Numbers of test rejections for simulations performed under the mechanistic model with dispersal parameter <i>γ</i> = 0.2.

<p>Grey bars: number of times that the null hypothesis was rejected and that the alternative was true; White bars: number of times that the null hypothesis was rejected and that the alternative was wrong. The rejection threshold was fixed at 0.05/3 (using Bonferroni’s correction). The number of sampling sites and the differences in the fitness coefficients are given under the x-axis of the top panels. Moreover, between each consecutive ticks, there are three bars corresponding, from left to right, to 1, 5 and 10 collected samples per sampling site. The results are provided for the bandwidth values (top left), (top right), (bottom left) and (bottom right).</p

Results of the ranking of pathogen strains observed within a natural epidemic of powdery mildew in <i>Plantago lanceolata</i>.

<p>The table provides frequencies of strains in the whole sample, estimated values of coefficients , and test <i>p</i>-values indicating the significance of the ranking between the pathogen strains. The strains were ordered with respect to the estimated values of .</p

Powdery mildew data and growth variable in a patch of <i>Plantago lanceolata</i> in the Åland islands.

<p>In all the panels the grey squares represent the grid cells covering the host population. Top panels: number of infected leaves in square cells at weeks 32 (left) and 34 (right) of year 2011 (dot size proportional to number of infected leaves that ranges between 0 and 137). The axis scales indicate the number of the cell from the most bottom-left cell. Bottom left: Growth variable (dot size linear in that ranges between −1.01 and 4.93). Bottom right: sites where samples were collected (46 samples in 22 sites; diamond: strain 1; plus: strain 2; triangle: strain 3; circle: strain 4; cross: strain 5).</p

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

Description of symbols used in the model.

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

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