Merge pull request #97 from InsightRX/RXR-2092-add-tinf-to-sc

add t_inf to sc doses in new_regimen

DESCRIPTION

@@ -8,6 +8,7 @@ Authors@R: c(
         person("Jasmine", "Hughes", email = "[email protected]", role = "aut"),
         person("Dominic", "Tong", email = "[email protected]", role = "aut"),
         person("Kara", "Woo", email = "[email protected]", role = c("aut")),
+        person("Jordan", "Brooks", email = "[email protected]", role = "aut"),
         person("InsightRX", role = c("cph", "fnd")))
 Depends: R (>= 3.0.2)
 Imports: Rcpp (>= 0.12.9), BH, data.table, stringr, MASS,

R/new_regimen.R

@@ -68,10 +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 = 1
-    } else if (any(is.na(t_inf))) {
-      t_inf[is.na(t_inf)] <- 1
+    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) {
@@ -121,7 +127,7 @@ 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")) {
+  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

tests/testthat/test_new_regimen.R

@@ -67,3 +67,51 @@ 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$t_inf, rep(0.5,5))
+})
+
+test_that("t_inf imputed correctly", {
+  reg1 <- new_regimen(
+    amt = 100,
+    times = c(0, 12, 24, 36, 48, 60, 72, 84),
+    type = c("sc", "infusion", "im", "sc", "infusion", "im","bolus","oral")
+  )
+  reg2 <- new_regimen(
+    amt = 100,
+    times = c(0, 12, 24, 36, 48, 60, 72, 84),
+    type = c("sc", "infusion", "im", "sc", "infusion", "im","bolus","oral"),
+    t_inf = c(2/60, 2.5, 3/60, NA, NA, NA, NA, NA)
+  )
+  reg3 <- new_regimen(
+    amt = 100,
+    times = c(0, 12, 24, 36, 48, 60, 72, 84),
+    type = c("sc", "infusion", "im", "sc", "infusion", "im","bolus","oral"),
+    t_inf = numeric(0)
+  )
+  reg4 <- new_regimen(
+    amt = 100,
+    times = c(0, 12, 24, 36, 48, 60, 72, 84),
+    type = c("sc", "infusion", "im", "sc", "infusion", "im","bolus","oral"),
+    t_inf = NULL
+  )
+  reg5 <- new_regimen(
+    amt = 100,
+    times = c(0, 12, 24, 36),
+    type = c("sc", "infusion", "im", "unknown_drug_type"),
+    t_inf = c(2/60, 2.5, 3/60, NA)
+  )
+  expect_equal(reg1$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))
+})
+