Initial steps to help with choosing parameters for intervals

NEWS.md

@@ -6,6 +6,12 @@ the dosing including dose amount and route.
 
 # PKNCA (development version)
 
+## New features
+
+* `choose_params()` is a new function that helps choose the parameters to use
+  based on parameters you want to calculate based on dosing route, number of
+  doses, and other choices.
+
 ## Minor changes (unlikely to affect PKNCA use)
 
 * Units for fraction excretion parameter (fe) are now accurately captured as

R/assertions.R

@@ -196,6 +196,23 @@ assert_aucmethod <- function(method = c("lin up/log down", "linear", "lin-log"))
   match.arg(method)
 }
 
+#' Assert that a character vector only contains PKNCA parameter names
+#' @param param A vector of parameter names to check
+assert_param_name <- function(param) {
+  missing_param <- setdiff(param, names(get.interval.cols()))
+  if (length(missing_param) > 0) {
+    stop(
+      paste(missing_param, collapse = ", "),
+      ngettext(
+        length(missing_param),
+        msg1 = " is not a valid PKNCA parameter name",
+        msg2 = " are not valid PKNCA parameter names"
+      )
+    )
+  }
+  param
+}
+
 #' Assert that an object is a PKNCAdata object
 #' @param object The PKNCAdata object
 #' @returns The PKNCAdata object (confirmed to be usable)

R/interval_model.R

@@ -0,0 +1,56 @@
+#' Choose parameters for an interval
+#'
+#' @inheritParams assert_choose_params_control
+#' @inheritParams assert_choose_params_auc_choices
+#' @inheritParams assert_choose_params_iv_choices
+choose_params <- function(route, num_doses, sample_type, clast_type, auc_choices, iv_choices) {
+  control <- assert_choose_params_control(route, num_doses, sample_type, clast_type)
+  auc_choices <- assert_choose_params_auc_choices(auc_choices, route = control$route, clast_type = control$clast_type)
+  iv_choices <- assert_choose_params_iv_choices(iv_choices, route = control$route)
+}
+
+#' Verify parameter options for choose_params
+#'
+#' @param route The route of administration
+#' @param num_doses Were "single" or "multiple" doses administered
+#' @param sample_type Was this a "spot" sample (typical for serum, plasma, and
+#'   blood) or an "interval" sample (typical for urine and feces)
+#' @param clast_type Should "pred"icted or "obs"erved clast be used?
+#' @returns A list of valid parameters
+assert_choose_params_control <- function(route, num_doses, sample_type, clast_type) {
+  checkmate::assert_choice(route, choices = c("extravascular", "intravascular"), null.ok = FALSE)
+  checkmate::assert_choice(num_doses, choices = c("single", "multiple"), null.ok = FALSE)
+  checkmate::assert_choice(sample_type, choices = c("spot", "interval"), null.ok = FALSE)
+  checkmate::assert_choice(clast_type, choices = c("pred", "obs"), null.ok = FALSE)
+}
+
+#' @describeIn assert_choose_params_control Choose valid AUC types
+#'
+#' @param auc_choices Zero or more types of AUC to calculate ("all", "inf", "last")
+#' @param auc_prefix "auc" or "aumc" to indicate what type of AUC calculation it will be
+#' @returns A character vector of AUC types to calculate
+assert_choose_params_auc_choices <- function(auc_choices, route, clast_type, auc_prefix) {
+  if (is.null(auc_choices)) {
+    return(character())
+  }
+  auc_choices <- unique(checkmate::assert_subset(auc_choices, choices = c("all", "inf", "last")))
+  which_inf <- which(auc_choices %in% "inf")
+  if (length(which_inf) > 0) {
+    auc_choices[which_inf] <- paste(auc_choices[which_inf], clast_type, sep = ".")
+  }
+  auc_prefix <- checkmate::assert_choice(auc_prefix, choices = c("auc", "aumc"))
+  if (route %in% "intravascular") {
+    ret <- paste0(auc_prefix, "iv")
+  } else {
+    ret <- auc_prefix
+  }
+  ret <- paste0(ret, auc_choices)
+  assert_param_name(ret)
+}
+
+#' Choose IV-specific parameters
+#'
+#' @param iv_choices intravenous-specific parameter names ("c0", "ceoi")
+assert_choose_params_iv_choices <- function(iv_choices) {
+  unique(checkmate::assert_subset(x = iv_choices, choices = c("c0", "ceoi"))
+}

tests/testthat/test-assertions.R

@@ -99,6 +99,17 @@ test_that("assert_lambdaz", {
   )
 })
 
+test_that("assert_param_name", {
+  expect_error(
+    assert_param_name("foo"),
+    regexp = "foo is not a valid PKNCA parameter name"
+  )
+  expect_error(
+    assert_param_name(c("foo", "bar")),
+    regexp = "foo, bar are not valid PKNCA parameter names"
+  )
+})
+
 test_that("assert_PKNCAdata", {
   expect_error(
     assert_PKNCAdata("A"),
@@ -113,12 +124,12 @@ test_that("element_find", {
     element_find(values5),
     element_find(values10)
   )
-  
+
   expect_equal(
     element_find(values5),
     "Elements 1, 2, 3, 4, 5"
   )
-  
+
   expect_equal(
     element_find(values10),
     "Elements 1, 2, 3, 4, 5"

tests/testthat/test-interval_model.R

@@ -0,0 +1,47 @@
+test_that("assert_choose_params_auc_choices", {
+  # no parameters are required
+  expect_equal(
+    assert_choose_params_auc_choices(auc_choices = NULL),
+    character()
+  )
+  # multiple parmaeters may be returned
+  expect_equal(
+    assert_choose_params_auc_choices(auc_choices = c("last", "all", "inf"), route = "intravascular", clast_type = "pred", auc_prefix = "auc"),
+    c("aucivlast", "aucivall", "aucivinf.pred")
+  )
+  # Verify that all valid choices return valid parameter names
+  for (current_auc_choices in c("all", "inf", "last")) {
+    for (current_route in c("extravascular", "intravascular")) {
+      for (current_clast_type in c("pred", "obs")) {
+        for (current_auc_prefix in c("auc", "aumc")) {
+          # TODO: multiple AUMC IV parameters do not exist
+          if (current_auc_prefix == "aumc" && current_route == "intravascular") {
+            expect_error(
+              assert_choose_params_auc_choices(
+                auc_choices = current_auc_choices,
+                route = current_route,
+                clast_type = current_clast_type,
+                auc_prefix = current_auc_prefix
+              ),
+              regexp = "not .*valid PKNCA parameter name"
+            )
+          } else {
+            expect_error(
+              assert_choose_params_auc_choices(
+                auc_choices = current_auc_choices,
+                route = current_route,
+                clast_type = current_clast_type,
+                auc_prefix = current_auc_prefix
+              ),
+              NA
+            )
+          }
+        }
+      }
+    }
+  }
+  expect_equal(
+    assert_choose_params_auc_choices(auc_choices = "inf", route = "extravascular", clast_type = "pred", auc_prefix = "auc"),
+    "aucinf.pred"
+  )
+})