From dde74ea087a8dca842724a2b53aa2a60616d715e Mon Sep 17 00:00:00 2001
From: Jordan Brooks <jordan.brooks@insight-rx.com>
Date: Mon, 3 Jun 2024 23:13:54 +0000
Subject: [PATCH 1/8] add t_inf to sc doses in new_regimen

---
 R/new_regimen.R                   | 11 +++++++++++
 tests/testthat/test_new_regimen.R | 10 ++++++++++
 2 files changed, 21 insertions(+)

diff --git a/R/new_regimen.R b/R/new_regimen.R
index 06c86c2d..12b91edd 100644
--- a/R/new_regimen.R
+++ b/R/new_regimen.R
@@ -73,6 +73,11 @@ new_regimen <- function(
     } else if (any(is.na(t_inf))) {
       t_inf[is.na(t_inf)] <- 1
     }
+    if(any(type == "sc") && (is.null(t_inf) || length(t_inf) == 0)) {
+      reg$t_inf = 1/60
+    } else if (any(is.na(t_inf))) {
+      t_inf[is.na(t_inf)] <- 1/60
+    }
   }
   if(ss) {
     if(is.null(amt) || is.null(interval)) {
@@ -135,6 +140,12 @@ new_regimen <- function(
     reg$t_inf[reg$type == "oral"] <- 0
     reg$rate[reg$type == "oral"] <- 0
   }
+  if(any(reg$type == "sc")) {
+    if(any(reg$t_inf == 0)) {
+      reg$t_inf[reg$t_inf == 0] <- 1/60
+      reg$rate[reg$t_inf == 0] <- 60
+    }
+  }
   if(!is.null(cmt)) {
     if(length(cmt) != length(reg$dose_times)) {
       cmt <- rep(cmt[1], length(reg$dose_times))
diff --git a/tests/testthat/test_new_regimen.R b/tests/testthat/test_new_regimen.R
index 0b15c050..edde21f4 100644
--- a/tests/testthat/test_new_regimen.R
+++ b/tests/testthat/test_new_regimen.R
@@ -67,3 +67,13 @@ test_that("new_regimen can take arbitrary values for `type`", {
 test_that("do not creat regimens of `type` 'covariate'", {
   expect_error(new_regimen(100, times = 0, type = "covariate"))
 })
+
+test_that("sc doses accept an infusion length argument'", {
+  reg1 <- new_regimen(
+    amt = 100,
+    times = c(0, 12, 24, 36, 48),
+    type = "sc",
+    t_inf = 30/60
+  )
+  expect_equal(reg1$t_inf, rep(0.5,5))
+})

From bc6056382cfcd52c5722d476305eff61cceb623b Mon Sep 17 00:00:00 2001
From: jasmineirx <jasmine@insight-rx.com>
Date: Tue, 4 Jun 2024 12:31:03 -0400
Subject: [PATCH 2/8] add a couple of edge cases to test

---
 tests/testthat/test_new_regimen.R | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/tests/testthat/test_new_regimen.R b/tests/testthat/test_new_regimen.R
index edde21f4..7bf08a3c 100644
--- a/tests/testthat/test_new_regimen.R
+++ b/tests/testthat/test_new_regimen.R
@@ -77,3 +77,19 @@ test_that("sc doses accept an infusion length argument'", {
   )
   expect_equal(reg1$t_inf, rep(0.5,5))
 })
+
+test_that("t_inf imputed correctly", {
+  reg1 <- new_regimen(
+    amt = 100,
+    times = c(0, 12, 24, 36, 48),
+    type = c("sc", "infusion", "sc", "infusion", "sc")
+  )
+  reg2 <- new_regimen(
+    amt = 100,
+    times = c(0, 12, 24, 36, 48),
+    type = c("sc", "infusion", "sc", "infusion", "sc"),
+    t_inf = c(2/60, 2.5, NA, NA, 0)
+  )
+  expect_equal(reg1$t_inf, c(1/60, 1, 1/60, 1, 1/60))
+  expect_equal(reg2$t_inf, c(2/60, 2.5, 1/60, 1, 1/60))
+})

From 880e4164b037fe9c70ac34cf3efd641e5b4a6d69 Mon Sep 17 00:00:00 2001
From: Jordan Brooks <jordan.brooks@insight-rx.com>
Date: Thu, 6 Jun 2024 19:29:06 +0000
Subject: [PATCH 3/8] updated logic to cover mixed regimen type automatic t_inf
 assignment

---
 R/new_regimen.R                   | 37 ++++++++++++++++++++-----------
 tests/testthat/test_new_regimen.R | 15 +++++++------
 2 files changed, 32 insertions(+), 20 deletions(-)

diff --git a/R/new_regimen.R b/R/new_regimen.R
index 12b91edd..729fce3b 100644
--- a/R/new_regimen.R
+++ b/R/new_regimen.R
@@ -69,14 +69,29 @@ new_regimen <- function(
       stop("'covariate' is a protected type and cannot be used for doses.")
     }
     if(any(type == "infusion") && (is.null(t_inf) || length(t_inf) == 0)) {
-      reg$t_inf = 1
+      reg$t_inf[reg$type=="infusion"] = 1
     } else if (any(is.na(t_inf))) {
-      t_inf[is.na(t_inf)] <- 1
+      reg$t_inf[(reg$type=="infusion" & is.na(t_inf))] <- 1
     }
     if(any(type == "sc") && (is.null(t_inf) || length(t_inf) == 0)) {
-      reg$t_inf = 1/60
+      reg$t_inf[reg$type=="sc"] = 1/60
     } else if (any(is.na(t_inf))) {
-      t_inf[is.na(t_inf)] <- 1/60
+      reg$t_inf[(reg$type=="sc" & is.na(reg$t_inf))] <- 1/60
+    }
+    if(any(type == "im") & (is.null(t_inf) || length(t_inf) == 0)) {
+      reg$t_inf[reg$type=="im"] = 1/60
+    } else if (any(is.na(t_inf))) {
+      reg$t_inf[(reg$type=="im" & is.na(reg$t_inf))] <- 1/60
+    }
+    if(any(type == "bolus") && (is.null(t_inf) || length(t_inf) == 0)) {
+      reg$t_inf[reg$type=="bolus"] = 0
+    } else if (any(is.na(t_inf))) {
+      reg$t_inf[(reg$type=="bolus" & is.na(reg$t_inf))] <- 0
+    }
+    if(any(type == "oral") && (is.null(t_inf) || length(t_inf) == 0)) {
+      reg$t_inf[reg$type=="oral"] = 0
+    } else if (any(is.na(t_inf))) {
+      reg$t_inf[(reg$type=="oral" & is.na(reg$t_inf))] <- 0
     }
   }
   if(ss) {
@@ -126,10 +141,12 @@ new_regimen <- function(
   if(length(reg$type) != length(reg$dose_times)) {
     reg$type <- rep(reg$type[1], length(reg$dose_times))
   }
-  if(any(reg$type == "infusion")) {
+  if(any(reg$type == "infusion" | reg$type == "sc" | reg$type == "im")) {
     if(any(reg$t_inf == 0)) {
-      reg$t_inf[reg$t_inf == 0] <- 1/60
-      reg$rate[reg$t_inf == 0] <- 60
+      reg$t_inf[reg$t_inf == 0 & (type =="sc" | type =="im")] <- 1/60
+      reg$rate[reg$t_inf == 0 & (type =="sc" | type =="im")] <- 60
+      reg$t_inf[reg$t_inf == 0 & type == "infusion"] <- 1/60
+      reg$rate[reg$t_inf == 0 & type == "infusion"] <- 60
     }
   }
   if(any(reg$type == "bolus")) {
@@ -140,12 +157,6 @@ new_regimen <- function(
     reg$t_inf[reg$type == "oral"] <- 0
     reg$rate[reg$type == "oral"] <- 0
   }
-  if(any(reg$type == "sc")) {
-    if(any(reg$t_inf == 0)) {
-      reg$t_inf[reg$t_inf == 0] <- 1/60
-      reg$rate[reg$t_inf == 0] <- 60
-    }
-  }
   if(!is.null(cmt)) {
     if(length(cmt) != length(reg$dose_times)) {
       cmt <- rep(cmt[1], length(reg$dose_times))
diff --git a/tests/testthat/test_new_regimen.R b/tests/testthat/test_new_regimen.R
index 7bf08a3c..ba7867b8 100644
--- a/tests/testthat/test_new_regimen.R
+++ b/tests/testthat/test_new_regimen.R
@@ -81,15 +81,16 @@ test_that("sc doses accept an infusion length argument'", {
 test_that("t_inf imputed correctly", {
   reg1 <- new_regimen(
     amt = 100,
-    times = c(0, 12, 24, 36, 48),
-    type = c("sc", "infusion", "sc", "infusion", "sc")
+    times = c(0, 12, 24, 36, 48, 60, 72, 84),
+    type = c("sc", "infusion", "im", "sc", "infusion", "im","bolus","oral")
   )
   reg2 <- new_regimen(
     amt = 100,
-    times = c(0, 12, 24, 36, 48),
-    type = c("sc", "infusion", "sc", "infusion", "sc"),
-    t_inf = c(2/60, 2.5, NA, NA, 0)
+    times = c(0, 12, 24, 36, 48, 60, 72, 84),
+    type = c("sc", "infusion", "im", "sc", "infusion", "im","bolus","oral"),
+    t_inf = c(2/60, 2.5, 3/60, NA, NA, NA, NA, NA)
   )
-  expect_equal(reg1$t_inf, c(1/60, 1, 1/60, 1, 1/60))
-  expect_equal(reg2$t_inf, c(2/60, 2.5, 1/60, 1, 1/60))
+  expect_equal(reg1$t_inf, c(1/60, 1, 1/60, 1/60, 1, 1/60, 0, 0))
+  expect_equal(reg2$t_inf, c(2/60, 2.5, 3/60, 1/60, 1, 1/60, 0, 0))
 })
+

From 1693710a14c19bad04d2aaea80638713d7826495 Mon Sep 17 00:00:00 2001
From: Jordan Brooks <jordan.brooks@insight-rx.com>
Date: Thu, 6 Jun 2024 19:35:18 +0000
Subject: [PATCH 4/8] altered logic when t_inf==0 to update to 1/60 for
 infusion, sc, and im

---
 R/new_regimen.R | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/R/new_regimen.R b/R/new_regimen.R
index 729fce3b..134f9e66 100644
--- a/R/new_regimen.R
+++ b/R/new_regimen.R
@@ -143,10 +143,8 @@ new_regimen <- function(
   }
   if(any(reg$type == "infusion" | reg$type == "sc" | reg$type == "im")) {
     if(any(reg$t_inf == 0)) {
-      reg$t_inf[reg$t_inf == 0 & (type =="sc" | type =="im")] <- 1/60
-      reg$rate[reg$t_inf == 0 & (type =="sc" | type =="im")] <- 60
-      reg$t_inf[reg$t_inf == 0 & type == "infusion"] <- 1/60
-      reg$rate[reg$t_inf == 0 & type == "infusion"] <- 60
+      reg$t_inf[reg$t_inf == 0] <- 1/60
+      reg$rate[reg$t_inf == 0] <- 60
     }
   }
   if(any(reg$type == "bolus")) {

From 92313aeae7fea7e7eb2858f56b8eecd6e7ebe984 Mon Sep 17 00:00:00 2001
From: JordanBrooks33 <129786148+JordanBrooks33@users.noreply.github.com>
Date: Thu, 6 Jun 2024 13:47:14 -0700
Subject: [PATCH 5/8] Update R/new_regimen.R

Co-authored-by: Jasmine Hughes <43552465+jasmineirx@users.noreply.github.com>
---
 R/new_regimen.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/new_regimen.R b/R/new_regimen.R
index 134f9e66..cde336a3 100644
--- a/R/new_regimen.R
+++ b/R/new_regimen.R
@@ -141,7 +141,7 @@ new_regimen <- function(
   if(length(reg$type) != length(reg$dose_times)) {
     reg$type <- rep(reg$type[1], length(reg$dose_times))
   }
-  if(any(reg$type == "infusion" | reg$type == "sc" | reg$type == "im")) {
+  if(any(reg$type %in% c("infusion", "sc", "im"))) {
     if(any(reg$t_inf == 0)) {
       reg$t_inf[reg$t_inf == 0] <- 1/60
       reg$rate[reg$t_inf == 0] <- 60

From 5bbf857d08e9f58f420459b3f74bf256911504f7 Mon Sep 17 00:00:00 2001
From: JordanBrooks33 <129786148+JordanBrooks33@users.noreply.github.com>
Date: Thu, 6 Jun 2024 13:48:17 -0700
Subject: [PATCH 6/8] Update R/new_regimen.R

Co-authored-by: Jasmine Hughes <43552465+jasmineirx@users.noreply.github.com>
---
 R/new_regimen.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/new_regimen.R b/R/new_regimen.R
index cde336a3..ed4d4838 100644
--- a/R/new_regimen.R
+++ b/R/new_regimen.R
@@ -69,7 +69,7 @@ new_regimen <- function(
       stop("'covariate' is a protected type and cannot be used for doses.")
     }
     if(any(type == "infusion") && (is.null(t_inf) || length(t_inf) == 0)) {
-      reg$t_inf[reg$type=="infusion"] = 1
+      reg$t_inf[reg$type == "infusion"] <- 1
     } else if (any(is.na(t_inf))) {
       reg$t_inf[(reg$type=="infusion" & is.na(t_inf))] <- 1
     }

From 9aceaf807c3ff1bdf25dfb1855456e16705b2b29 Mon Sep 17 00:00:00 2001
From: Jordan Brooks <jordan.brooks@insight-rx.com>
Date: Thu, 6 Jun 2024 20:51:39 +0000
Subject: [PATCH 7/8] cleaned up repetitive formatting

---
 R/new_regimen.R | 34 ++++++++++------------------------
 1 file changed, 10 insertions(+), 24 deletions(-)

diff --git a/R/new_regimen.R b/R/new_regimen.R
index ed4d4838..79c5ab65 100644
--- a/R/new_regimen.R
+++ b/R/new_regimen.R
@@ -68,30 +68,16 @@ new_regimen <- function(
     if (any(reg$type == "covariate")) {
       stop("'covariate' is a protected type and cannot be used for doses.")
     }
-    if(any(type == "infusion") && (is.null(t_inf) || length(t_inf) == 0)) {
-      reg$t_inf[reg$type == "infusion"] <- 1
-    } else if (any(is.na(t_inf))) {
-      reg$t_inf[(reg$type=="infusion" & is.na(t_inf))] <- 1
-    }
-    if(any(type == "sc") && (is.null(t_inf) || length(t_inf) == 0)) {
-      reg$t_inf[reg$type=="sc"] = 1/60
-    } else if (any(is.na(t_inf))) {
-      reg$t_inf[(reg$type=="sc" & is.na(reg$t_inf))] <- 1/60
-    }
-    if(any(type == "im") & (is.null(t_inf) || length(t_inf) == 0)) {
-      reg$t_inf[reg$type=="im"] = 1/60
-    } else if (any(is.na(t_inf))) {
-      reg$t_inf[(reg$type=="im" & is.na(reg$t_inf))] <- 1/60
-    }
-    if(any(type == "bolus") && (is.null(t_inf) || length(t_inf) == 0)) {
-      reg$t_inf[reg$type=="bolus"] = 0
-    } else if (any(is.na(t_inf))) {
-      reg$t_inf[(reg$type=="bolus" & is.na(reg$t_inf))] <- 0
-    }
-    if(any(type == "oral") && (is.null(t_inf) || length(t_inf) == 0)) {
-      reg$t_inf[reg$type=="oral"] = 0
-    } else if (any(is.na(t_inf))) {
-      reg$t_inf[(reg$type=="oral" & is.na(reg$t_inf))] <- 0
+    if (is.null(t_inf) || length(t_inf) == 0) {
+      reg$t_inf <- rep(NA_real_, length(reg$type))
+    }
+    if (any(is.na(reg$t_inf))) {
+      # impute using standard values for each dose type
+      impute_t_inf <- c(infusion = 1, sc = 1/60, im = 1/60, oral = 0, bolus = 0)
+      idx <- which(is.na(reg$t_inf))
+      reg$t_inf[idx] <- impute_t_inf[reg$type[idx]]
+      # set unrecognized types to 1
+      reg$t_inf[is.na(reg$t_inf)] <- 1
     }
   }
   if(ss) {

From 8c43c2d4e732bf41397ee253f5837c8ae52d6241 Mon Sep 17 00:00:00 2001
From: jasmineirx <jasmine@insight-rx.com>
Date: Fri, 7 Jun 2024 12:07:30 -0400
Subject: [PATCH 8/8] add contributor; tests for edge cases

---
 DESCRIPTION                       |  1 +
 tests/testthat/test_new_regimen.R | 21 +++++++++++++++++++++
 2 files changed, 22 insertions(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index b903c19d..f45788a7 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -8,6 +8,7 @@ Authors@R: c(
         person("Jasmine", "Hughes", email = "jasmine@insight-rx.com", role = "aut"),
         person("Dominic", "Tong", email = "dominic@insight-rx.com", role = "aut"),
         person("Kara", "Woo", email = "kara@insight-rx.com", role = c("aut")),
+        person("Jordan", "Brooks", email = "jordan.brooks@insight-rx.com", role = "aut"),
         person("InsightRX", role = c("cph", "fnd")))
 Depends: R (>= 3.0.2)
 Imports: Rcpp (>= 0.12.9), BH, data.table, stringr, MASS,
diff --git a/tests/testthat/test_new_regimen.R b/tests/testthat/test_new_regimen.R
index ba7867b8..f5559b87 100644
--- a/tests/testthat/test_new_regimen.R
+++ b/tests/testthat/test_new_regimen.R
@@ -90,7 +90,28 @@ test_that("t_inf imputed correctly", {
     type = c("sc", "infusion", "im", "sc", "infusion", "im","bolus","oral"),
     t_inf = c(2/60, 2.5, 3/60, NA, NA, NA, NA, NA)
   )
+  reg3 <- new_regimen(
+    amt = 100,
+    times = c(0, 12, 24, 36, 48, 60, 72, 84),
+    type = c("sc", "infusion", "im", "sc", "infusion", "im","bolus","oral"),
+    t_inf = numeric(0)
+  )
+  reg4 <- new_regimen(
+    amt = 100,
+    times = c(0, 12, 24, 36, 48, 60, 72, 84),
+    type = c("sc", "infusion", "im", "sc", "infusion", "im","bolus","oral"),
+    t_inf = NULL
+  )
+  reg5 <- new_regimen(
+    amt = 100,
+    times = c(0, 12, 24, 36),
+    type = c("sc", "infusion", "im", "unknown_drug_type"),
+    t_inf = c(2/60, 2.5, 3/60, NA)
+  )
   expect_equal(reg1$t_inf, c(1/60, 1, 1/60, 1/60, 1, 1/60, 0, 0))
   expect_equal(reg2$t_inf, c(2/60, 2.5, 3/60, 1/60, 1, 1/60, 0, 0))
+  expect_equal(reg3$t_inf, c(1/60, 1, 1/60, 1/60, 1, 1/60, 0, 0))
+  expect_equal(reg4$t_inf, c(1/60, 1, 1/60, 1/60, 1, 1/60, 0, 0))
+  expect_equal(reg5$t_inf, c(2/60, 2.5, 3/60, 1))
 })