Epidemiological and genomic parameters for ten major outbreak causing pathogens.

<p>Epidemiological and genomic parameters for ten major outbreak causing pathogens.</p

Impact of transmission divergence on outbreak reconstruction.

<p>Transmission divergence is defined as the number of mutations separating pathogen WGS sampled from transmission pairs. <b>A) Change in accuracy of outbreak reconstruction.</b> Accuracy of outbreak reconstruction is defined as the proportion of correctly assigned ancestries in the consensus transmission tree, itself defined as the tree with the most frequent posterior infector for each infectee. Coloured points represent individual simulated outbreaks. The solid black line represents the fitted relationship of the form <i>i</i>—<i>i</i>*exp(-<i>a</i>*<i>K</i>), where <i>K</i> is the transmission divergence and <i>a</i> and <i>i</i> the fitting variables. Dotted black lines represent the corresponding 95% prediction interval. <b>B) Change in posterior entropy.</b> Posterior entropy is related to the number of plausible posterior infectors for a given case. Lower average entropy indicates greater statistical confidence in the proposed transmission tree. The solid black line represents the fitted relationship of the form <i>i</i>*exp(-<i>a</i>*<i>K</i>)—<i>i</i>, where <i>K</i> is the transmission divergence and <i>a</i> and <i>i</i> the fitting variables.</p

Impact of the proportion of unique sequences on outbreak reconstruction.

<p><b>A) Change in accuracy of outbreak reconstruction.</b> Accuracy of outbreak reconstruction is defined as the proportion of correctly assigned ancestries in the consensus transmission tree, itself defined as the tree with the most frequent posterior infector for each infectee. Coloured points represent individual simulated outbreaks. The solid black line represents the fitted linear model, the dotted black lines the 95% prediction interval. <b>B) Change in posterior entropy.</b> Posterior entropy is related to the number of plausible posterior infectors for a given case. Lower average entropy indicates greater statistical confidence in the proposed transmission tree. The solid black line represents the fitted linear model, the dotted black lines the 95% prediction interval.</p

epicontacts

<p>A collection of tools for representing epidemiological contact data, composed of case line lists and contacts between cases. Also contains procedures for data handling, interactive graphics, and statistics.</p