Data & scripts_v2

ZIP folder containing all scripts, data and simulation results used in this study

Estimation output for the 2007 UK outbreak.

<p>Top left: posterior probabilities of transmissions (dot sizes proportional to probabilities). Top right: tree with the highest posterior probability mapped in space (black arrows). Bottom: posterior distributions (histograms) of mean latency duration (; left) and mean transmission distance (; right); dotted-dashed curves: prior distributions; solid lines: posterior medians; dotted lines: posterior quantiles 0.025 and 0.975.</p

Estimation output for the simulated outbreak.

<p>Top left: true transmissions (circles) and posterior probabilities of transmissions (dot sizes are proportional to probabilities). Top right: tree with the highest posterior probability (solid arrows); Only transmission is not consistent with the true tree (the true transmission is dashed arrow). Bottom: posterior distributions (histograms) of mean latency duration (; left) and mean transmission distance (; right); dashed lines: true values; dotted-dashed curves: prior distributions; solid lines: posterior medians; dotted lines: posterior quantiles 0.025 and 0.975.</p

Estimation output for the 2001 UK outbreak (Darlington cluster).

<p>Top left: posterior probabilities of transmissions (dot sizes proportional to probabilities). Top right: tree with the highest posterior probability mapped in space (black arrows). Bottom: posterior distributions (histograms) of mean latency duration (; left) and mean transmission distance (; right); dotted-dashed curves: prior distributions; solid lines: posterior medians; dotted lines: posterior quantiles 0.025 and 0.975.</p

Direct acyclic graph illustrating the dependencies in the model.

<p>Bold letters are used to represent sets of variables, with one variable per farm, e.g. . For a full description of the symbols, see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002768#pcbi-1002768-t002" target="_blank">Table 2</a>.</p

Description of symbols used in the model.

<p>Description of symbols used in the model.</p

Performance of the estimation algorithm over three series of 100 simulations (test, 2007, 2001).

<p>Performance of the estimation algorithm over three series of 100 simulations (test, 2007, 2001).</p

Summary statistics for parameters estimated from the survey data.

<p>Summary statistics for parameters estimated from the survey data.</p

Comparison of simulated and estimated dispersal kernels.

<p>From left to right: kernels with the minimum, lower quartile, median, upper quartile and maximum Kullback-Leibler (KL) distances (posterior mean), as estimated (red) under the most exhaustive scheme (Θ₄), based on simulated epidemics with short-, medium- and long-range kernels (from top to bottom; black). Kernels are represented by their marginal cumulative distribution function <i>F</i>^1<i>D</i> (with distance from the source represented on the log₁₀ scale). The mean KL distance is indicated for each estimation.</p

Susceptible-Exposed-Hidden-Detected-Removed (<i>SEHDR</i>) model of an individual’s epidemiological status.

<p>At <i>T</i>₀, patch <i>i</i> is planted with infectious (<i>I</i>) or susceptible (<i>S</i>) individuals with probabilities <i>p</i>_<i>i</i> and 1-<i>p</i>_<i>i</i>, respectively. An individual passes between compartments at event times <i>T</i>_<i>E</i>, <i>T</i>_<i>H</i>, <i>T</i>_<i>D</i> and <i>T</i>_<i>R</i>. Apart from <i>T</i>₀, only the detection time <i>T</i>_<i>D</i> can be known (yellow); all other event times are censored (blue). Infectious individuals from both within and outside the patch contribute to the force of infection , which is the expected number of infectious events affecting an individual over time interval (<i>t</i>_<i>r</i>−1, <i>t</i>_<i>r</i>]. The probability that a given susceptible (<i>S</i>) individual becomes exposed (<i>E</i>) in this time interval is 1-exp(-), assuming independent infection events. A latent period of duration <i>T</i>_<i>H</i>-<i>T</i>_<i>E</i> follows, after which the individual becomes infectious (<i>H</i>). Infectious individuals are removed (<i>R</i>) only after detection (<i>D</i>) or when the entire patch is removed. For simplicity, the <i>i</i> and <i>t</i>_<i>r</i> subscripts are omitted in the figure.</p