From b5063cb4717718976022052d8e3e7abcda6f4131 Mon Sep 17 00:00:00 2001
From: Sam <s.e.abbott12@gmail.com>
Date: Thu, 19 Dec 2024 17:04:28 +0000
Subject: [PATCH] change over opts and create interface

---
 R/create.R |  2 +-
 R/opts.R   | 22 ++++++++++++++++------
 2 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/R/create.R b/R/create.R
index 789bbb444..88da040c8 100644
--- a/R/create.R
+++ b/R/create.R
@@ -280,7 +280,7 @@ create_rt_data <- function(rt = rt_opts(), breakpoints = NULL,
     breakpoints = breakpoints,
     future_fixed =  as.numeric(future_rt$fixed),
     fixed_from = future_rt$from,
-    pop = rt$pop,
+    pop = as.integer(rt$pop != Fixed(0)),
     stationary =  as.numeric(rt$gp_on == "R0"),
     future_time = horizon - future_rt$from
   )
diff --git a/R/opts.R b/R/opts.R
index 613a6452f..7ed86568d 100644
--- a/R/opts.R
+++ b/R/opts.R
@@ -320,9 +320,9 @@ trunc_opts <- function(dist = Fixed(0), default_cdf_cutoff = 0.001,
 #' conservative estimate of break point changes (alter this by setting
 #' `gp = NULL`).
 #'
-#' @param pop Integer, defaults to 0. Susceptible population initially present.
-#' Used to adjust Rt estimates when otherwise fixed based on the proportion of
-#' the population that is susceptible. When set to 0 no population adjustment
+#' @param pop A `<dist_spec>` giving the initial susceptible population size.
+#' Used to adjust Rt estimates based on the proportion of the population that
+#' is susceptible. Defaults to `Fixed(0)` which means no population adjustment
 #' is done.
 #'
 #' @param gp_on Character string, defaulting to  "R_t-1". Indicates how the
@@ -354,13 +354,12 @@ rt_opts <- function(prior = LogNormal(mean = 1, sd = 1),
                     use_breakpoints = TRUE,
                     future = "latest",
                     gp_on = c("R_t-1", "R0"),
-                    pop = 0) {
+                    pop = Fixed(0)) {
   rt <- list(
     use_rt = use_rt,
     rw = rw,
     use_breakpoints = use_breakpoints,
     future = future,
-    pop = pop,
     gp_on = arg_match(gp_on)
   )
 
@@ -388,6 +387,17 @@ rt_opts <- function(prior = LogNormal(mean = 1, sd = 1),
     prior <- LogNormal(mean = prior$mean, sd = prior$sd)
   }
 
+  if (is.numeric(pop)) {
+    cli_warn(
+      c(
+        "!" = "Specifying {.var pop} as a numeric value is deprecated.",
+        "i" = "Use a {.cls dist_spec} instead, e.g. Fixed({pop})."
+      )
+    )
+    pop <- Fixed(pop)
+  }
+  rt$pop <- pop
+
   if (rt$use_rt) {
     rt$prior <- prior
   } else {
@@ -698,7 +708,7 @@ obs_opts <- function(family = c("negbin", "poisson"),
     cli_abort(
       c(
         "!" = "Specifying {.var phi} as a vector of length 2 is deprecated.",
-        "i" = "Mean and SD should be given as list elements."
+        "i" = "Use a {.cls dist_spec} instead, e.g. Normal(mean = {phi[1]}, sd = {phi[2]})."
       )
     )
   }