156 research outputs found

    Northwich time-series data.

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    <p>Dashed lines are the time points in which the forward simulation resets in the epidemics = ‘break’ argument for a threshold for three.</p

    Output results from the runtsir function for London.

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    <p>Subplots A) and B) are the cumulative births against cumulative cases regression and estimated reporting rate, the C) and D) are the profiled from <i>Z</i><sub><i>t</i></sub> and then reconstructed <i>S</i>, E) is 26-point <i>β</i><sub><i>t</i></sub> with the <i>α</i> and mean <i>β</i> (indicated as ) estimate, and F) and G) are the data (blue) against 10 randomly chosen stochastic simulations (red) and the (inverse) data against mean of the simulations with confidence intervals.</p

    Sampling scales for acute RNA viruses and the associated phylodynamic processes that viral genome sequence data and host sampling can elucidate.

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    <p>Sampling scales for acute RNA viruses and the associated phylodynamic processes that viral genome sequence data and host sampling can elucidate.</p

    The forward simulations for the Northwich time-series data under an epidemic-ahead fit using a threshold of three.

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    <p>The color coding in the panels shown here are the same as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185528#pone.0185528.g001" target="_blank">Fig 1</a>.</p

    Summary and description of the main functions in the tsiR package.

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    <p>Summary and description of the main functions in the tsiR package.</p

    Fluctuating genetic diversity of influenza A virus.

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    <p>The figure shows a Bayesian skyline plot of changing levels of genetic diversity through time for the HA gene (165 sequences) of A/H3N2 virus sampled from the state of New York, US, during the period 2001–2003. The <i>y</i>-axes depict relative genetic diversity (<i>N</i><sub>e</sub><i>t</i>, where <i>N</i><sub>e</sub> is the effective population size, and <i>t</i> the generation time from infected host to infected host), which can be considered a measure of effective population size under strictly neutral evolution. Peaks of genetic diversity, reflecting the seasonal occurrence of influenza, are clearly visible. See <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000505#pcbi.1000505-Rambaut1" target="_blank">[30]</a> for a more detailed analysis.</p

    Heat map illustrating how incidence of epidemics change with changing birth rate and amplitude.

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    <p>The contour plot illustrates the transition from annual to biennial epidemics. The timing of the epidemic did not change significantly with changing birth rate () and amplitude (). ( = 0,  = 1000,  = 0).</p

    Bifurcation diagrams showing the impact of varying birth amplitude () on the periodicity of the epidemics.

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    <p>Simulations use extrapolated initial conditions (the numbers of susceptibles, exposed, infectives, and recovered at the end of one simulation are used to start the next simulation <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075806#pone.0075806-Keeling1" target="_blank">[27]</a>). In Panel A the first simulation is at  = 0 (left hand of the x axis), then is increased in the subsequent simulations; to further sample the bifurcation structure, Panel B reverses this order, starting at  = 1. Black points represent the relative size of the incidence peaks, blue circles represent the period of the attractor, while the background is a heat map of the power spectral densities where the color red signifies higher power. In Panel B, at high levels of , there are both annual and biennial components present but the power is stronger for the biennial component. ( = 35/1000,  = 0,  = 1000,  = 0).</p

    One-dimensional bifurcations of the effect of varying values given different baseline values of (0.1, 0.2, 0.3, 0.4) and (in phase, anti-phase).

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    <p>Black points represent the relative size of the epidemic peaks, blue circles represent the period of the attractor, while the background is a heat map of the the power spectral densities where the color red signifies higher power. In all of the figures, the presence of an annual and biennial component is always present even though, for instance, an attractor may have a period of four years. The bottom panel in each of the figures shows the main Lyapunov exponent, when the system bifurcates the Lyapunov exponent equals zero (touches the horizontal line), when the Lyapunov exponent is greater than zero the dynamics are said to be chaotic. ( = 30/1000,  = 1000 in all panels).</p
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