Fix 701 (#717)

NEWS.md

@@ -8,6 +8,10 @@
 
 - `epinow()` now returns the "timing" output in a "time difference"" format that is easier to understand and work with. By @jamesmbaazam in #688 and reviewed by @sbfnk.
 
+## Bug fixes
+
+- a bug was fixed where `forecast_secondary()` did not work with fixed delays. By @sbfnk in #717 and reviewed by @sbfnk.
+
 ## Documentation
 
 - Updated the documentation of the dots argument of the `stan_sampling_opts()` to add that the dots are passed to `cmdstanr::sample()`. By @jamesmbaazam in #699 and reviewed by @sbfnk.

R/estimate_secondary.R

@@ -645,7 +645,7 @@ forecast_secondary <- function(estimate,
 
   # allocate empty parameters
   data <- allocate_empty(
-    data, c("frac_obs", "delay_param", "rep_phi"),
+    data, c("frac_obs", "delay_params", "rep_phi"),
     n = data$n
   )
   data$all_dates <- as.integer(all_dates)

tests/testthat/test-estimate_secondary.R

@@ -35,6 +35,12 @@ params <- c(
 
 inc_posterior <- inc$posterior[variable %in% params]
 
+# fit model to example data with a fixed delay
+inc_fixed <- estimate_secondary(inc_cases[1:60],
+  delays = delay_opts(Gamma(mean = 15, sd = 5, max = 30)),
+  verbose = FALSE
+)
+
 #### Prevalence data example ####
 
 # make some example prevalence data
@@ -178,6 +184,15 @@ test_that("forecast_secondary can return values from simulated data and plot
   expect_error(plot(inc_preds, new_obs = inc_cases, from = "2020-05-01"), NA)
 })
 
+test_that("forecast_secondary works with fixed delays", {
+  inc_preds <- forecast_secondary(
+    inc_fixed, inc_cases[seq(61, .N)][, value := primary]
+  )
+  expect_equal(names(inc_preds), c("samples", "forecast", "predictions"))
+  # validation plot of observations vs estimates
+  expect_error(plot(inc_preds, new_obs = inc_cases, from = "2020-05-01"), NA)
+})
+
 test_that("forecast_secondary can return values from simulated data when using
            the cmdstanr backend", {
   skip_on_os("windows")