The function creates a list of user-defined parameters.
create_parameter_list(no_predictors = 16, dependent_variable = "FOI", resample_grid_size = 20, grid_size = 5, no_samples = 1, vec_phis_R0_1 = c(1, 1, 0, 0), vec_phis_R0_2 = c(1, 1, 1, 1), prop_sympt = c(0.45, 0.85, 0.15, 0.15), prop_hosp = c(0.04, 0.1, 0.04, 0.04), FOI_grid = seq(0.002, 0.2, 0.002), sf_vals = seq(1, 0.1, -0.1), sat_functions_shapes = c(0, 5, 1600000), no_trees = 500, min_node_size = 20, all_wgt = 1, pseudoAbs_value = c(FOI = -0.02, R0_1 = 0.5, R0_2 = 0.5, R0_3 = 0.5, Z = -0.02), foi_offset = 0.03, EM_iter = 10, base_info = c("cell", "latitude", "longitude", "population", "ID_0", "ID_1", "ID_2"), extra_params = NULL)
| no_predictors | number of selected covariates used for model fitting and making predictions. |
|---|---|
| dependent_variable | character string of the fitted response variable (FOI). |
| resample_grid_size | resolution of the foi predictions (in km). Default = 20 (1/6 degree). |
| grid_size | size of the grid used for block bootstrapping. |
| no_samples | number of bootstrap samples. |
| vec_phis_R0_1 | numeric vector of length = 4 of the relative infectiousness of primary, secondary, tertiary and quaternary dengue infections, when assuming only primary and secondary infections are infectious. |
| vec_phis_R0_2 | numeric vector of length = 4 of the relative infectiousness of primary, secondary, tertiary and quaternary dengue infections, when assuming all four infections are infectious. |
| prop_sympt | numeric vector of length = 4 of the proportions of primary, secondary, tertiary and quaternary infections which are symptomatic. |
| prop_hosp | numeric vector of length = 4 of the proportions of primary, secondary, tertiary and quaternary infections requiring hospitalization. |
| FOI_grid | numeric vector of force of infection values used for mapping FOI to number of infections, cases hopsitalizations and R0. |
| sf_vals | scaling factor used to model the effect of transmission-reducing interventions. |
| sat_functions_shapes | parameters of the saturating function used for setting pseudo absences case weights. |
| no_trees | number of trees of the random forest model passed to |
| min_node_size | minimal node size of the random forest model passed to |
| all_wgt | numeric value of case weights for all data points. |
| pseudoAbs_value | numeric value of pseudo absences for different response variables. |
| foi_offset | numeric value to offset model FOI predictions during fitting with Expectation Maximization. |
| EM_iter | number of iterations of the Expectation Maximization algorithm |
| base_info | character string of key ID variable in the 1/6 degree resolution global covariate dataset. |
| extra_params | list of additional parameters. Default = NULL. |