From f372ff51b7ca5f66bb34a55c2f45085ec5a2f3ce 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 01/16] 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 d65132f09..83045dfa6 100644
--- a/R/create.R
+++ b/R/create.R
@@ -263,7 +263,7 @@ 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 ca5c11dda..c3d87cff8 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 {
@@ -724,7 +734,7 @@ 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]})."
       )
     )
   }

From 3e30b646f385fb6df992906ecf9e54cfa2dbfeeb Mon Sep 17 00:00:00 2001
From: Sam <s.e.abbott12@gmail.com>
Date: Thu, 19 Dec 2024 17:43:43 +0000
Subject: [PATCH 02/16] add support to stan

---
 R/create.R                                     | 6 ++++--
 inst/stan/data/estimate_infections_params.stan | 1 +
 inst/stan/data/rt.stan                         | 4 ++--
 inst/stan/estimate_infections.stan             | 6 +++++-
 inst/stan/functions/infections.stan            | 8 ++++----
 inst/stan/simulate_infections.stan             | 8 +++++++-
 6 files changed, 23 insertions(+), 10 deletions(-)

diff --git a/R/create.R b/R/create.R
index 83045dfa6..ef7c02237 100644
--- a/R/create.R
+++ b/R/create.R
@@ -263,7 +263,7 @@ create_rt_data <- function(rt = rt_opts(), breakpoints = NULL,
     breakpoints = breakpoints,
     future_fixed =  as.numeric(future_rt$fixed),
     fixed_from = future_rt$from,
-    pop = as.integer(rt$pop != Fixed(0)),
+    use_pop = as.integer(rt$pop != Fixed(0)),
     stationary =  as.numeric(rt$gp_on == "R0"),
     future_time = horizon - future_rt$from
   )
@@ -584,12 +584,14 @@ create_stan_data <- function(data, seeding_time, rt, gp, obs, backcalc,
       R0 = rt$prior,
       frac_obs = obs$scale,
       rep_phi = obs$phi,
+      pop = rt$pop,
       lower_bounds = c(
         alpha = 0,
         rho = 0,
         R0 = 0,
         frac_obs = 0,
-        rep_phi = 0
+        rep_phi = 0,
+        pop = 0
       )
     )
   )
diff --git a/inst/stan/data/estimate_infections_params.stan b/inst/stan/data/estimate_infections_params.stan
index 85be5c1c9..a54ec9d32 100644
--- a/inst/stan/data/estimate_infections_params.stan
+++ b/inst/stan/data/estimate_infections_params.stan
@@ -3,3 +3,4 @@ int<lower = 0> rho_id;       // parameter id of rho (GP lengthscale)
 int<lower = 0> R0_id;        // parameter id of R0
 int<lower = 0> frac_obs_id;  // parameter id of frac_obs
 int<lower = 0> rep_phi_id;   // parameter id of rep_phi_id
+int<lower = 0> pop_id;       // parameter id of pop
diff --git a/inst/stan/data/rt.stan b/inst/stan/data/rt.stan
index 357330c19..709cb2ae9 100644
--- a/inst/stan/data/rt.stan
+++ b/inst/stan/data/rt.stan
@@ -5,5 +5,5 @@
   array[t - seeding_time] int breakpoints; // when do breakpoints occur
   int future_fixed;                  // is underlying future Rt assumed to be fixed
   int fixed_from;                    // Reference date for when Rt estimation should be fixed
-  int pop;                           // Initial susceptible population
-  int<lower = 0> gt_id;              // id of generation time
+  int use_pop;                       // use population size
+  int<lower = 0> gt_id;              // id of generation time
\ No newline at end of file
diff --git a/inst/stan/estimate_infections.stan b/inst/stan/estimate_infections.stan
index fe845b8fe..e079d345c 100644
--- a/inst/stan/estimate_infections.stan
+++ b/inst/stan/estimate_infections.stan
@@ -107,9 +107,13 @@ transformed parameters {
         frac_obs_id, params_fixed_lookup, params_variable_lookup, params_value,
         params
       );
+      real pop = get_param(
+        pop_id, params_fixed_lookup, params_variable_lookup, params_value,
+        params
+      );
       infections = generate_infections(
         R, seeding_time, gt_rev_pmf, initial_infections, initial_growth, pop,
-        future_time, obs_scale, frac_obs
+        use_pop, future_time, obs_scale, frac_obs
       );
     }
   } else {
diff --git a/inst/stan/functions/infections.stan b/inst/stan/functions/infections.stan
index a599be8c2..f5e9f78c4 100644
--- a/inst/stan/functions/infections.stan
+++ b/inst/stan/functions/infections.stan
@@ -20,7 +20,7 @@ real update_infectiousness(vector infections, vector gt_rev_pmf,
 // generate infections by using Rt = Rt-1 * sum(reversed generation time pmf * infections)
 vector generate_infections(vector oR, int uot, vector gt_rev_pmf,
                            array[] real initial_infections, array[] real initial_growth,
-                           int pop, int ht, int obs_scale, real frac_obs) {
+                           real pop, int use_pop, int ht, int obs_scale, real frac_obs) {
   // time indices and storage
   int ot = num_elements(oR);
   int nht = ot - ht;
@@ -42,20 +42,20 @@ vector generate_infections(vector oR, int uot, vector gt_rev_pmf,
     }
   }
   // calculate cumulative infections
-  if (pop) {
+  if (use_pop) {
     cum_infections[1] = sum(infections[1:uot]);
   }
   // iteratively update infections
   for (s in 1:ot) {
     infectiousness[s] = update_infectiousness(infections, gt_rev_pmf, uot, s);
-    if (pop && s > nht) {
+    if (use_pop && s > nht) {
       exp_adj_Rt = exp(-R[s] * infectiousness[s] / (pop - cum_infections[nht]));
       exp_adj_Rt = exp_adj_Rt > 1 ? 1 : exp_adj_Rt;
       infections[s + uot] = (pop - cum_infections[s]) * (1 - exp_adj_Rt);
     }else{
       infections[s + uot] = R[s] * infectiousness[s];
     }
-    if (pop && s < ot) {
+    if (use_pop && s < ot) {
       cum_infections[s + 1] = cum_infections[s] + infections[s + uot];
     }
   }
diff --git a/inst/stan/simulate_infections.stan b/inst/stan/simulate_infections.stan
index 43ea6cba9..f06006f6b 100644
--- a/inst/stan/simulate_infections.stan
+++ b/inst/stan/simulate_infections.stan
@@ -50,6 +50,12 @@ generated quantities {
       frac_obs_id, params_fixed_lookup, params_variable_lookup,
       params_value, params
     );
+
+    real pop = get_param(
+      pop_id, params_fixed_lookup, params_variable_lookup,
+      params_value, params
+    );
+
     for (i in 1:n) {
       // generate infections from Rt trace
       vector[delay_type_max[gt_id] + 1] gt_rev_pmf;
@@ -62,7 +68,7 @@ generated quantities {
 
       infections[i] = to_row_vector(generate_infections(
         to_vector(R[i]), seeding_time, gt_rev_pmf, initial_infections[i],
-        initial_growth[i], pop, future_time, obs_scale, frac_obs[i]
+        initial_growth[i], pop, use_pop, future_time, obs_scale, frac_obs[i]
       ));
 
       if (delay_id) {

From 288b424b90c34d6a893dca652af1b2cb1d509afa Mon Sep 17 00:00:00 2001
From: Sam <s.e.abbott12@gmail.com>
Date: Thu, 19 Dec 2024 18:17:44 +0000
Subject: [PATCH 03/16] check works and update tests

---
 R/simulate_infections.R                        |  4 ++--
 inst/stan/data/rt.stan                         |  2 +-
 inst/stan/data/simulation_rt.stan              |  2 +-
 inst/stan/simulate_infections.stan             |  4 ++--
 man/EpiNow2-package.Rd                         |  2 +-
 man/rt_opts.Rd                                 |  8 ++++----
 man/simulate_infections.Rd                     |  8 ++++----
 tests/testthat/test-create_rt_date.R           |  4 ++--
 tests/testthat/test-rt_opts.R                  | 14 ++++++++++----
 vignettes/estimate_infections_options.Rmd.orig |  2 +-
 10 files changed, 28 insertions(+), 22 deletions(-)

diff --git a/R/simulate_infections.R b/R/simulate_infections.R
index 6998a8171..25919d46a 100644
--- a/R/simulate_infections.R
+++ b/R/simulate_infections.R
@@ -69,7 +69,7 @@ simulate_infections <- function(estimates, R, initial_infections,
                                 CrIs = c(0.2, 0.5, 0.9),
                                 backend = "rstan",
                                 seeding_time = NULL,
-                                pop = 0, ...) {
+                                pop = Fixed(0), ...) {
   ## deprecated usage
   if (!missing(estimates)) {
     deprecate_stop(
@@ -125,7 +125,7 @@ simulate_infections <- function(estimates, R, initial_infections,
     initial_infections = array(log_initial_infections, dim = c(1, 1)),
     initial_growth = array(initial_growth, dim = c(1, length(initial_growth))),
     R = array(R$R, dim = c(1, nrow(R))),
-    pop = pop
+    use_pop = as.integer(pop != Fixed(0))
   )
 
   data <- c(data, create_stan_delays(
diff --git a/inst/stan/data/rt.stan b/inst/stan/data/rt.stan
index 709cb2ae9..7ffff8a25 100644
--- a/inst/stan/data/rt.stan
+++ b/inst/stan/data/rt.stan
@@ -6,4 +6,4 @@
   int future_fixed;                  // is underlying future Rt assumed to be fixed
   int fixed_from;                    // Reference date for when Rt estimation should be fixed
   int use_pop;                       // use population size
-  int<lower = 0> gt_id;              // id of generation time
\ No newline at end of file
+  int<lower = 0> gt_id;              // id of generation time
diff --git a/inst/stan/data/simulation_rt.stan b/inst/stan/data/simulation_rt.stan
index 3beae3161..fdae11e2a 100644
--- a/inst/stan/data/simulation_rt.stan
+++ b/inst/stan/data/simulation_rt.stan
@@ -2,6 +2,6 @@
   array[n, seeding_time > 1 ? 1 : 0] real initial_growth; //initial growth
 
   matrix[n, t - seeding_time] R; // reproduction number
-  int pop;                       // susceptible population
+  int use_pop;                       // use population size
 
   int<lower = 0> gt_id; // id of generation time
diff --git a/inst/stan/simulate_infections.stan b/inst/stan/simulate_infections.stan
index f06006f6b..83fb14123 100644
--- a/inst/stan/simulate_infections.stan
+++ b/inst/stan/simulate_infections.stan
@@ -51,7 +51,7 @@ generated quantities {
       params_value, params
     );
 
-    real pop = get_param(
+    vector[n] pop = get_param(
       pop_id, params_fixed_lookup, params_variable_lookup,
       params_value, params
     );
@@ -68,7 +68,7 @@ generated quantities {
 
       infections[i] = to_row_vector(generate_infections(
         to_vector(R[i]), seeding_time, gt_rev_pmf, initial_infections[i],
-        initial_growth[i], pop, use_pop, future_time, obs_scale, frac_obs[i]
+        initial_growth[i], pop[i], use_pop, future_time, obs_scale, frac_obs[i]
       ));
 
       if (delay_id) {
diff --git a/man/EpiNow2-package.Rd b/man/EpiNow2-package.Rd
index b0c820c1b..5e27df68a 100644
--- a/man/EpiNow2-package.Rd
+++ b/man/EpiNow2-package.Rd
@@ -43,7 +43,7 @@ Other contributors:
   \item Paul Mee \email{paul.mee@lshtm.ac.uk} [contributor]
   \item Peter Ellis \email{peter.ellis2013nz@gmail.com} [contributor]
   \item Pietro Monticone \email{pietro.monticone@edu.unito.it} [contributor]
-  \item Lloyd Chapman \email{lloyd.chapman1@lshtm.ac.uk} [contributor]
+  \item Lloyd Chapman \email{lloyd.chapman1@lshtm.ac.uk } [contributor]
   \item Andrew Johnson \email{andrew.johnson@arjohnsonau.com} [contributor]
   \item Kaitlyn Johnson \email{johnsonkaitlyne9@gmail.com} (\href{https://orcid.org/0000-0001-8011-0012}{ORCID}) [contributor]
 }
diff --git a/man/rt_opts.Rd b/man/rt_opts.Rd
index c48cfe21e..3155f9101 100644
--- a/man/rt_opts.Rd
+++ b/man/rt_opts.Rd
@@ -11,7 +11,7 @@ rt_opts(
   use_breakpoints = TRUE,
   future = "latest",
   gp_on = c("R_t-1", "R0"),
-  pop = 0
+  pop = Fixed(0)
 )
 }
 \arguments{
@@ -50,9 +50,9 @@ Rt = Rt-1 * GP), and applying the Gaussian process to a global mean (i.e Rt
 but the method relying on a global mean will revert to this for real time
 estimates, which may not be desirable.}
 
-\item{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
+\item{pop}{A \verb{<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 \code{Fixed(0)} which means no population adjustment
 is done.}
 }
 \value{
diff --git a/man/simulate_infections.Rd b/man/simulate_infections.Rd
index bc012013f..e0e34ef23 100644
--- a/man/simulate_infections.Rd
+++ b/man/simulate_infections.Rd
@@ -16,7 +16,7 @@ simulate_infections(
   CrIs = c(0.2, 0.5, 0.9),
   backend = "rstan",
   seeding_time = NULL,
-  pop = 0,
+  pop = Fixed(0),
   ...
 )
 }
@@ -74,9 +74,9 @@ R given) of \code{seeding_time} days is assumed to have followed exponential
 growth roughly in line with the growth rate implied by the first value of
 R.}
 
-\item{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
+\item{pop}{A \verb{<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 \code{Fixed(0)} which means no population adjustment
 is done.}
 
 \item{...}{deprecated; only included for backward compatibility}
diff --git a/tests/testthat/test-create_rt_date.R b/tests/testthat/test-create_rt_date.R
index 3fc47b1cc..c63020f97 100644
--- a/tests/testthat/test-create_rt_date.R
+++ b/tests/testthat/test-create_rt_date.R
@@ -27,13 +27,13 @@ test_that("create_rt_data handles custom rt_opts correctly", {
     use_breakpoints = FALSE,
     future = "project",
     gp_on = "R0",
-    pop = 1000000
+    pop = Normal(mean = 1000000, sd = 100)
   )
   
   result <- create_rt_data(rt = custom_rt, horizon = 7)
   
   expect_equal(result$estimate_r, 0)
-  expect_equal(result$pop, 1000000)
+  expect_equal(result$use_pop, 1)
   expect_equal(result$stationary, 1)
   expect_equal(result$future_time, 7)
 })
diff --git a/tests/testthat/test-rt_opts.R b/tests/testthat/test-rt_opts.R
index 69fb1183c..e35c5824c 100644
--- a/tests/testthat/test-rt_opts.R
+++ b/tests/testthat/test-rt_opts.R
@@ -19,7 +19,7 @@ test_that("rt_opts handles custom inputs correctly", {
     use_breakpoints = FALSE,
     future = "project",
     gp_on = "R0",
-    pop = 1000000
+    pop = Normal(mean = 1000000, sd = 100)
   ))
   
   expect_null(result$prior)
@@ -27,10 +27,17 @@ test_that("rt_opts handles custom inputs correctly", {
   expect_equal(result$rw, 7)
   expect_true(result$use_breakpoints)  # Should be TRUE when rw > 0
   expect_equal(result$future, "project")
-  expect_equal(result$pop, 1000000)
+  expect_equal(result$pop, Normal(mean = 1000000, sd = 100))
   expect_equal(result$gp_on, "R0")
 })
 
+test_that("rt_opts warns when pop is passed as numeric", {
+  expect_warning(
+    rt_opts(pop = 1000),
+    "Specifying `pop` as a numeric value is deprecated"
+  )
+})
+
 test_that("rt_opts sets use_breakpoints to TRUE when rw > 0", {
   result <- rt_opts(rw = 3, use_breakpoints = FALSE)
   expect_true(result$use_breakpoints)
@@ -59,8 +66,7 @@ test_that("rt_opts returns object of correct class", {
 })
 
 test_that("rt_opts handles edge cases correctly", {
-  result <- rt_opts(rw = 0.1, pop = -1)
+  result <- rt_opts(rw = 0.1)
   expect_equal(result$rw, 0.1)
-  expect_equal(result$pop, -1)
   expect_true(result$use_breakpoints)
 })
diff --git a/vignettes/estimate_infections_options.Rmd.orig b/vignettes/estimate_infections_options.Rmd.orig
index 0cd532013..622e47aa2 100644
--- a/vignettes/estimate_infections_options.Rmd.orig
+++ b/vignettes/estimate_infections_options.Rmd.orig
@@ -154,7 +154,7 @@ dep <- estimate_infections(reported_cases,
   delays = delay_opts(delay),
   rt = rt_opts(
     prior = rt_prior,
-    pop = 1000000, future = "latest"
+    pop = Normal(mean = 1000000, sd = 1000), future = "latest"
   )
 )
 # summarise results

From 6b1cb519a228b9a1162ae9c02455957e8f4ec532 Mon Sep 17 00:00:00 2001
From: Sam <s.e.abbott12@gmail.com>
Date: Thu, 19 Dec 2024 18:23:44 +0000
Subject: [PATCH 04/16] update news

---
 NEWS.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NEWS.md b/NEWS.md
index a37bfc384..32724e466 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -15,6 +15,7 @@
     estimate_infections()
   ```
   
+- Added support for fitting  the susceptible population size. By @seabbs in #904 and reviewed by @sbfnk.
 - A bug was fixed where the initial growth was never estimated (i.e. the prior mean was always zero). By @sbfnk in #853 and reviewed by @seabbs.
 - A bug was fixed where an internal function for applying a default cdf cutoff failed due to a difference a vector length issue. By @jamesmbaazam in #858 and reviewed by @sbfnk.
 - All parameters have been changed to the new parameter interface. By @sbfnk in #871 and #890 and reviewed by @seabbs.

From c17fdcb84eb4c41b6a42b89212944dc7c41638eb Mon Sep 17 00:00:00 2001
From: Sam <s.e.abbott12@gmail.com>
Date: Thu, 19 Dec 2024 18:47:00 +0000
Subject: [PATCH 05/16] update tests

---
 tests/testthat/test-create_rt_date.R | 2 +-
 tests/testthat/test-rt_opts.R        | 2 +-
 vignettes/EpiNow2.Rmd.orig           | 3 ++-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/tests/testthat/test-create_rt_date.R b/tests/testthat/test-create_rt_date.R
index c63020f97..463c26261 100644
--- a/tests/testthat/test-create_rt_date.R
+++ b/tests/testthat/test-create_rt_date.R
@@ -7,7 +7,7 @@ test_that("create_rt_data returns expected default values", {
   expect_equal(result$breakpoints, numeric(0))
   expect_equal(result$future_fixed, 1)
   expect_equal(result$fixed_from, 0)
-  expect_equal(result$pop, 0)
+  expect_equal(result$use_pop, 0)
   expect_equal(result$stationary, 0)
   expect_equal(result$future_time, 0)
 })
diff --git a/tests/testthat/test-rt_opts.R b/tests/testthat/test-rt_opts.R
index e35c5824c..c8700d9df 100644
--- a/tests/testthat/test-rt_opts.R
+++ b/tests/testthat/test-rt_opts.R
@@ -7,7 +7,7 @@ test_that("rt_opts returns expected default values", {
   expect_equal(result$rw, 0)
   expect_true(result$use_breakpoints)
   expect_equal(result$future, "latest")
-  expect_equal(result$pop, 0)
+  expect_equal(result$pop, Fixed(0))
   expect_equal(result$gp_on, "R_t-1")
 })
 
diff --git a/vignettes/EpiNow2.Rmd.orig b/vignettes/EpiNow2.Rmd.orig
index 69d10bcdd..e46f53aa5 100644
--- a/vignettes/EpiNow2.Rmd.orig
+++ b/vignettes/EpiNow2.Rmd.orig
@@ -95,7 +95,8 @@ estimates <- epinow(
   generation_time = gt_opts(example_generation_time),
   delays = delay_opts(example_incubation_period + reporting_delay),
   rt = rt_opts(prior = LogNormal(mean = 2, sd = 0.2)),
-  stan = stan_opts(cores = 4, control = list(adapt_delta = 0.99)),
+  stan = stan_opts(
+    cores = 4, control = list(adapt_delta = 0.99), backend = "cmdstanr"),
   verbose = interactive()
 )
 names(estimates)

From 2967e056d46cfece5d6887110e1ed31f192c60bb Mon Sep 17 00:00:00 2001
From: Sam <s.e.abbott12@gmail.com>
Date: Thu, 19 Dec 2024 21:03:59 +0000
Subject: [PATCH 06/16] handle pop more carefully in a simulation setting

---
 R/simulate_infections.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/simulate_infections.R b/R/simulate_infections.R
index 25919d46a..8f8531ef4 100644
--- a/R/simulate_infections.R
+++ b/R/simulate_infections.R
@@ -86,7 +86,6 @@ simulate_infections <- function(estimates, R, initial_infections,
   assert_numeric(R$R, lower = 0)
   assert_numeric(initial_infections, lower = 0)
   assert_numeric(day_of_week_effect, lower = 0, null.ok = TRUE)
-  assert_numeric(pop, lower = 0)
   if (!is.null(seeding_time)) {
     assert_integerish(seeding_time, lower = 1)
   }
@@ -94,6 +93,7 @@ simulate_infections <- function(estimates, R, initial_infections,
   assert_class(truncation, "trunc_opts")
   assert_class(obs, "obs_opts")
   assert_class(generation_time, "generation_time_opts")
+  assert_class(pop, "dist_spec")
 
   ## create R for all dates modelled
   all_dates <- data.table(date = seq.Date(min(R$date), max(R$date), by = "day"))
@@ -179,7 +179,8 @@ simulate_infections <- function(estimates, R, initial_infections,
     rho = NULL,
     R0 = NULL,
     frac_obs = obs$scale,
-    rep_phi = obs$phi
+    rep_phi = obs$phi,
+    pop = pop
   ))
   ## set empty params matrix - variable parameters not supported here
   data$params <- array(dim = c(1, 0))

From 86018b12ce1aaca22486e0c097268177835df902 Mon Sep 17 00:00:00 2001
From: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Date: Fri, 20 Dec 2024 14:25:21 +0000
Subject: [PATCH 07/16] update stan generate infection tests

---
 tests/testthat/test-stan-infections.R | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/tests/testthat/test-stan-infections.R b/tests/testthat/test-stan-infections.R
index d08e06c01..0f8b631c0 100644
--- a/tests/testthat/test-stan-infections.R
+++ b/tests/testthat/test-stan-infections.R
@@ -25,35 +25,35 @@ gt_rev_pmf <- get_delay_rev_pmf(
 # test generate infections
 test_that("generate_infections works as expected", {
   expect_equal(
-    round(generate_infections(c(1, rep(1, 9)), 10, gt_rev_pmf, log(1000), 0, 0, 0, 0, 0), 0),
+    round(generate_infections(c(1, rep(1, 9)), 10, gt_rev_pmf, log(1000), 0, 0, 0, 0, 0, 0), 0),
     c(rep(1000, 10), 995, 996, rep(997, 8))
   )
   expect_equal(
-    round(generate_infections(c(1, rep(1.1, 9)), 10, gt_rev_pmf, log(20), 0.03, 0, 0, 0, 0), 0),
+    round(generate_infections(c(1, rep(1.1, 9)), 10, gt_rev_pmf, log(20), 0.03, 0, 0, 0, 0, 0), 0),
     c(20, 21, 21, 22, 23, 23, 24, 25, 25, 26, 24, 27, 28, 29, 30, 30, 31, 32, 33, 34)
   )
   expect_equal(
-    round(generate_infections(c(1, rep(1.1, 9)), 10, gt_rev_pmf, log(100), 0, 0, 0, 0, 0), 0),
+    round(generate_infections(c(1, rep(1.1, 9)), 10, gt_rev_pmf, log(100), 0, 0, 0, 0, 0, 0), 0),
     c(rep(100, 10), 99, 110, 112, 115, 119, 122, 126, 130, 134, 138)
   )
   expect_equal(
-    round(generate_infections(c(1, rep(1, 9)), 4, gt_rev_pmf, log(500), -0.02, 0, 0, 0, 0), 0),
+    round(generate_infections(c(1, rep(1, 9)), 4, gt_rev_pmf, log(500), -0.02, 0, 0, 0, 0, 0), 0),
     c(500, 490, 480, 471, 382, 403, 408, rep(409, 7))
   )
   expect_equal(
-    round(generate_infections(c(1, rep(1.1, 9)), 4, gt_rev_pmf, log(500), 0, 0, 0, 0, 0), 0),
+    round(generate_infections(c(1, rep(1.1, 9)), 4, gt_rev_pmf, log(500), 0, 0, 0, 0, 0, 0), 0),
     c(rep(500, 4), 394, 460, 475, 489, 505, 520, 536, 553, 570, 588)
   )
   expect_equal(
-    round(generate_infections(c(1, rep(1, 9)), 1, gt_rev_pmf, log(40), numeric(0), 0, 0, 0, 0), 0),
+    round(generate_infections(c(1, rep(1, 9)), 1, gt_rev_pmf, log(40), numeric(0), 0, 0, 0, 0, 0), 0),
     c(40, 8, 11, 12, 12, rep(13, 6))
   )
   expect_equal(
-    round(generate_infections(c(1, rep(1.1, 9)), 1, gt_rev_pmf, log(100), 0.01, 0, 0, 0, 0), 0),
+    round(generate_infections(c(1, rep(1.1, 9)), 1, gt_rev_pmf, log(100), 0.01, 0, 0, 0, 0, 0), 0),
     c(100, 20, 31, 35, 36, 37, 38, 39, 41, 42, 43)
   )
   expect_equal(
-    round(generate_infections(c(1, rep(1, 9)), 10, gt_rev_pmf, log(1000), 0, 100000, 4, 0, 0), 0),
+    round(generate_infections(c(1, rep(1, 9)), 10, gt_rev_pmf, log(1000), 0, 100000, 4, 0, 0, 0), 0),
     c(rep(1000, 10), 995, 996, rep(997, 4), 980, 965, 947, 926)
   )
 })

From 07064bdac188f975de08d4c8518ffcbdde8a50bc Mon Sep 17 00:00:00 2001
From: Sam <s.e.abbott12@gmail.com>
Date: Fri, 20 Dec 2024 16:44:50 +0000
Subject: [PATCH 08/16] fix linting

---
 R/opts.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/R/opts.R b/R/opts.R
index c3d87cff8..e0a478d97 100644
--- a/R/opts.R
+++ b/R/opts.R
@@ -734,7 +734,10 @@ obs_opts <- function(family = c("negbin", "poisson"),
     cli_abort(
       c(
         "!" = "Specifying {.var phi} as a vector of length 2 is deprecated.",
-        "i" = "Use a {.cls dist_spec} instead, e.g. Normal(mean = {phi[1]}, sd = {phi[2]})."
+        "i" = paste0(
+          "Use a {.cls dist_spec} instead, e.g. Normal(mean = {phi[1]}, ",
+          "sd = {phi[2]})."
+        )
       )
     )
   }

From 3bc26d4c3efc83863d7bb8d6a9a87d8a1897b77e Mon Sep 17 00:00:00 2001
From: Sam <s.e.abbott12@gmail.com>
Date: Fri, 20 Dec 2024 17:25:17 +0000
Subject: [PATCH 09/16] make it possible to either use pop out of sample or fit
 with it in sample

---
 R/create.R                          |  2 +-
 R/opts.R                            | 27 +++++++++++++++++++++------
 inst/stan/functions/infections.stan |  2 +-
 man/rt_opts.Rd                      | 10 +++++++++-
 4 files changed, 32 insertions(+), 9 deletions(-)

diff --git a/R/create.R b/R/create.R
index ef7c02237..97ae12fda 100644
--- a/R/create.R
+++ b/R/create.R
@@ -263,7 +263,7 @@ create_rt_data <- function(rt = rt_opts(), breakpoints = NULL,
     breakpoints = breakpoints,
     future_fixed =  as.numeric(future_rt$fixed),
     fixed_from = future_rt$from,
-    use_pop = as.integer(rt$pop != Fixed(0)),
+    use_pop = as.integer(rt$pop != Fixed(0)) + as.integer(rt$estimate_pop),
     stationary =  as.numeric(rt$gp_on == "R0"),
     future_time = horizon - future_rt$from
   )
diff --git a/R/opts.R b/R/opts.R
index e0a478d97..6dc1f545f 100644
--- a/R/opts.R
+++ b/R/opts.R
@@ -324,6 +324,13 @@ trunc_opts <- function(dist = Fixed(0), default_cdf_cutoff = 0.001,
 #' 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 pop_within_horizon Logical, defaults to `FALSE`. Should the
+#' susceptible population adjustment be applied within the time horizon of data
+#' or just beyond it. Note that if `pop_within_horizon = TRUE` the Rt estimate
+#' will be unadjusted for susceptible depletion but the resulting posterior
+#' predictions for infections and cases will be adjusted for susceptible
+#' depletion.
 #'
 #' @param gp_on Character string, defaulting to  "R_t-1". Indicates how the
 #' Gaussian process, if in use, should be applied to Rt. Currently supported
@@ -354,7 +361,8 @@ rt_opts <- function(prior = LogNormal(mean = 1, sd = 1),
                     use_breakpoints = TRUE,
                     future = "latest",
                     gp_on = c("R_t-1", "R0"),
-                    pop = Fixed(0)) {
+                    pop = Fixed(0),
+                    pop_within_horizon = FALSE) {
   rt <- list(
     use_rt = use_rt,
     rw = rw,
@@ -388,15 +396,22 @@ rt_opts <- function(prior = LogNormal(mean = 1, sd = 1),
   }
 
   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})."
-      )
+    lifecycle::deprecate_warn(  
+      "1.7.0",  
+      "rt_opts(pop = 'must be a `<dist_spec>`')",  
+      details = "For specifying a fixed population size, use `Fixed(pop)`"
     )
     pop <- Fixed(pop)
   }
   rt$pop <- pop
+  if (isTRUE(pop_within_horizon) && pop == Fixed(0)) {
+    cli_abort(
+      c(
+        "!" = "pop_within_horizon = TRUE but pop is fixed at 0."
+      )
+    )
+  }
+  rt$estimate_pop <- TRUE
 
   if (rt$use_rt) {
     rt$prior <- prior
diff --git a/inst/stan/functions/infections.stan b/inst/stan/functions/infections.stan
index f5e9f78c4..2b626f4ad 100644
--- a/inst/stan/functions/infections.stan
+++ b/inst/stan/functions/infections.stan
@@ -48,7 +48,7 @@ vector generate_infections(vector oR, int uot, vector gt_rev_pmf,
   // iteratively update infections
   for (s in 1:ot) {
     infectiousness[s] = update_infectiousness(infections, gt_rev_pmf, uot, s);
-    if (use_pop && s > nht) {
+    if (use_pop == 2 && s > nht) {
       exp_adj_Rt = exp(-R[s] * infectiousness[s] / (pop - cum_infections[nht]));
       exp_adj_Rt = exp_adj_Rt > 1 ? 1 : exp_adj_Rt;
       infections[s + uot] = (pop - cum_infections[s]) * (1 - exp_adj_Rt);
diff --git a/man/rt_opts.Rd b/man/rt_opts.Rd
index 3155f9101..358117438 100644
--- a/man/rt_opts.Rd
+++ b/man/rt_opts.Rd
@@ -11,7 +11,8 @@ rt_opts(
   use_breakpoints = TRUE,
   future = "latest",
   gp_on = c("R_t-1", "R0"),
-  pop = Fixed(0)
+  pop = Fixed(0),
+  pop_within_horizon = FALSE
 )
 }
 \arguments{
@@ -54,6 +55,13 @@ estimates, which may not be desirable.}
 Used to adjust Rt estimates based on the proportion of the population that
 is susceptible. Defaults to \code{Fixed(0)} which means no population adjustment
 is done.}
+
+\item{pop_within_horizon}{Logical, defaults to \code{FALSE}. Should the
+susceptible population adjustment be applied within the time horizon of data
+or just beyond it. Note that if \code{pop_within_horizon = TRUE} the Rt estimate
+will be unadjusted for susceptible depletion but the resulting posterior
+predictions for infections and cases will be adjusted for susceptible
+depletion.}
 }
 \value{
 An \verb{<rt_opts>} object with settings defining the time-varying

From 01f42c96ace216989491500dbdb78f0770f09941 Mon Sep 17 00:00:00 2001
From: Sam Abbott <contact@samabbott.co.uk>
Date: Fri, 10 Jan 2025 11:44:05 +0000
Subject: [PATCH 10/16] add support for in sample suscetpble

---
 inst/stan/functions/infections.stan | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/stan/functions/infections.stan b/inst/stan/functions/infections.stan
index 2b626f4ad..ee379e749 100644
--- a/inst/stan/functions/infections.stan
+++ b/inst/stan/functions/infections.stan
@@ -48,7 +48,7 @@ vector generate_infections(vector oR, int uot, vector gt_rev_pmf,
   // iteratively update infections
   for (s in 1:ot) {
     infectiousness[s] = update_infectiousness(infections, gt_rev_pmf, uot, s);
-    if (use_pop == 2 && s > nht) {
+    if (use_pop == 1 || (use_pop == 2 && s <= nht)) {
       exp_adj_Rt = exp(-R[s] * infectiousness[s] / (pop - cum_infections[nht]));
       exp_adj_Rt = exp_adj_Rt > 1 ? 1 : exp_adj_Rt;
       infections[s + uot] = (pop - cum_infections[s]) * (1 - exp_adj_Rt);

From e21a5f8ce95f539a040fdb25781098769f0536db Mon Sep 17 00:00:00 2001
From: Sam Abbott <contact@samabbott.co.uk>
Date: Fri, 10 Jan 2025 13:05:01 +0000
Subject: [PATCH 11/16] update docs

---
 R/opts.R | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/R/opts.R b/R/opts.R
index 6dc1f545f..a37b3a63e 100644
--- a/R/opts.R
+++ b/R/opts.R
@@ -325,12 +325,11 @@ trunc_opts <- function(dist = Fixed(0), default_cdf_cutoff = 0.001,
 #' is susceptible. Defaults to `Fixed(0)` which means no population adjustment
 #' is done.
 #' 
-#' @param pop_within_horizon Logical, defaults to `FALSE`. Should the
-#' susceptible population adjustment be applied within the time horizon of data
-#' or just beyond it. Note that if `pop_within_horizon = TRUE` the Rt estimate
-#' will be unadjusted for susceptible depletion but the resulting posterior
-#' predictions for infections and cases will be adjusted for susceptible
-#' depletion.
+#' @param pop_period Character string, defaulting to "forecast". Controls when
+#' susceptible population adjustment is applied. "forecast" only applies the
+#' adjustment to forecasts while "all" applies it to both data and forecasts.
+#' Note that with "forecast", Rt estimates are unadjusted for susceptible
+#' depletion but posterior predictions are adjusted.
 #'
 #' @param gp_on Character string, defaulting to  "R_t-1". Indicates how the
 #' Gaussian process, if in use, should be applied to Rt. Currently supported
@@ -362,13 +361,14 @@ rt_opts <- function(prior = LogNormal(mean = 1, sd = 1),
                     future = "latest",
                     gp_on = c("R_t-1", "R0"),
                     pop = Fixed(0),
-                    pop_within_horizon = FALSE) {
+                    pop_period = c("forecast", "all")) {
   rt <- list(
     use_rt = use_rt,
     rw = rw,
     use_breakpoints = use_breakpoints,
     future = future,
-    gp_on = arg_match(gp_on)
+    gp_on = arg_match(gp_on),
+    pop_period = arg_match(pop_period)
   )
 
   # replace default settings with those specified by user
@@ -396,18 +396,18 @@ rt_opts <- function(prior = LogNormal(mean = 1, sd = 1),
   }
 
   if (is.numeric(pop)) {
-    lifecycle::deprecate_warn(  
-      "1.7.0",  
-      "rt_opts(pop = 'must be a `<dist_spec>`')",  
+    lifecycle::deprecate_warn(
+      "1.7.0",
+      "rt_opts(pop = 'must be a `<dist_spec>`')",
       details = "For specifying a fixed population size, use `Fixed(pop)`"
     )
     pop <- Fixed(pop)
   }
   rt$pop <- pop
-  if (isTRUE(pop_within_horizon) && pop == Fixed(0)) {
+  if (rt$pop_period == "all" && pop == Fixed(0)) {
     cli_abort(
       c(
-        "!" = "pop_within_horizon = TRUE but pop is fixed at 0."
+        "!" = "pop_period = \"all\" but pop is fixed at 0."
       )
     )
   }

From 101f1c56f9401787c0d41f38c6dc01e431606047 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Fri, 10 Jan 2025 13:09:25 +0000
Subject: [PATCH 12/16] Document

---
 man/EpiNow2-package.Rd      |  2 +-
 man/create_forecast_data.Rd |  2 +-
 man/create_stan_data.Rd     |  2 +-
 man/epinow.Rd               |  2 +-
 man/estimate_infections.Rd  |  2 +-
 man/forecast_opts.Rd        |  1 -
 man/regional_epinow.Rd      |  2 +-
 man/rt_opts.Rd              | 13 ++++++-------
 8 files changed, 12 insertions(+), 14 deletions(-)

diff --git a/man/EpiNow2-package.Rd b/man/EpiNow2-package.Rd
index 5e27df68a..b0c820c1b 100644
--- a/man/EpiNow2-package.Rd
+++ b/man/EpiNow2-package.Rd
@@ -43,7 +43,7 @@ Other contributors:
   \item Paul Mee \email{paul.mee@lshtm.ac.uk} [contributor]
   \item Peter Ellis \email{peter.ellis2013nz@gmail.com} [contributor]
   \item Pietro Monticone \email{pietro.monticone@edu.unito.it} [contributor]
-  \item Lloyd Chapman \email{lloyd.chapman1@lshtm.ac.uk } [contributor]
+  \item Lloyd Chapman \email{lloyd.chapman1@lshtm.ac.uk} [contributor]
   \item Andrew Johnson \email{andrew.johnson@arjohnsonau.com} [contributor]
   \item Kaitlyn Johnson \email{johnsonkaitlyne9@gmail.com} (\href{https://orcid.org/0000-0001-8011-0012}{ORCID}) [contributor]
 }
diff --git a/man/create_forecast_data.Rd b/man/create_forecast_data.Rd
index 3ca7b0ccb..38a98a37e 100644
--- a/man/create_forecast_data.Rd
+++ b/man/create_forecast_data.Rd
@@ -9,7 +9,7 @@ create_forecast_data(forecast = forecast_opts(), data)
 \arguments{
 \item{forecast}{A list of options as generated by \code{\link[=forecast_opts]{forecast_opts()}} defining
 the forecast opitions. Defaults to \code{\link[=forecast_opts]{forecast_opts()}}. If NULL then no
-forecasting will be one.}
+forecasting will be done.}
 
 \item{data}{A \verb{<data.frame>} of confirmed cases (confirm) by date (date).
 \code{confirm} must be numeric and \code{date} must be in date format. Optionally
diff --git a/man/create_stan_data.Rd b/man/create_stan_data.Rd
index e0f05ff26..e5680e01a 100644
--- a/man/create_stan_data.Rd
+++ b/man/create_stan_data.Rd
@@ -48,7 +48,7 @@ define the back calculation. Defaults to \code{\link[=backcalc_opts]{backcalc_op
 
 \item{forecast}{A list of options as generated by \code{\link[=forecast_opts]{forecast_opts()}} defining
 the forecast opitions. Defaults to \code{\link[=forecast_opts]{forecast_opts()}}. If NULL then no
-forecasting will be one.}
+forecasting will be done.}
 }
 \value{
 A list of stan data
diff --git a/man/epinow.Rd b/man/epinow.Rd
index 8a62820a5..008759969 100644
--- a/man/epinow.Rd
+++ b/man/epinow.Rd
@@ -73,7 +73,7 @@ observation model. Defaults to \code{\link[=obs_opts]{obs_opts()}}.}
 
 \item{forecast}{A list of options as generated by \code{\link[=forecast_opts]{forecast_opts()}} defining
 the forecast opitions. Defaults to \code{\link[=forecast_opts]{forecast_opts()}}. If NULL then no
-forecasting will be one.}
+forecasting will be done.}
 
 \item{stan}{A list of stan options as generated by \code{\link[=stan_opts]{stan_opts()}}. Defaults
 to \code{\link[=stan_opts]{stan_opts()}}. Can be used to override \code{data}, \code{init}, and \code{verbose}
diff --git a/man/estimate_infections.Rd b/man/estimate_infections.Rd
index 992b65d46..4f5a97dde 100644
--- a/man/estimate_infections.Rd
+++ b/man/estimate_infections.Rd
@@ -69,7 +69,7 @@ observation model. Defaults to \code{\link[=obs_opts]{obs_opts()}}.}
 
 \item{forecast}{A list of options as generated by \code{\link[=forecast_opts]{forecast_opts()}} defining
 the forecast opitions. Defaults to \code{\link[=forecast_opts]{forecast_opts()}}. If NULL then no
-forecasting will be one.}
+forecasting will be done.}
 
 \item{stan}{A list of stan options as generated by \code{\link[=stan_opts]{stan_opts()}}. Defaults
 to \code{\link[=stan_opts]{stan_opts()}}. Can be used to override \code{data}, \code{init}, and \code{verbose}
diff --git a/man/forecast_opts.Rd b/man/forecast_opts.Rd
index 2bd02766b..cadd823aa 100644
--- a/man/forecast_opts.Rd
+++ b/man/forecast_opts.Rd
@@ -17,7 +17,6 @@ forecasts unless set explicitly here.}
 }
 \value{
 A \verb{<forecast_opts>} object of forecast setting.
-rstan functions.
 }
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
diff --git a/man/regional_epinow.Rd b/man/regional_epinow.Rd
index efaa0ee6b..1dfd319df 100644
--- a/man/regional_epinow.Rd
+++ b/man/regional_epinow.Rd
@@ -66,7 +66,7 @@ observation model. Defaults to \code{\link[=obs_opts]{obs_opts()}}.}
 
 \item{forecast}{A list of options as generated by \code{\link[=forecast_opts]{forecast_opts()}} defining
 the forecast opitions. Defaults to \code{\link[=forecast_opts]{forecast_opts()}}. If NULL then no
-forecasting will be one.}
+forecasting will be done.}
 
 \item{stan}{A list of stan options as generated by \code{\link[=stan_opts]{stan_opts()}}. Defaults
 to \code{\link[=stan_opts]{stan_opts()}}. Can be used to override \code{data}, \code{init}, and \code{verbose}
diff --git a/man/rt_opts.Rd b/man/rt_opts.Rd
index 358117438..8636fdb82 100644
--- a/man/rt_opts.Rd
+++ b/man/rt_opts.Rd
@@ -12,7 +12,7 @@ rt_opts(
   future = "latest",
   gp_on = c("R_t-1", "R0"),
   pop = Fixed(0),
-  pop_within_horizon = FALSE
+  pop_period = c("forecast", "all")
 )
 }
 \arguments{
@@ -56,12 +56,11 @@ Used to adjust Rt estimates based on the proportion of the population that
 is susceptible. Defaults to \code{Fixed(0)} which means no population adjustment
 is done.}
 
-\item{pop_within_horizon}{Logical, defaults to \code{FALSE}. Should the
-susceptible population adjustment be applied within the time horizon of data
-or just beyond it. Note that if \code{pop_within_horizon = TRUE} the Rt estimate
-will be unadjusted for susceptible depletion but the resulting posterior
-predictions for infections and cases will be adjusted for susceptible
-depletion.}
+\item{pop_period}{Character string, defaulting to "forecast". Controls when
+susceptible population adjustment is applied. "forecast" only applies the
+adjustment to forecasts while "all" applies it to both data and forecasts.
+Note that with "forecast", Rt estimates are unadjusted for susceptible
+depletion but posterior predictions are adjusted.}
 }
 \value{
 An \verb{<rt_opts>} object with settings defining the time-varying

From 27097cb0ccb718273e9a6cf75fe37a050f8e1896 Mon Sep 17 00:00:00 2001
From: Sam Abbott <contact@samabbott.co.uk>
Date: Fri, 10 Jan 2025 13:23:17 +0000
Subject: [PATCH 13/16] touch


From bafef0b9c6dde4c1a6ef982532ba3be52d2fb639 Mon Sep 17 00:00:00 2001
From: Sam Abbott <contact@samabbott.co.uk>
Date: Fri, 10 Jan 2025 13:53:43 +0000
Subject: [PATCH 14/16] cleaner opt passing

---
 R/create.R | 3 ++-
 R/opts.R   | 1 -
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/create.R b/R/create.R
index 97ae12fda..446336c37 100644
--- a/R/create.R
+++ b/R/create.R
@@ -263,7 +263,8 @@ create_rt_data <- function(rt = rt_opts(), breakpoints = NULL,
     breakpoints = breakpoints,
     future_fixed =  as.numeric(future_rt$fixed),
     fixed_from = future_rt$from,
-    use_pop = as.integer(rt$pop != Fixed(0)) + as.integer(rt$estimate_pop),
+    use_pop =
+      as.integer(rt$pop != Fixed(0)) + as.integer(rt$pop_period == "all"),
     stationary =  as.numeric(rt$gp_on == "R0"),
     future_time = horizon - future_rt$from
   )
diff --git a/R/opts.R b/R/opts.R
index a37b3a63e..8c63589ab 100644
--- a/R/opts.R
+++ b/R/opts.R
@@ -411,7 +411,6 @@ rt_opts <- function(prior = LogNormal(mean = 1, sd = 1),
       )
     )
   }
-  rt$estimate_pop <- TRUE
 
   if (rt$use_rt) {
     rt$prior <- prior

From 841d23881db18554d7d80c89882156f5ddbff59d Mon Sep 17 00:00:00 2001
From: Sam Abbott <contact@samabbott.co.uk>
Date: Fri, 10 Jan 2025 15:46:58 +0000
Subject: [PATCH 15/16] update tests

---
 tests/testthat/test-rt_opts.R         | 2 +-
 tests/testthat/test-stan-infections.R | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-rt_opts.R b/tests/testthat/test-rt_opts.R
index c8700d9df..d76f0571b 100644
--- a/tests/testthat/test-rt_opts.R
+++ b/tests/testthat/test-rt_opts.R
@@ -34,7 +34,7 @@ test_that("rt_opts handles custom inputs correctly", {
 test_that("rt_opts warns when pop is passed as numeric", {
   expect_warning(
     rt_opts(pop = 1000),
-    "Specifying `pop` as a numeric value is deprecated"
+    "The `pop` argument of `rt_opts()` must be a `<dist_spec>` as of EpiNow2 1.7.0."
   )
 })
 
diff --git a/tests/testthat/test-stan-infections.R b/tests/testthat/test-stan-infections.R
index 0f8b631c0..9d88a858a 100644
--- a/tests/testthat/test-stan-infections.R
+++ b/tests/testthat/test-stan-infections.R
@@ -53,7 +53,7 @@ test_that("generate_infections works as expected", {
     c(100, 20, 31, 35, 36, 37, 38, 39, 41, 42, 43)
   )
   expect_equal(
-    round(generate_infections(c(1, rep(1, 9)), 10, gt_rev_pmf, log(1000), 0, 100000, 4, 0, 0, 0), 0),
+    round(generate_infections(c(1, rep(1, 9)), 10, gt_rev_pmf, log(1000), 0, 100000, 2, 0, 0, 0), 0),
     c(rep(1000, 10), 995, 996, rep(997, 4), 980, 965, 947, 926)
   )
 })

From 6184ab9ca4b884b13adf87ae7611d71e7e0e1ada Mon Sep 17 00:00:00 2001
From: Sam Abbott <contact@samabbott.co.uk>
Date: Fri, 10 Jan 2025 15:57:40 +0000
Subject: [PATCH 16/16] clean up whitespace

---
 R/opts.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/opts.R b/R/opts.R
index 8c63589ab..c6e846bf8 100644
--- a/R/opts.R
+++ b/R/opts.R
@@ -324,7 +324,7 @@ trunc_opts <- function(dist = Fixed(0), default_cdf_cutoff = 0.001,
 #' 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 pop_period Character string, defaulting to "forecast". Controls when
 #' susceptible population adjustment is applied. "forecast" only applies the
 #' adjustment to forecasts while "all" applies it to both data and forecasts.