Optimal experimental designs for estimating genetic and non-genetic effects underlying infectious disease transmission

Table 2 Data/model scenarios

Data	Design	Residual	Group effect	Fixed effect	Information source
Inf. + Rec	Single group (no dominance estimate)	✕	✕	✕	Figure 3
Inf. + Rec	Pure (no dominance estimate)	✕	✕	✕	Figure 4
Inf. + Rec	Mixed (no dominance estimate)	✕	✕	✕	Figure 5
Inf. + Rec	Pure/mixed (no dominance estimate)	✓	✓	✓	Figure 6
Inf. + Rec	Pure (dominance estimate)	✕	✕	✕	Additional file 9: Fig. S3
Inf. + Rec	Mixed (dominance estimate)	✕	✕	✕	Additional file 10: Fig. S4
Inf. + Rec	Pure/mixed (no dominance estimate)	✓	✕	✕	Additional file 11: Figs. S5–S8
Inf. + Rec	Pure/mixed (no dominance estimate)	✕	✓	✕	Additional file 11: Figs. S5–S7
Inf. + Rec	Pure/mixed (no dominance estimate)	✕	✕	✓	Additional file 11: Figs. S5–S7
Rec. (no Inf.)	Pure/mixed (no dominance estimate)	✕	✕	✕	Additional file 11: Figs. S5–S7
Periodic DS checks	Pure/mixed (no dominance estimate)	✕	✕	✕	Additional file 11: Figs. S5–S7
Inf. + Rec	Pure/mixed (no dominance estimate)	✓	✓	✓	Additional file 11: Figs. S5–S7
Inf. + Rec	Pure/mixed (dominance estimate)	✓	✓	✓	Additional file 12: Fig. S9
Inf. + Rec	HWE	✕	✕	✕	Additional file 15: Fig. S12

This table summarises all the data/model scenarios used in this paper. The columns are as follows: Data (“Inf. + Rec.” means that infection and recovery times of all individuals are assumed to be known exactly, “Rec.” means only recovery times are known, and “Periodic DS checks” means the disease status of individuals is periodically checked); Design (this includes the five optimal designed illustrated in Fig. 2 as well as “HWE”, in which individuals are randomly allocated genotypes assuming Hardy–Weinberg equilibrium); Residual (a tick (✓) is indicated if the model incorporates the residuals \({\varvec{\upvarepsilon}}\) =(\({{\varvec{\upvarepsilon}}}_{{\varvec{g}}}\), \({{\varvec{\upvarepsilon}}}_{{\varvec{f}}}\), \({{\varvec{\upvarepsilon}}}_{{\varvec{r}}}\)) in Eq. (2)); Group effect (a tick (✓) is indicated if the model incorporates the random group effect \({G}_{z}\) in Eq. (1)); Fixed effect (a tick (✓) is indicated if the model incorporates a fixed effect \(\mathbf{b}\) = (\({\mathbf{b}}_{{\varvec{g}}}\), \({\mathbf{b}}_{{\varvec{f}}}\), \({\mathbf{b}}_{{\varvec{r}}}\)) in Eq. (2)); and Information source (indicates the figure in the main text and in Additional files that relates to the corresponding scenario)

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