check works and update tests

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(

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
+  int<lower = 0> gt_id;              // id of generation time

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

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
+        initial_growth[i], pop[i], use_pop, future_time
       ));
 
       if (delay_id) {

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)
 })

tests/testthat/test-rt_opts.R

@@ -19,18 +19,25 @@ 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$prior)
   expect_false(result$use_rt)
   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)
 })

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