test limits

seroanalytics · Nov 4, 2024 · 53f7bc9 · 53f7bc9
1 parent 2943703
commit 53f7bc9
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Showing 2 changed files with 37 additions and 1 deletion.
diff --git a/R/biokinetics.R b/R/biokinetics.R
@@ -45,7 +45,7 @@ biokinetics <- R6::R6Class(
         private$lower_limit <- min(private$data$value)
       } else {
         min_value <- min(private$data$value)
-        if (max_value > upper_limit) {
+        if (min_value < lower_limit) {
           warning(sprintf("Data contains a value of %s which is smaller than the lower detection limit %s",
                           min_value, lower_limit))
         }

diff --git a/tests/testthat/test-data.R b/tests/testthat/test-data.R
@@ -65,3 +65,39 @@ test_that("Log scale data is passed directly to stan", {
   stan_data <- mod$get_stan_data()
   expect_equal(stan_data$value, dat$value, ignore_attr = TRUE)
 })
+
+test_that("Highest value is used as default upper limit", {
+  dat <- data.table::fread(system.file("delta_full.rds", package = "epikinetics"))
+  mod <- biokinetics$new(data = dat, lower_detection_limit = 2)
+  stan_data <- mod$get_stan_data()
+  expect_equal(stan_data$upper_limit, log2(max(dat$value)/2))
+  expect_equal(stan_data$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$new(data = dat, upper_detection_limit = 10)},
+                 "Data contains a value of 2560 which is greater than the upper detection limit 10")
+  stan_data <- mod$get_stan_data()
+  expect_equal(stan_data$upper_limit, log2(10/5))
+  expect_equal(stan_data$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$lower_limit, 0)
+})
+
+test_that("Warns if data contains values below the lower limit", {
+  dat <- data.table::fread(system.file("delta_full.rds", package = "epikinetics"))
+  expect_warning({mod <- biokinetics$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")
+  stan_data <- mod$get_stan_data()
+  expect_equal(stan_data$upper_limit, log2(2560/10))
+  expect_equal(stan_data$lower_limit, 0)
+})