Update tests

Author: kristinawlai

tests/testthat/test-autoplot.summary.seroincidence.by.R

@@ -15,7 +15,7 @@ test_that(
     noise <-
       example_noise_params_pk
 
-    est2 <- estimate_scr_by(
+    est2 <- est_seroincidence_by(
       strata = c("catchment", "ageCat"),
       pop_data = xs_data,
       curve_params = curve,
@@ -70,7 +70,7 @@ test_that(
     noise <-
       example_noise_params_pk
 
-    est2 <- estimate_scr_by(
+    est2 <- est_seroincidence_by(
       strata = c("catchment", "ageCat"),
       pop_data = xs_data,
       curve_params = curve,
@@ -111,7 +111,7 @@ test_that(
     noise <-
       example_noise_params_pk
 
-    est2 <- estimate_scr_by(
+    est2 <- est_seroincidence_by(
       strata = c("catchment", "ageCat"),
       pop_data = xs_data,
       curve_params = curve,
@@ -154,7 +154,7 @@ test_that(
     noise <-
       example_noise_params_pk
 
-    est2 <- estimate_scr_by(
+    est2 <- est_seroincidence_by(
       strata = c("catchment", "ageCat"),
       pop_data = xs_data,
       curve_params = curve,
@@ -198,7 +198,7 @@ test_that(
     noise <-
       example_noise_params_pk
 
-    est2 <- estimate_scr_by(
+    est2 <- est_seroincidence_by(
       strata = c("catchment", "ageCat"),
       pop_data = xs_data,
       curve_params = curve,

tests/testthat/test-est_seroincidence_by.R

@@ -1,11 +1,11 @@
 test_that(
-  desc = "estimate_scr_by() warns about missing data",
+  desc = "est_seroincidence_by() warns about missing data",
   code = {
 
     withr::local_package("dplyr")
     withr::local_package("readr")
 
-    estimate_scr_by(
+    est_seroincidence_by(
       pop_data =
         sees_pop_data_pk_100 |>
         dplyr::filter(catchment == "kgh" | antigen_iso == "HlyE_IgA"),
@@ -22,13 +22,13 @@ test_that(
 )
 
 
-test_that("estimate_scr_by() warns about missing data", {
+test_that("est_seroincidence_by() warns about missing data", {
 
   withr::local_package("dplyr")
   withr::local_package("readr")
 
 
-  estimate_scr_by(
+  est_seroincidence_by(
     pop_data = sees_pop_data_pk_100 |>
       tail(-1),
     curve_params = typhoid_curves_nostrat_100,
@@ -41,9 +41,9 @@ test_that("estimate_scr_by() warns about missing data", {
     expect_warning(class = "incomplete-obs")
 })
 
-test_that("`estimate_scr_by()` warns user when strata is missing", {
+test_that("`est_seroincidence_by()` warns user when strata is missing", {
   expect_warning(
-    estimate_scr_by(
+    est_seroincidence_by(
       pop_data = sees_pop_data_pk_100,
       curve_params = typhoid_curves_nostrat_100,
       noise_params = example_noise_params_pk,
@@ -54,11 +54,11 @@ test_that("`estimate_scr_by()` warns user when strata is missing", {
 })
 
 test_that(
-  "`estimate_scr_by()` aborts when elements that don't exactly
+  "`est_seroincidence_by()` aborts when elements that don't exactly
           match the columns of `pop_data` are provided",
   {
     expect_error(
-      object = estimate_scr_by(
+      object = est_seroincidence_by(
         strata = c("ag", "catch", "Count"),
         pop_data = sees_pop_data_pk_100,
         curve_params = typhoid_curves_nostrat_100,
@@ -76,10 +76,10 @@ test_that(
 
 
 test_that(
-  desc = "`estimate_scr_by()` produces consistent results for typhoid data",
+  desc = "`est_seroincidence_by()` produces consistent results for typhoid data",
   code = {
     withr::local_options(width = 80)
-    typhoid_results <- estimate_scr_by(
+    typhoid_results <- est_seroincidence_by(
       strata = "catchment",
       pop_data = sees_pop_data_pk_100,
       curve_param = typhoid_curves_nostrat_100,
@@ -99,10 +99,10 @@ test_that(
 )
 
 test_that(
-  "`estimate_scr_by()` produces expected results
+  "`est_seroincidence_by()` produces expected results
           regardless of whether varnames have been standardized.",
   {
-    est_true <- estimate_scr_by(
+    est_true <- est_seroincidence_by(
       strata = c("catchment"),
       pop_data = sees_pop_data_pk_100,
       curve_params = typhoid_curves_nostrat_100,
@@ -113,7 +113,7 @@ test_that(
       num_cores = 1 # Allow for parallel processing to decrease run time
     )
 
-    est_false <- estimate_scr_by(
+    est_false <- est_seroincidence_by(
       strata = c("catchment"),
       pop_data = sees_pop_data_pk_100_old_names,
       curve_params = typhoid_curves_nostrat_100,
@@ -130,11 +130,11 @@ test_that(
 
 
 test_that(
-  "`estimate_scr_by()` produces expected results
+  "`est_seroincidence_by()` produces expected results
           regardless of whether using parallel processing or not.",
   {
 
-    ests_1_core <- estimate_scr_by(
+    ests_1_core <- est_seroincidence_by(
       strata = c("catchment"),
       pop_data = sees_pop_data_pk_100,
       curve_params = typhoid_curves_nostrat_100,
@@ -145,7 +145,7 @@ test_that(
       num_cores = 1
     )
 
-    ests_2_cores <- estimate_scr_by(
+    ests_2_cores <- est_seroincidence_by(
       strata = c("catchment"),
       pop_data = sees_pop_data_pk_100_old_names,
       curve_params = typhoid_curves_nostrat_100,
@@ -161,15 +161,15 @@ test_that(
 )
 
 test_that(
-  "`estimate_scr_by()` produces expected results
+  "`est_seroincidence_by()` produces expected results
           regardless of whether using verbose messaging or not.
           with single core.",
   {
 
     capture.output(
       file = nullfile(),
       {
-        ests_verbose_sc <- estimate_scr_by(
+        ests_verbose_sc <- est_seroincidence_by(
           strata = c("catchment"),
           pop_data = sees_pop_data_pk_100,
           curve_params = typhoid_curves_nostrat_100,
@@ -183,7 +183,7 @@ test_that(
       }
     )
 
-    ests_non_verbose_sc <- estimate_scr_by(
+    ests_non_verbose_sc <- est_seroincidence_by(
       verbose = FALSE,
       strata = c("catchment"),
       pop_data = sees_pop_data_pk_100_old_names,
@@ -200,12 +200,12 @@ test_that(
 )
 
 test_that(
-  "`estimate_scr_by()` produces expected results
+  "`est_seroincidence_by()` produces expected results
           regardless of whether using verbose messaging or not
           with multi-core processing.",
   {
 
-    ests_verbose_mc <- estimate_scr_by(
+    ests_verbose_mc <- est_seroincidence_by(
       strata = c("catchment"),
       pop_data = sees_pop_data_pk_100,
       curve_params = typhoid_curves_nostrat_100,
@@ -218,7 +218,7 @@ test_that(
     ) |>
       suppressMessages()
 
-    ests_non_verbose_mc <- estimate_scr_by(
+    ests_non_verbose_mc <- est_seroincidence_by(
       verbose = FALSE,
       strata = c("catchment"),
       pop_data = sees_pop_data_pk_100_old_names,
@@ -241,7 +241,7 @@ test_that(
 test_that(
   "a warning is produced when `strata = NULL",
   code = {
-    estimate_scr_by(
+    est_seroincidence_by(
       strata = NULL,
       pop_data = sees_pop_data_pk_100,
       curve_param = typhoid_curves_nostrat_100,
@@ -260,7 +260,7 @@ test_that("results are consistent with `strata = NULL`", {
     antigen_isos = c("HlyE_IgG", "HlyE_IgA")
   )
 
-  typhoid_results_nullstrata <- estimate_scr_by(
+  typhoid_results_nullstrata <- est_seroincidence_by(
     strata = NULL,
     pop_data = sees_pop_data_pk_100,
     curve_param = typhoid_curves_nostrat_100,

tests/testthat/test-print.seroincidence.by.R

@@ -3,7 +3,7 @@ test_that(
   code = {
 
     withr::local_options(width = 80)
-    typhoid_results <- estimate_scr_by(
+    typhoid_results <- est_seroincidence_by(
       strata = "catchment",
       pop_data = sees_pop_data_pk_100,
       curve_param = typhoid_curves_nostrat_100,

tests/testthat/test-print.summary.seroincidence.by.R

@@ -1,6 +1,6 @@
 test_that("print method works consistently", {
   withr::local_options(width = 80)
-  typhoid_results <- estimate_scr_by(
+  typhoid_results <- est_seroincidence_by(
     strata = "catchment",
     pop_data = sees_pop_data_pk_100,
     curve_param = typhoid_curves_nostrat_100,

tests/testthat/test-summary.seroincidence.by.R

@@ -1,7 +1,7 @@
 test_that("`summary.seroincidence.by()` produces consistent results",
           {
             typhoid_results <-
-              estimate_scr_by(
+              est_seroincidence_by(
                 strata = "catchment",
                 pop_data = sees_pop_data_pk_100,
                 curve_param = typhoid_curves_nostrat_100,