From e1d4ed52e63d72f3724e8c2aeb1849d93d24f27e Mon Sep 17 00:00:00 2001
From: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Date: Thu, 17 Oct 2024 13:36:21 +0100
Subject: [PATCH] refine wording (where GP applies depends on model)

---
 R/opts.R       | 7 ++++---
 man/gp_opts.Rd | 7 ++++---
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/R/opts.R b/R/opts.R
index a5698925b..7e9f0aa94 100644
--- a/R/opts.R
+++ b/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,
diff --git a/man/gp_opts.Rd b/man/gp_opts.Rd
index 45160a893..57866fde8 100644
--- a/man/gp_opts.Rd
+++ b/man/gp_opts.Rd
@@ -12,7 +12,7 @@ gp_opts(
   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,
@@ -47,11 +47,12 @@ this is smaller.}
 
 \item{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).}
 
 \item{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 (\code{alpha_mean}).}
 
 \item{kernel}{Character string, the type of kernel required. Currently
 supporting the Matern kernel ("matern"), squared exponential kernel ("se"),