refine wording (where GP applies depends on model)

R/opts.R

@@ -455,11 +455,12 @@ backcalc_opts <- function(prior = c("reports", "none", "infections"),
 #'
 #' @param alpha_mean Numeric, defaults to 0. The mean of the magnitude parameter
 #' of the Gaussian process kernel. Should be approximately the expected standard
-#' deviation of the logged Rt.
+#' deviation of the Gaussian process (logged Rt in case of the renewal model,
+#' logged infections in case of the nonmechanistic model).
 #'
 #' @param alpha_sd Numeric, defaults to 0.1. The standard deviation of the
 #' magnitude parameter of the Gaussian process kernel. Can be tuned to adjust
-#' the uncertainty about the expected standard deviation of the logged Rt.
+#' how far alpha is allowed to deviate form its prior mean (`alpha_mean`).
 #'
 #' @param kernel Character string, the type of kernel required. Currently
 #' supporting the Matern kernel ("matern"), squared exponential kernel ("se"),
@@ -508,7 +509,7 @@ gp_opts <- function(basis_prop = 0.2,
                     ls_min = 0,
                     ls_max = 60,
                     alpha_mean = 0,
-                    alpha_sd = 0.01,
+                    alpha_sd = 0.05,
                     kernel = c("matern", "se", "ou", "periodic"),
                     matern_order = 3 / 2,
                     matern_type,