p><p>^bOR not adjusted for age group effect.</p><p>Multiple logistic regression odds ratios (OR) to investigate factors associated with the prevalence of morbidity assessed using different diagnostic tools.</p

Non-metric multidimensional scaling (NMDS) ordination in 2-dimensional configurations by sex, age-group and <i>S. haematobium</i> infection status determined using parasitological (A) and serological diagnostic techniques (B).

<p>Subgroup centres are represented by the bigger closed (●), or open (○) points, and the distance between these centres is proportional to the level of dissimilarities between subgroups.</p