instead of manually setting disp_subclin to disp_com in scenario_sim,…

… set argument default in scenario_sim, outbreak_model and outbreak_step

R/outbreak_model.R

@@ -18,7 +18,9 @@
 #' @param disp_com numeric dispersion parameter for non-isolated cases
 #' (must be >0)
 #' @param disp_subclin numeric dispersion parameter for sub-clincial
-#' non-isolated cases (must be >0)
+#' non-isolated cases (must be >0). Default of `disp_subclin` is to be equal to
+#' clinical cases (`disp_com`), this unless specified dispersion for
+#' sub-clinical cases will be equal to non-isolated cases.
 #' @param k numeric skew parameter for sampling the serial interval from the
 #' incubation period
 #' @param delay_shape numeric shape parameter of delay distribution
@@ -70,7 +72,7 @@ outbreak_model <- function(num_initial_cases,
                            r0subclin = r0community,
                            disp_iso,
                            disp_com,
-                           disp_subclin,
+                           disp_subclin = disp_com,
                            k,
                            delay_shape,
                            delay_scale,

R/outbreak_step.R

@@ -44,7 +44,7 @@ outbreak_step <- function(case_data,
                           r0subclin = r0community,
                           disp_iso,
                           disp_com,
-                          disp_subclin,
+                          disp_subclin = disp_com,
                           k,
                           prop_asym,
                           quarantine,

R/scenario_sim.R

@@ -56,14 +56,8 @@ scenario_sim <- function(n_sim,
                          prop_asym,
                          quarantine,
                          r0subclin = r0community,
-                         disp_subclin = NULL) {
+                         disp_subclin = disp_com) {
 
-
-
-
-  if (is.null(disp_subclin)) {
-    disp_subclin <- disp_com
-  }
   # Run n_sim number of model runs and put them all together in a big data.frame
   res <- purrr::map(
     .x = 1:n_sim, ~ outbreak_model(