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We used default modelling settings as far as possible (Additional file 1: Appendix 1).
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As well as allowing us to model setting-specific transmission, the line list made it possible to directly calculate the case fatality ratio (CFR) in different settings.
Lineage-specific rates of substitution were then calculated with BASEML, with the same model settings as previously described, and a set species tree topology [ 90- 92].
For Models B and C, in each gene we chose each of all possible SNP pairs in turn to be the causal SNP pair, resulting in nearly 80,000 trait model settings in total for main and validation sets.
The chain heating parameter was set at 0.3 and apart from the model settings, the default settings were retained.
Furthermore, it allows the user to view model settings before the model has been assigned to a data set, whereas the show_model and get_model commands do not.
This data set is called the validation set and is used to compare the performance of candidate models or model settings.
Finally, they allow for a wide range of model settings.
See Sugimoto et al.21,24 for further details of the model settings.
Realistic model settings are required for accurate financial evaluation.
Most of the standard model settings were used, based on the previous successful implementation at Midway Atoll28.
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