tests for log scale

seroanalytics · Nov 4, 2024 · c73495a · c73495a
1 parent 53f7bc9
commit c73495a
Showing 1 changed file with 22 additions and 9 deletions.
diff --git a/tests/testthat/test-data.R b/tests/testthat/test-data.R
@@ -70,34 +70,47 @@ test_that("Highest value is used as default upper limit", {
   dat <- data.table::fread(system.file("delta_full.rds", package = "epikinetics"))
   mod <- biokinetics$new(data = dat, lower_detection_limit = 2)
   stan_data <- mod$get_stan_data()
-  expect_equal(stan_data$upper_limit, log2(max(dat$value)/2))
+  expect_equal(stan_data$upper_limit, log2(max(dat$value) / 2))
   expect_equal(stan_data$lower_limit, 0)
 })
 
 test_that("Warns if data contains values above the upper limit", {
   dat <- data.table::fread(system.file("delta_full.rds", package = "epikinetics"))
-  expect_warning({mod <- biokinetics$new(data = dat, upper_detection_limit = 10)},
+  expect_warning({ mod <- biokinetics$new(data = dat, upper_detection_limit = 10) },
                  "Data contains a value of 2560 which is greater than the upper detection limit 10")
   stan_data <- mod$get_stan_data()
-  expect_equal(stan_data$upper_limit, log2(10/5))
+  expect_equal(stan_data$upper_limit, log2(10 / 5))
   expect_equal(stan_data$lower_limit, 0)
 })
 
 test_that("Smallest value is used as default lower limit", {
   dat <- data.table::fread(system.file("delta_full.rds", package = "epikinetics"))
   mod <- biokinetics$new(data = dat, upper_detection_limit = 3000)
   stan_data <- mod$get_stan_data()
-  expect_equal(stan_data$upper_limit, log2(3000/min(dat$value)))
+  expect_equal(stan_data$upper_limit, log2(3000 / min(dat$value)))
   expect_equal(stan_data$lower_limit, 0)
 })
 
 test_that("Warns if data contains values below the lower limit", {
   dat <- data.table::fread(system.file("delta_full.rds", package = "epikinetics"))
-  expect_warning({mod <- biokinetics$new(data = dat,
-                                         upper_detection_limit = 2560,
-                                         lower_detection_limit = 10)},
-                 "Data contains a value of 5 which is smaller than the lower detection limit 10")
+  expect_warning({ mod <- biokinetics$new(data = dat,
+                                          upper_detection_limit = 2560,
+                                          lower_detection_limit = 10) },
+    "Data contains a value of 5 which is smaller than the lower detection limit 10")
   stan_data <- mod$get_stan_data()
-  expect_equal(stan_data$upper_limit, log2(2560/10))
+  expect_equal(stan_data$upper_limit, log2(2560 / 10))
   expect_equal(stan_data$lower_limit, 0)
 })
+
+test_that("Detection limits are passed to stan without transformation if using log data", {
+  dat <- data.table::fread(system.file("delta_full.rds", package = "epikinetics"))
+  mod <- biokinetics$new(data = convert_log2_scale(dat,
+                                                   lower_limit = 2,
+                                                   vars_to_transform = "value"),
+                         scale = "log",
+                         lower_detection_limit = 1,
+                         upper_detection_limit = 15)
+  stan_data <- mod$get_stan_data()
+  expect_equal(stan_data$upper_limit, 15)
+  expect_equal(stan_data$lower_limit, 1)
+})