Genotype-specific scrapie risk and corresponding estimates for the relative susceptibility.

<p>Estimates, obtained in Ref. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139436#pone.0139436.ref015" target="_blank">15</a>] from culled-flocks data, of the genotype-specific risk of being tested scrapie positive, for genotypes (or groups of genotypes) without ARR allele, relative to the ARQ*/VRQ group of genotypes.</p

Scale parameter distribution.

<p>Histogram of 22 estimated values for the transmission scale parameter <i>ρ</i>₀. The dashed line is a Weibull frequency distribution with mean and variance equal to the mean and variance of the <i>ρ</i>₀ estimates for <i>Se</i> = 0.75.</p

Threshold pattern.

<p>Expected within-flock infection prevalence against the “expected” within-flock reproduction number <math><mrow><mi>β</mi><mo stretchy="true">¯</mo><mi>β</mi><mrow><mo>−</mo><mn>1</mn></mrow><msubsup><mi>R</mi><mn>0</mn>w</msubsup></mrow></math>. The expected within-flock infection prevalence is computed by weighing the genotype-specific detected infection prevalence in tested animals by the frequency of the genotype in genotyped animals. As this computation uses detected prevalence it assumes <i>Se</i> = 1.</p

Dependence on sensitivity parameter.

<p>Mean (left-hand panel) and coefficient of variation (right-hand panel) of estimated <i>ρ</i>₀ values as a function of the sensitivity <i>Se</i>.</p

Distribution of the within-flock reproduction number.

<p>Histogram of 22 estimated values for the reproduction number <math><mrow><msubsup><mi>R</mi><mn>0</mn><mi>w</mi></msubsup></mrow></math>.</p

The fraction of the total number of new infections as estimated by Boender et al. (2007) from the 2003 epidemic data attributable to the wind-borne route for various choices of a cut-off distance up until which the new infections are occurring.

<p>The fraction of the total number of new infections as estimated by Boender et al. (2007) from the 2003 epidemic data attributable to the wind-borne route for various choices of a cut-off distance up until which the new infections are occurring.</p

The distance-dependent probability of infection for the parameter values given in <b>Table 1</b> and the Boender et al. (2007) transmission kernel (and its 95% confidence bounds).

<p>The calculation caters for the prolonged infectiousness of the wind-dispersed material beyond the (direct-contact) infectious period of the source farm.</p

Default parameter values used in the model calculations.

<p>*parameter value estimated from the data in the indicated reference.</p

Estimated transmission kernels λ^c and their confidence bounds.

<p>The basic kernel parameterization is given by <i>c = </i>0 in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095278#pone.0095278.e004" target="_blank">Equation (1</a>) and (2) without farm-size dependence (dashed blue line) and the best-fit kernel <i>c = </i>5 (solid red line), where N_S is set equal to the average size of the farms in the OA (1038.3) and N_I to the average size of the infected farms in the OA (1515.7), with their confidence bounds (thinner lines).</p

The number of contacts, the estimated per-contact transmission probabilities (95% CI), and the percentage of infections caused for the potentially infectious contacts during the HPAI (H7N7) epidemic in the Netherlands in 2003.

<p>The number of contacts, the estimated per-contact transmission probabilities (95% CI), and the percentage of infections caused for the potentially infectious contacts during the HPAI (H7N7) epidemic in the Netherlands in 2003.</p