rename truncate -> truncate_obs

epiforecasts · seabbs · Aug 9, 2024 · Aug 7, 2024 · Aug 7, 2024 · Aug 7, 2024
commit 6e5dff3076e57e963f06a41be8dcd7a770f84405
diff --git a/inst/stan/estimate_infections.stan b/inst/stan/estimate_infections.stan
@@ -143,7 +143,7 @@ transformed parameters {
       );
     }
     profile("truncate") {
-      obs_reports = truncate(reports[1:ot], trunc_rev_cmf, 0);
+      obs_reports = truncate_obs(reports[1:ot], trunc_rev_cmf, 0);
     }
   } else {
     obs_reports = reports[1:ot];

diff --git a/inst/stan/estimate_secondary.stan b/inst/stan/estimate_secondary.stan
@@ -78,7 +78,7 @@ transformed parameters {
       delay_np_pmf_groups, delay_params, delay_params_groups, delay_dist,
       0, 1, 1
     );
-    secondary = truncate(secondary, trunc_rev_cmf, 0);
+    secondary = truncate_obs(secondary, trunc_rev_cmf, 0);
  }
 }
 

diff --git a/inst/stan/estimate_truncation.stan b/inst/stan/estimate_truncation.stan
@@ -47,12 +47,12 @@ transformed parameters{
   vector[t] last_obs;
   // reconstruct latest data without truncation
 
-  last_obs = truncate(to_vector(obs[, obs_sets]), trunc_rev_cmf, 1);
+  last_obs = truncate_obs(to_vector(obs[, obs_sets]), trunc_rev_cmf, 1);
   // apply truncation to latest dataset to map back to previous data sets and
   // add noise term
   for (i in 1:(obs_sets - 1)) {
     trunc_obs[1:(end_t[i] - start_t[i] + 1), i] =
-      truncate(last_obs[start_t[i]:end_t[i]], trunc_rev_cmf, 0) + sigma;
+      truncate_obs(last_obs[start_t[i]:end_t[i]], trunc_rev_cmf, 0) + sigma;
    }
   }
 }
@@ -80,7 +80,7 @@ generated quantities {
   matrix[delay_type_max[trunc_id] + 1, obs_sets - 1] gen_obs;
   // reconstruct all truncated datasets using posterior of the truncation distribution
   for (i in 1:obs_sets) {
-    recon_obs[1:(end_t[i] - start_t[i] + 1), i] = truncate(
+    recon_obs[1:(end_t[i] - start_t[i] + 1), i] = truncate_obs(
       to_vector(obs[start_t[i]:end_t[i], i]), trunc_rev_cmf, 1
     );
   }

diff --git a/inst/stan/functions/observation_model.stan b/inst/stan/functions/observation_model.stan
@@ -50,7 +50,7 @@ vector scale_obs(vector reports, real frac_obs) {
  *
  * @return A vector of truncated reports.
  */
-vector truncate(vector reports, vector trunc_rev_cmf, int reconstruct) {
+vector truncate_obs(vector reports, vector trunc_rev_cmf, int reconstruct) {
   int t = num_elements(reports);
   int trunc_max = num_elements(trunc_rev_cmf);
   vector[t] trunc_reports = reports;

diff --git a/inst/stan/simulate_infections.stan b/inst/stan/simulate_infections.stan
@@ -82,7 +82,7 @@ generated quantities {
         delay_np_pmf_groups, delay_params[i], delay_params_groups, delay_dist,
         0, 1, 1
       );
-      reports[i] = to_row_vector(truncate(
+      reports[i] = to_row_vector(truncate_obs(
         to_vector(reports[i]), trunc_rev_cmf, 0)
       );
     }

diff --git a/inst/stan/simulate_secondary.stan b/inst/stan/simulate_secondary.stan
@@ -73,7 +73,7 @@ generated quantities {
         delay_np_pmf_groups, delay_params[i], delay_params_groups, delay_dist,
         0, 1, 1
       );
-      secondary = truncate(
+      secondary = truncate_obs(
         secondary, trunc_rev_cmf, 0
       );
     }

diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
@@ -12,8 +12,6 @@ if (identical(Sys.getenv("NOT_CRAN"), "true")) {
         target_dir = system.file("stan/functions", package = "EpiNow2")
       )
     )
-    # avoid problems due to base::truncate
-    stan_truncate <- truncate
   }
 }
 

diff --git a/tests/testthat/test-stan-truncate.R b/tests/testthat/test-stan-truncate.R
@@ -1,30 +1,30 @@
 skip_on_cran()
 skip_on_os("windows")
 
-test_that("truncate() can perform truncation as expected", {
+test_that("truncate_obs() can perform truncation as expected", {
   reports <- c(10, 20, 30, 40, 50)
   trunc_rev_cmf <- c(1, 0.8, 0.5, 0.2)
   expected <- c(reports[1], reports[2:5] * trunc_rev_cmf)
-  expect_equal(stan_truncate(reports, trunc_rev_cmf, FALSE), expected)
+  expect_equal(truncate_obs(reports, trunc_rev_cmf, FALSE), expected)
 })
 
-test_that("truncate() can perform reconstruction as expected", {
+test_that("truncate_obs() can perform reconstruction as expected", {
   reports <- c(10, 20, 15, 8, 10)
   trunc_rev_cmf <- c(1, 0.8, 0.5, 0.2)
   expected <- c(reports[1], reports[2:5] / trunc_rev_cmf)
-  expect_equal(stan_truncate(reports, trunc_rev_cmf, TRUE), expected)
+  expect_equal(truncate_obs(reports, trunc_rev_cmf, TRUE), expected)
 })
 
-test_that("truncate() can handle longer trunc_rev_cmf than reports", {
+test_that("truncate_obs() can handle longer trunc_rev_cmf than reports", {
   reports <- c(10, 20, 30)
   trunc_rev_cmf <- c(1, 0.8, 0.5, 0.2, 0.1)
   expected <- reports * trunc_rev_cmf[3:5]
-  expect_equal(stan_truncate(reports, trunc_rev_cmf, FALSE), expected)
+  expect_equal(truncate_obs(reports, trunc_rev_cmf, FALSE), expected)
 })
 
-test_that("truncate() can handle reconstruction with longer trunc_rev_cmf than reports", {
+test_that("truncate_obs() can handle reconstruction with longer trunc_rev_cmf than reports", {
   reports <- c(10, 16, 15)
   trunc_rev_cmf <- c(1, 0.8, 0.5, 0.2, 0.1)
   expected <- reports / trunc_rev_cmf[3:5]
-  expect_equal(stan_truncate(reports, trunc_rev_cmf, TRUE), expected)
+  expect_equal(truncate_obs(reports, trunc_rev_cmf, TRUE), expected)
 })
-Original file line number
+Diff line change
@@ Expand Up / @@ -78,7 +78,7 @@ transformed parameters { @@
           delay_np_pmf_groups, delay_params, delay_params_groups, delay_dist,
 , 1, 1
         );
-        secondary = truncate(secondary, trunc_rev_cmf, 0);
+        secondary = truncate_obs(secondary, trunc_rev_cmf, 0);
      }
     }
@@ Expand Down @@