EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering
Fig 4
(a) Proportion of replicates that capture the true value of the parameter within their HPD intervals (y-axis) of increasing credible mass alpha (x-axis), for the parameters: β infection parameter (green), γ recovery parameter (blue), φ case sampling rate (yellow) and ψ sequence sampling rate (orange). For the infection rate parameter β (which varies over time), the y-axis reflects the average proportion of the β trajectory captured in the HPD interval across all replicates (b) Mean inferred value and 95% HPD interval of the parameter (y-axis) plotted against the true value of the parameter (x-axis). For the infection parameter β, a subset of 1000 values of βt is shown for clarity in the plot as β varied over time in the simulations and models, so each replicate resulted in the inference of many βt values. For both graphs the grey dotted line indicates the ‘perfect’ result: perfect calibration for (a) and perfect agreement between true and inferred parameters for (b).