Merge pull request #105 from InsightRX/RXR-1876-warning-infusion

RXR-1876 fix warning infusion

R/regimen_to_nm.R

@@ -37,14 +37,14 @@ regimen_to_nm <- function(
       suppressWarnings(
         bioav_dose <- as.numeric(bioav[dose_cmt])
       )
-      if(!any(is.na(bioav_dose))) {
-        if(!all(bioav_dose == 1)) {
-          dat$RATE <- dat$RATE * bioav_dose
-          message("Recalculating infusion rates to reflect bioavailability for infusion.")
+      if(any(is.na(bioav_dose))) {
+        if(any(is.na(bioav_dose) & reg$t_inf > 0)) { # only warn when it actually concerns an infusion
+          warning("For compartments where bioavailability is specified as model parameter and not as a number, any infusion rates are not corrected for bioavailability.")
         }
-      } else {
-        warning("Bioavailability not specified correctly, cannot correct infusion rates.")
+        bioav_dose[is.na(bioav_dose)] <- 1
       }
+      dat$RATE <- dat$RATE * bioav_dose
+      message("Recalculating infusion rates to reflect bioavailability for infusion.")
     }
   }
   if(!is.null(t_obs)) {

tests/testthat/test_regimen_to_nm.R

@@ -33,7 +33,7 @@ test_that("regimen with infusion correctly recalculates rates when bioavailabili
       t_obs = c(1, 2, 3),
       bioav = "F1"
     ),
-    "Bioavailability not specified correctly"
+    "For compartments where bioavailability is specified"
   )
   expected_cols <- c(
     "ID",
@@ -95,3 +95,34 @@ test_that("rate is calculated for any regimen with an infusion length", {
   expect_equal(c$RATE, c(0, 0, 0, 0, 0, 10, 20, 0))
 })
 
+test_that("throws warning when bioav specified as model parameter and need to convert RATE, but not when not needed", {
+  a <- new_regimen(
+    amt = 10,
+    time = c(1, 2, 3, 4),
+    t_inf = c(0, 0, 1, 1),
+    type = c("oral", "oral", "infusion", "infusion")
+  )
+  expect_message({
+    b <- regimen_to_nm(
+      a,
+      dose_cmt = c(1, 1, 2, 2),
+      t_obs = c(1, 2, 3),
+      bioav = c("Fi", 1)
+    )
+  }, "Recalculating infusion rates")
+  a2 <- new_regimen(
+    amt = 10,
+    time = c(1, 2, 3, 4),
+    t_inf = c(1, 1, 1, 1),  # now an infusion in the sc compartment and infusion lengths are >0, should throw warning!
+    type = c("sc", "sc", "infusion", "infusion")
+  )
+  expect_warning(
+    regimen_to_nm(
+      a2,
+      dose_cmt = c(1, 1, 2, 2),
+      t_obs = c(1, 2, 3),
+      bioav = c("Fi", 1)
+    ),
+    "For compartments where bioavailability is specified"
+  )
+})