Merge pull request #474 from Gero1999/473-fe_not_calculated_without_ae

Fix: fe and clr not calculated if ae not included in intervals (#473)

Author: billdenney

NEWS.md

@@ -14,6 +14,7 @@ the dosing including dose amount and route.
 
 * `get_halflife_points()` now correctly accounts for start time != 0 and sets
   times outside of any interval to `NA` (#470)
+* `pk.nca` will calculate `fe` and `clr` even if their dependant parameters (e.g, `ae`) were not requested to be calculated in the intervals (#473)
 
 ## New features
 

R/pk.calc.urine.R

@@ -78,6 +78,7 @@ add.interval.col("clr.last",
                  unit_type="renal_clearance",
                  pretty_name="Renal clearance (from AUClast)",
                  formalsmap=list(auc="auclast"),
+                 depends = c("ae", "auclast"),
                  desc="The renal clearance calculated using AUClast")
 PKNCA.set.summary(
   name="clr.last",
@@ -91,6 +92,7 @@ add.interval.col("clr.obs",
                  unit_type="renal_clearance",
                  pretty_name="Renal clearance (from AUCinf,obs)",
                  formalsmap=list(auc="aucinf.obs"),
+                 depends = c("ae", "aucinf.obs"),
                  desc="The renal clearance calculated using AUCinf,obs")
 PKNCA.set.summary(
   name="clr.obs",
@@ -104,6 +106,7 @@ add.interval.col("clr.pred",
                  unit_type="renal_clearance",
                  pretty_name="Renal clearance (from AUCinf,pred)",
                  formalsmap=list(auc="aucinf.pred"),
+                 depends = c("ae", "aucinf.pred"),
                  desc="The renal clearance calculated using AUCinf,pred")
 PKNCA.set.summary(
   name="clr.pred",
@@ -131,6 +134,7 @@ add.interval.col("fe",
                  unit_type="amount_dose",
                  pretty_name="Fraction excreted",
                  values=c(FALSE, TRUE),
+                 depends = "ae",
                  desc="The fraction of the dose excreted")
 PKNCA.set.summary(
   name="fe",

tests/testthat/test-pk.calc.all.R

@@ -757,6 +757,38 @@ test_that("do not give rbind error when interval columns have attributes (#381)"
   )
 })
 
+
+test_that("pk.nca can be run for each parameter independently (#473)", {
+
+  d_conc <- Theoph[Theoph$Subject %in% "1", ]
+  d_conc <- rbind(d_conc, mutate(d_conc, Time = Time + 25))
+  d_conc$volume <- 1
+  d_conc$duration <- 1
+  d_dose <- data.frame(Subject = "1", Time = c(0, 25), Dose = 5, duration = 1)
+
+  o_conc <- PKNCAconc(d_conc, formula = conc~Time|Subject, volume = "volume", duration = "duration")
+  o_dose <- PKNCAdose(d_dose, formula = Dose~Time|Subject, route = "intravascular", duration = "duration")
+
+  non_pknca_covered_params <- c(
+    "f", "time_above", "mrt.md.obs", "mrt.md.pred", "sparse_auclast", "sparse_auc_se", "sparse_auc_df",
+    "vss.md.obs", "vss.md.pred", "ceoi"
+  )
+  all_params <- setdiff(names(get.interval.cols()), c("start", "end", non_pknca_covered_params))
+  intervals <- data.frame(start = c(0, 25), end = c(25, Inf))
+
+  for (param in all_params){
+    intervals_with_param <- intervals
+    intervals_with_param[[param]] <- TRUE
+    o_data <- PKNCAdata(o_conc, o_dose, intervals = intervals_with_param)
+
+    expect_no_error(param_res <- pk.nca(o_data))
+    expect_false(
+      all(is.na(param_res$result$PPORRES)),
+      info = paste0("Parameter ", param, " can be calculated independently")
+    )
+  }
+})
+
 test_that("Cannot include and exclude half-life points at the same time (#406)", {
   o_conc <- PKNCAconc(data = data.frame(conc = 1, time = 0, inex = TRUE), conc~time, include_half.life = "inex", exclude_half.life = "inex")
   d_interval <- data.frame(start = 0, end = Inf, half.life = TRUE)