integration tests and minor issues

epiforecasts · Aug 15, 2024 · ecf8965 · ecf8965
1 parent fa7d2f4
commit ecf8965
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Showing 3 changed files with 24 additions and 8 deletions.
diff --git a/R/create.R b/R/create.R
@@ -615,12 +615,15 @@ create_initial_conditions <- function(data) {
         meanlog = data$ls_meanlog,
         sdlog = ifelse(data$ls_sdlog > 0, data$ls_sdlog, 0.01)
       ))
-
-      out$rescaled_rho <- array(data.table::fcase(
-        out$rescaled_rho > data$ls_max, data$ls_max - 0.001,
-        out$rescaled_rho < data$ls_min, data$ls_min + 0.001,
-        default = out$rescaled_rho
-        ))
+      if (data$gp_type != 3) {
+        out$rescaled_rho <- array(data.table::fcase(
+          out$rescaled_rho > data$ls_max, data$ls_max - 0.001,
+          out$rescaled_rho < data$ls_min, data$ls_min + 0.001,
+          default = out$rescaled_rho
+          ))
+      }else{
+        out$rescaled_rho <- array(numeric(0))
+      }
 
       out$alpha <- array(
         truncnorm::rtruncnorm(

diff --git a/inst/stan/estimate_infections.stan b/inst/stan/estimate_infections.stan
@@ -213,7 +213,7 @@ generated quantities {
   vector[fixed ? 0 : 1] rho;
 
   profile("generated quantities") {
-    if (!fixed) {
+    if (!fixed && gp_type != 3) {
       vector[noise_terms] x = linspaced_vector(noise_terms, 1, noise_terms);
       rho[1] = rescaled_rho[1] * sd(x);
     }

diff --git a/tests/testthat/test-estimate_infections.R b/tests/testthat/test-estimate_infections.R
@@ -38,6 +38,20 @@ test_that("estimate_infections successfully returns estimates using default sett
   test_estimate_infections(reported_cases)
 })
 
+test_that("estimate_infections successfully returns estimates using a Matern 5/2 kernel", {
+  skip_on_cran()
+  test_estimate_infections(
+    reported_cases, gp = gp_opts(kernel = "matern", matern_order = 5 / 2)
+  )
+})
+
+test_that("estimate_infections successfully returns estimates using a Linear kernel", {
+  skip_on_cran()
+  test_estimate_infections(
+    reported_cases, gp = gp_opts(kernel = "linear")
+  )
+})
+
 test_that("estimate_infections successfully returns estimates when passed NA values", {
   skip_on_cran()
   reported_cases_na <- data.table::copy(reported_cases)
@@ -85,7 +99,6 @@ test_that("estimate_infections successfully returns estimates using a single bre
   )
 })
 
-
 test_that("estimate_infections successfully returns estimates using a random walk", {
   skip_on_cran()
   test_estimate_infections(reported_cases, gp = NULL, rt = rt_opts(rw = 7))