From 9836b87f71ae003973ebc86f213c9dae65a5a0b2 Mon Sep 17 00:00:00 2001
From: Ron Keizer <ron@insight-rx.com>
Date: Thu, 7 Mar 2024 20:51:33 -0800
Subject: [PATCH 1/8] implement infusion duration scaling

---
 NAMESPACE                   |  1 +
 R/apply_duration_scale.R    | 54 +++++++++++++++++++++++++++++++++++++
 R/new_ode_model.R           |  1 +
 R/sim.R                     |  8 ++++++
 inst/template/R/model.R     |  7 ++++-
 man/apply_duration_scale.Rd | 34 +++++++++++++++++++++++
 6 files changed, 104 insertions(+), 1 deletion(-)
 create mode 100644 R/apply_duration_scale.R
 create mode 100644 man/apply_duration_scale.Rd

diff --git a/NAMESPACE b/NAMESPACE
index bf35b7dc..f9230d73 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -14,6 +14,7 @@ export(advan)
 export(advan_create_data)
 export(advan_parse_output)
 export(advan_process_infusion_doses)
+export(apply_duration_scale)
 export(apply_lagtime)
 export(calc_auc_analytic)
 export(calc_ss_analytic)
diff --git a/R/apply_duration_scale.R b/R/apply_duration_scale.R
new file mode 100644
index 00000000..42da2135
--- /dev/null
+++ b/R/apply_duration_scale.R
@@ -0,0 +1,54 @@
+#' Apply infusion duration scale to a regimen
+#'
+#' E.g. see Centanni et al. Clin Pharmacokinet 2024. An estimated scaling factor 
+#' for the length of the infusion was applied there in a model for vincristine.
+#' This is likely most relevant for very short infusions.
+#'
+#' Implementation is similar to handling of `lagtime`, i.e. the regimen that is the 
+#' input for the simulation function is updated.
+#'
+#' @param regimen PKPDsim regimen
+#' @param duration_scale infusion length scale.
+#' @param parameters parameter list, required if parameters are specified.
+#' @param cmt_mapping map of administration types to compartments, e.g. `list("oral" = 1, "infusion" = 2, "bolus" = 2)`.
+#'
+#' @export
+#'
+#' @return Original regimen with infusion lengths scaled by a factor
+#'
+apply_duration_scale <- function(
+  regimen,
+  duration_scale = NULL,
+  parameters,
+  cmt_mapping = NULL
+) {
+  if(is.null(regimen$t_inf)) {
+    warning("`duration_scale` is only relevant for infusion regimens with an infusion length > 0.")
+    return(regimen)
+  }
+  if(!is.null(duration_scale)) {
+    if(class(duration_scale) %in% c("numeric", "integer")) {
+      if(length(duration_scale) == 1) {
+        regimen$t_inf <- regimen$t_inf * duration_scale
+      } else {
+        regimen$t_inf <- regimen$t_inf * duration_scale[regimen$cmt]
+      }
+    }
+    if(class(duration_scale) %in% c("character")) {
+      if(length(duration_scale) == 1) {
+        regimen$t_inf <- regimen$t_inf * parameters[[duration_scale]]
+      } else {
+        if(is.null(regimen$cmt)) {
+          if(!is.null(cmt_mapping)) {
+            regimen$cmt <- as.numeric(cmt_mapping[regimen$type])
+          } else {
+            regimen$cmt <- rep(1, length(regimen$dose_times))
+          }
+        }
+        par_tmp <- parameters
+        regimen$t_inf <- regimen$t_inf + as.numeric(unlist(par_tmp[duration_scale[regimen$cmt]]))
+      }
+    }
+  }
+  return(regimen)
+}
diff --git a/R/new_ode_model.R b/R/new_ode_model.R
index 50e46fe8..2c4df7b9 100644
--- a/R/new_ode_model.R
+++ b/R/new_ode_model.R
@@ -371,6 +371,7 @@ new_ode_model <- function (model = NULL,
                        "\\[COVS\\]", covs,
                        "\\[FIXED\\]", fixed,
                        "\\[LAGTIME\\]", lagtime,
+                       "\\[DURATION_SCALE\\]", deparse(dose$duration_scale),
                        "\\[USE_IOV\\]", as.character(use_iov),
                        "\\[IOV\\]", PKPDsim::print_list(iov, FALSE),
                        "\\[DEVELOPMENT\\]", print_list(development, FALSE),
diff --git a/R/sim.R b/R/sim.R
index 147b3f25..9854fbc6 100644
--- a/R/sim.R
+++ b/R/sim.R
@@ -148,6 +148,14 @@ sim <- function (ode = NULL,
   if(!is.null(lagtime)) {
     regimen <- apply_lagtime(regimen, lagtime, parameters, attr(ode, "cmt_mapping"))
   }
+  if(!is.null(attr(ode, "dose")$duration_scale)) {
+    regimen <- apply_duration_scale(
+      regimen,
+      attr(ode, "dose")$duration_scale,
+      parameters,
+      attr(ode, "cmt_mapping")
+    )
+  }
   if(t_init != 0) regimen$dose_times <- regimen$dose_times + t_init
   p <- as.list(parameters)
   if(!is.null(t_obs)) {
diff --git a/inst/template/R/model.R b/inst/template/R/model.R
index b00ea8ae..7220675c 100644
--- a/inst/template/R/model.R
+++ b/inst/template/R/model.R
@@ -4,7 +4,12 @@ model <- function(mod = NULL) {
   attr(ret, "cpp") <- TRUE
   attr(ret, "size") <- [N_COMP]
   attr(ret, "obs") <- list("cmt" = [OBS_COMP], "scale" = "[OBS_SCALE]", "variable" = [OBS_VARIABLE])
-  attr(ret, "dose") <- list("cmt" = [DOSE_COMP], "bioav" = [DOSE_BIOAV], "duplicate" = [DOSE_DUPLICATE] )
+  attr(ret, "dose") <- list(
+    "cmt" = [DOSE_COMP], 
+    "bioav" = [DOSE_BIOAV], 
+    "duplicate" = [DOSE_DUPLICATE],
+    "duration_scale" = [DURATION_SCALE]
+  )
   attr(ret, "code") <- "[CODE]"
   attr(ret, "pk_code") <- "[PK_CODE]"
   attr(ret, "state_init") <- [STATE_INIT]
diff --git a/man/apply_duration_scale.Rd b/man/apply_duration_scale.Rd
new file mode 100644
index 00000000..94b46316
--- /dev/null
+++ b/man/apply_duration_scale.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/apply_duration_scale.R
+\name{apply_duration_scale}
+\alias{apply_duration_scale}
+\title{Apply infusion duration scale to a regimen}
+\usage{
+apply_duration_scale(
+  regimen,
+  duration_scale = NULL,
+  parameters,
+  cmt_mapping = NULL
+)
+}
+\arguments{
+\item{regimen}{PKPDsim regimen}
+
+\item{duration_scale}{infusion length scale.}
+
+\item{parameters}{parameter list, required if parameters are specified.}
+
+\item{cmt_mapping}{map of administration types to compartments, e.g. `list("oral" = 1, "infusion" = 2, "bolus" = 2)`.}
+}
+\value{
+Original regimen with infusion lengths scaled by a factor
+}
+\description{
+E.g. see Centanni et al. Clin Pharmacokinet 2024. An estimated scaling factor 
+for the length of the infusion was applied there in a model for vincristine.
+This is likely most relevant for very short infusions.
+}
+\details{
+Implementation is similar to handling of `lagtime`, i.e. the regimen that is the 
+input for the simulation function is updated.
+}

From 86f24137c1a8059c0ac0756df495a990c3067429 Mon Sep 17 00:00:00 2001
From: Ron Keizer <ron@insight-rx.com>
Date: Tue, 2 Apr 2024 09:41:46 -0700
Subject: [PATCH 2/8] rm lines not needed; add test

---
 R/apply_duration_scale.R                   | 25 ++++-------
 man/apply_duration_scale.Rd                | 16 +++----
 tests/testthat/test_apply_duration_scale.R | 49 ++++++++++++++++++++++
 3 files changed, 63 insertions(+), 27 deletions(-)
 create mode 100644 tests/testthat/test_apply_duration_scale.R

diff --git a/R/apply_duration_scale.R b/R/apply_duration_scale.R
index 42da2135..e3a4d1d2 100644
--- a/R/apply_duration_scale.R
+++ b/R/apply_duration_scale.R
@@ -1,16 +1,16 @@
 #' Apply infusion duration scale to a regimen
 #'
-#' E.g. see Centanni et al. Clin Pharmacokinet 2024. An estimated scaling factor 
+#' E.g. see Centanni et al. Clin Pharmacokinet 2024. An estimated scaling factor
 #' for the length of the infusion was applied there in a model for vincristine.
 #' This is likely most relevant for very short infusions.
 #'
-#' Implementation is similar to handling of `lagtime`, i.e. the regimen that is the 
+#' Implementation is similar to handling of `lagtime`, i.e. the regimen that is the
 #' input for the simulation function is updated.
 #'
 #' @param regimen PKPDsim regimen
 #' @param duration_scale infusion length scale.
-#' @param parameters parameter list, required if parameters are specified.
-#' @param cmt_mapping map of administration types to compartments, e.g. `list("oral" = 1, "infusion" = 2, "bolus" = 2)`.
+#' @param parameters parameter list, required if the duration scale is
+#' specified as a parameter.
 #'
 #' @export
 #'
@@ -19,10 +19,9 @@
 apply_duration_scale <- function(
   regimen,
   duration_scale = NULL,
-  parameters,
-  cmt_mapping = NULL
+  parameters = NULL
 ) {
-  if(is.null(regimen$t_inf)) {
+  if(is.null(regimen$t_inf) || all(regimen$t_inf == 0)) {
     warning("`duration_scale` is only relevant for infusion regimens with an infusion length > 0.")
     return(regimen)
   }
@@ -33,22 +32,16 @@ apply_duration_scale <- function(
       } else {
         regimen$t_inf <- regimen$t_inf * duration_scale[regimen$cmt]
       }
-    }
-    if(class(duration_scale) %in% c("character")) {
+    } else if(class(duration_scale) %in% c("character")) {
       if(length(duration_scale) == 1) {
         regimen$t_inf <- regimen$t_inf * parameters[[duration_scale]]
       } else {
-        if(is.null(regimen$cmt)) {
-          if(!is.null(cmt_mapping)) {
-            regimen$cmt <- as.numeric(cmt_mapping[regimen$type])
-          } else {
-            regimen$cmt <- rep(1, length(regimen$dose_times))
-          }
-        }
         par_tmp <- parameters
         regimen$t_inf <- regimen$t_inf + as.numeric(unlist(par_tmp[duration_scale[regimen$cmt]]))
       }
     }
+  } else {
+    warning("Please specify `duration_scale` to apply to regimen.")
   }
   return(regimen)
 }
diff --git a/man/apply_duration_scale.Rd b/man/apply_duration_scale.Rd
index 94b46316..f3a4a821 100644
--- a/man/apply_duration_scale.Rd
+++ b/man/apply_duration_scale.Rd
@@ -4,31 +4,25 @@
 \alias{apply_duration_scale}
 \title{Apply infusion duration scale to a regimen}
 \usage{
-apply_duration_scale(
-  regimen,
-  duration_scale = NULL,
-  parameters,
-  cmt_mapping = NULL
-)
+apply_duration_scale(regimen, duration_scale = NULL, parameters = NULL)
 }
 \arguments{
 \item{regimen}{PKPDsim regimen}
 
 \item{duration_scale}{infusion length scale.}
 
-\item{parameters}{parameter list, required if parameters are specified.}
-
-\item{cmt_mapping}{map of administration types to compartments, e.g. `list("oral" = 1, "infusion" = 2, "bolus" = 2)`.}
+\item{parameters}{parameter list, required if the duration scale is
+specified as a parameter.}
 }
 \value{
 Original regimen with infusion lengths scaled by a factor
 }
 \description{
-E.g. see Centanni et al. Clin Pharmacokinet 2024. An estimated scaling factor 
+E.g. see Centanni et al. Clin Pharmacokinet 2024. An estimated scaling factor
 for the length of the infusion was applied there in a model for vincristine.
 This is likely most relevant for very short infusions.
 }
 \details{
-Implementation is similar to handling of `lagtime`, i.e. the regimen that is the 
+Implementation is similar to handling of `lagtime`, i.e. the regimen that is the
 input for the simulation function is updated.
 }
diff --git a/tests/testthat/test_apply_duration_scale.R b/tests/testthat/test_apply_duration_scale.R
new file mode 100644
index 00000000..4470b6f5
--- /dev/null
+++ b/tests/testthat/test_apply_duration_scale.R
@@ -0,0 +1,49 @@
+reg_oral <- new_regimen(
+  amt = 1000,
+  n = 12,
+  interval = 12,
+  type = "oral"
+)
+reg_iv <- new_regimen(
+  amt = 1000,
+  n = 12,
+  interval = 12,
+  type = "infusion",
+  t_inf = 1
+)
+
+## null / error checks
+test_that("infusion length NULL warning", {
+  expect_warning(
+    dur0 <- apply_duration_scale(
+      regimen = reg_oral
+    )
+  )
+  expect_equal(dur0, reg_oral)
+})
+test_that("duration scale NULL warning", {
+  expect_warning(
+    dur1 <- apply_duration_scale(
+      regimen = reg_iv
+    )
+  )
+  expect_equal(dur1, reg_iv)
+})
+
+## Check functionality
+test_that("infusion length scaled", {
+  dur2 <- apply_duration_scale(
+    regimen = reg_iv,
+    duration_scale = 1.5
+  )
+  expect_equal(dur2$t_inf, rep(1.5, 12))
+})
+
+test_that("infusion length scaled using parameter", {
+  dur3 <- apply_duration_scale(
+    regimen = reg_iv,
+    duration_scale = "SCALE",
+    parameters = list(CL = 5, V = 50, SCALE = 1.6)
+  )
+  expect_equal(dur3$t_inf, rep(1.6, 12))
+})

From 449f4e619e0a535b47c0a3fa4b545bb0e1f529d7 Mon Sep 17 00:00:00 2001
From: jasmineirx <jasmine@insight-rx.com>
Date: Tue, 2 Apr 2024 14:24:27 -0400
Subject: [PATCH 3/8] add test for multi length scale

---
 tests/testthat/test_apply_duration_scale.R | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/tests/testthat/test_apply_duration_scale.R b/tests/testthat/test_apply_duration_scale.R
index 4470b6f5..17d94b3f 100644
--- a/tests/testthat/test_apply_duration_scale.R
+++ b/tests/testthat/test_apply_duration_scale.R
@@ -12,6 +12,15 @@ reg_iv <- new_regimen(
   t_inf = 1
 )
 
+reg_combo <- new_regimen(
+  amt = 1000,
+  n = 4,
+  interval = 12,
+  type = c("drug1", "drug2", "oral", "oral"),
+  cmt = c(2, 3, 1, 1),
+  t_inf = c(1, 1, 0, 0)
+)
+
 ## null / error checks
 test_that("infusion length NULL warning", {
   expect_warning(
@@ -47,3 +56,11 @@ test_that("infusion length scaled using parameter", {
   )
   expect_equal(dur3$t_inf, rep(1.6, 12))
 })
+
+test_that("infusion length scaled", {
+  dur4 <- apply_duration_scale(
+    regimen = reg_combo,
+    duration_scale = c(1, 1.5, 2)
+  )
+  expect_equal(dur4$t_inf, c(1.5, 2, 0))
+})

From ccb7003e8fc5ada5b3cfc3e07816a76627367cb8 Mon Sep 17 00:00:00 2001
From: Ron Keizer <ron@insight-rx.com>
Date: Tue, 2 Apr 2024 14:12:36 -0700
Subject: [PATCH 4/8] misc fixes

---
 R/apply_duration_scale.R                   |  9 +++++++++
 R/sim.R                                    |  4 +---
 man/apply_duration_scale.Rd                |  3 +++
 tests/testthat/test_apply_duration_scale.R | 13 +++++++++++--
 4 files changed, 24 insertions(+), 5 deletions(-)

diff --git a/R/apply_duration_scale.R b/R/apply_duration_scale.R
index e3a4d1d2..7c9ab84a 100644
--- a/R/apply_duration_scale.R
+++ b/R/apply_duration_scale.R
@@ -11,6 +11,8 @@
 #' @param duration_scale infusion length scale.
 #' @param parameters parameter list, required if the duration scale is
 #' specified as a parameter.
+#' @param cmt_mapping map of administration types to compartments, e.g.
+#' `list("oral" = 1, "infusion" = 2, "bolus" = 2)`.
 #'
 #' @export
 #'
@@ -33,6 +35,13 @@ apply_duration_scale <- function(
         regimen$t_inf <- regimen$t_inf * duration_scale[regimen$cmt]
       }
     } else if(class(duration_scale) %in% c("character")) {
+      if(is.null(regimen$cmt)) {
+        if(!is.null(cmt_mapping)) {
+          regimen$cmt <- as.numeric(cmt_mapping[regimen$type])
+        } else {
+          regimen$cmt <- rep(1, length(regimen$dose_times))
+        }
+      }
       if(length(duration_scale) == 1) {
         regimen$t_inf <- regimen$t_inf * parameters[[duration_scale]]
       } else {
diff --git a/R/sim.R b/R/sim.R
index 9854fbc6..46e31d6b 100644
--- a/R/sim.R
+++ b/R/sim.R
@@ -151,9 +151,7 @@ sim <- function (ode = NULL,
   if(!is.null(attr(ode, "dose")$duration_scale)) {
     regimen <- apply_duration_scale(
       regimen,
-      attr(ode, "dose")$duration_scale,
-      parameters,
-      attr(ode, "cmt_mapping")
+      attr(ode, "dose")$duration_scale
     )
   }
   if(t_init != 0) regimen$dose_times <- regimen$dose_times + t_init
diff --git a/man/apply_duration_scale.Rd b/man/apply_duration_scale.Rd
index f3a4a821..c6d5f680 100644
--- a/man/apply_duration_scale.Rd
+++ b/man/apply_duration_scale.Rd
@@ -13,6 +13,9 @@ apply_duration_scale(regimen, duration_scale = NULL, parameters = NULL)
 
 \item{parameters}{parameter list, required if the duration scale is
 specified as a parameter.}
+
+\item{cmt_mapping}{map of administration types to compartments, e.g.
+`list("oral" = 1, "infusion" = 2, "bolus" = 2)`.}
 }
 \value{
 Original regimen with infusion lengths scaled by a factor
diff --git a/tests/testthat/test_apply_duration_scale.R b/tests/testthat/test_apply_duration_scale.R
index 4470b6f5..0e69accf 100644
--- a/tests/testthat/test_apply_duration_scale.R
+++ b/tests/testthat/test_apply_duration_scale.R
@@ -9,7 +9,8 @@ reg_iv <- new_regimen(
   n = 12,
   interval = 12,
   type = "infusion",
-  t_inf = 1
+  t_inf = 1,
+  cmt = c(1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2)
 )
 
 ## null / error checks
@@ -39,8 +40,16 @@ test_that("infusion length scaled", {
   expect_equal(dur2$t_inf, rep(1.5, 12))
 })
 
-test_that("infusion length scaled using parameter", {
+test_that("infusion length scaled using vector", {
   dur3 <- apply_duration_scale(
+    regimen = reg_iv,
+    duration_scale = c(1.5, 1.0) # scale oral "infusions", but not "iv"
+  )
+  expect_equal(dur3$t_inf, rep(c(1.5, 1.0), 6))
+})
+
+test_that("infusion length scaled using parameter", {
+  dur4 <- apply_duration_scale(
     regimen = reg_iv,
     duration_scale = "SCALE",
     parameters = list(CL = 5, V = 50, SCALE = 1.6)

From 620815a701cea163bf458a85863839e37e1565b3 Mon Sep 17 00:00:00 2001
From: Ron Keizer <ron@insight-rx.com>
Date: Tue, 2 Apr 2024 15:26:15 -0700
Subject: [PATCH 5/8] clean up

---
 R/apply_duration_scale.R    | 3 ++-
 R/sim.R                     | 4 +++-
 man/apply_duration_scale.Rd | 7 ++++++-
 3 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/R/apply_duration_scale.R b/R/apply_duration_scale.R
index 7c9ab84a..7ef97714 100644
--- a/R/apply_duration_scale.R
+++ b/R/apply_duration_scale.R
@@ -21,7 +21,8 @@
 apply_duration_scale <- function(
   regimen,
   duration_scale = NULL,
-  parameters = NULL
+  parameters = NULL,
+  cmt_mapping = NULL
 ) {
   if(is.null(regimen$t_inf) || all(regimen$t_inf == 0)) {
     warning("`duration_scale` is only relevant for infusion regimens with an infusion length > 0.")
diff --git a/R/sim.R b/R/sim.R
index 46e31d6b..9854fbc6 100644
--- a/R/sim.R
+++ b/R/sim.R
@@ -151,7 +151,9 @@ sim <- function (ode = NULL,
   if(!is.null(attr(ode, "dose")$duration_scale)) {
     regimen <- apply_duration_scale(
       regimen,
-      attr(ode, "dose")$duration_scale
+      attr(ode, "dose")$duration_scale,
+      parameters,
+      attr(ode, "cmt_mapping")
     )
   }
   if(t_init != 0) regimen$dose_times <- regimen$dose_times + t_init
diff --git a/man/apply_duration_scale.Rd b/man/apply_duration_scale.Rd
index c6d5f680..05e4e46d 100644
--- a/man/apply_duration_scale.Rd
+++ b/man/apply_duration_scale.Rd
@@ -4,7 +4,12 @@
 \alias{apply_duration_scale}
 \title{Apply infusion duration scale to a regimen}
 \usage{
-apply_duration_scale(regimen, duration_scale = NULL, parameters = NULL)
+apply_duration_scale(
+  regimen,
+  duration_scale = NULL,
+  parameters = NULL,
+  cmt_mapping = NULL
+)
 }
 \arguments{
 \item{regimen}{PKPDsim regimen}

From 5069aca7962f4d0dc7f4d0e0e00ae30a96b25212 Mon Sep 17 00:00:00 2001
From: jasmineirx <jasmine@insight-rx.com>
Date: Wed, 3 Apr 2024 13:16:12 -0400
Subject: [PATCH 6/8] add tests, plus to multiplication

---
 R/apply_duration_scale.R                   |  2 +-
 tests/testthat/test_apply_duration_scale.R | 35 ++++++++++++++++++++--
 2 files changed, 33 insertions(+), 4 deletions(-)

diff --git a/R/apply_duration_scale.R b/R/apply_duration_scale.R
index 7ef97714..1f67db36 100644
--- a/R/apply_duration_scale.R
+++ b/R/apply_duration_scale.R
@@ -47,7 +47,7 @@ apply_duration_scale <- function(
         regimen$t_inf <- regimen$t_inf * parameters[[duration_scale]]
       } else {
         par_tmp <- parameters
-        regimen$t_inf <- regimen$t_inf + as.numeric(unlist(par_tmp[duration_scale[regimen$cmt]]))
+        regimen$t_inf <- regimen$t_inf * as.numeric(unlist(par_tmp[duration_scale[regimen$cmt]]))
       }
     }
   } else {
diff --git a/tests/testthat/test_apply_duration_scale.R b/tests/testthat/test_apply_duration_scale.R
index 7beb866b..36c50d84 100644
--- a/tests/testthat/test_apply_duration_scale.R
+++ b/tests/testthat/test_apply_duration_scale.R
@@ -63,13 +63,42 @@ test_that("infusion length scaled using parameter", {
     duration_scale = "SCALE",
     parameters = list(CL = 5, V = 50, SCALE = 1.6)
   )
-  expect_equal(dur3$t_inf, rep(1.6, 12))
+  expect_equal(dur4$t_inf, rep(1.6, 12))
 })
 
-test_that("infusion length scaled", {
+test_that("infusion length scaled, multiple cmts", {
   dur4 <- apply_duration_scale(
     regimen = reg_combo,
     duration_scale = c(1, 1.5, 2)
   )
-  expect_equal(dur4$t_inf, c(1.5, 2, 0))
+  expect_equal(dur4$t_inf, c(1.5, 2, 0, 0))
+})
+
+test_that("infusion length scaled, multiple cmts, no cmt", {
+  reg_combo$cmt <- NULL
+  dur5 <- apply_duration_scale(
+    regimen = reg_combo,
+    duration_scale = "SCALE",
+    parameters = list(CL = 5, V = 50, SCALE = 1.6),
+    cmt_mapping = c("drug1" = 2, "drug2" = 3, "oral" = 1)
+  )
+  dur6 <- apply_duration_scale(
+    regimen = reg_combo,
+    duration_scale = c("SCALE1", "SCALE2", "SCALE3"),
+    parameters = list(CL = 5, V = 50, SCALE1 = 1.6, SCALE2 = 1.7, SCALE3 = 1.8),
+    cmt_mapping = c("drug1" = 2, "drug2" = 3, "oral" = 1)
+  )
+  expect_equal(dur5$t_inf, c(1.6, 1.6, 0, 0))
+  expect_equal(dur6$t_inf, c(1.7, 1.8, 0, 0))
+})
+
+test_that("infusion length scaled, no cmt, no cmt_mapping", {
+  reg_combo$cmt <- NULL
+  dur7 <- apply_duration_scale(
+    regimen = reg_combo,
+    duration_scale = c("SCALE1", "SCALE2", "SCALE3"),
+    parameters = list(CL = 5, V = 50, SCALE1 = 1.6, SCALE2 = 1.7, SCALE3 = 1.8),
+    cmt_mapping = NULL
+  )
+  expect_equal(dur7$t_inf, c(1.6, 1.6, 0, 0))
 })

From 95a5cb0c712b493fd77e170390b72c86eabbb314 Mon Sep 17 00:00:00 2001
From: Ron Keizer <ron@insight-rx.com>
Date: Wed, 3 Apr 2024 10:20:40 -0700
Subject: [PATCH 7/8] fix test; clean up unrelated warnings in other test

---
 tests/testthat/test_apply_duration_scale.R | 4 ++--
 tests/testthat/test_timevar_cov.R          | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test_apply_duration_scale.R b/tests/testthat/test_apply_duration_scale.R
index 7beb866b..f1d00010 100644
--- a/tests/testthat/test_apply_duration_scale.R
+++ b/tests/testthat/test_apply_duration_scale.R
@@ -63,7 +63,7 @@ test_that("infusion length scaled using parameter", {
     duration_scale = "SCALE",
     parameters = list(CL = 5, V = 50, SCALE = 1.6)
   )
-  expect_equal(dur3$t_inf, rep(1.6, 12))
+  expect_equal(dur4$t_inf, rep(1.6, 12))
 })
 
 test_that("infusion length scaled", {
@@ -71,5 +71,5 @@ test_that("infusion length scaled", {
     regimen = reg_combo,
     duration_scale = c(1, 1.5, 2)
   )
-  expect_equal(dur4$t_inf, c(1.5, 2, 0))
+  expect_equal(dur4$t_inf, c(1.5, 2, 0, 0))
 })
diff --git a/tests/testthat/test_timevar_cov.R b/tests/testthat/test_timevar_cov.R
index 7e91ae32..60866dbc 100644
--- a/tests/testthat/test_timevar_cov.R
+++ b/tests/testthat/test_timevar_cov.R
@@ -16,7 +16,7 @@ mod <- new_ode_model(
   pk_code = "CLi = CL + CRCL",
   obs = list(cmt = 2, scale = "V"),
   covariates = list(CRCL = new_covariate(5)), declare_variables = "CLi",
-  cpp = TRUE
+  cpp = FALSE
 )
 
 test_that("timevarying covariates handled", {
@@ -103,7 +103,7 @@ test_that("timevarying covariates are interpolated and affect PK", {
   ## Check interpolated covariates actually affect simulated conc
   expect_equal(
     round(sim2_inter$y, 3)[1:10],
-    c(0, 0.32, 0.611, 0.788, 1.205, 1.531, 1.708, 2.098, 2.379, 2.503),
+    c(0, 0.32, 0.611, 0.788, 1.205, 1.531, 1.708, 2.098, 2.379, 2.503)
   )
   expect_equal(
     round(sim2_locf$y, 3)[1:10],

From e1cdc8449fae749f4ce1f0e0a4533c106be6c79d Mon Sep 17 00:00:00 2001
From: jasmineirx <jasmine@insight-rx.com>
Date: Wed, 3 Apr 2024 13:22:13 -0400
Subject: [PATCH 8/8] minor cleanup

---
 R/apply_duration_scale.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/R/apply_duration_scale.R b/R/apply_duration_scale.R
index 1f67db36..8971b5cb 100644
--- a/R/apply_duration_scale.R
+++ b/R/apply_duration_scale.R
@@ -46,8 +46,7 @@ apply_duration_scale <- function(
       if(length(duration_scale) == 1) {
         regimen$t_inf <- regimen$t_inf * parameters[[duration_scale]]
       } else {
-        par_tmp <- parameters
-        regimen$t_inf <- regimen$t_inf * as.numeric(unlist(par_tmp[duration_scale[regimen$cmt]]))
+        regimen$t_inf <- regimen$t_inf * as.numeric(unlist(parameters[duration_scale[regimen$cmt]]))
       }
     }
   } else {