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add t_inf to sc doses in new_regimen #97

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merged 8 commits into from
Jun 10, 2024
Merged

add t_inf to sc doses in new_regimen #97

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dde74ea
add t_inf to sc doses in new_regimen
JordanBrooks33 Jun 3, 2024
bc60563
add a couple of edge cases to test
jasmineirx Jun 4, 2024
880e416
updated logic to cover mixed regimen type automatic t_inf assignment
JordanBrooks33 Jun 6, 2024
1693710
altered logic when t_inf==0 to update to 1/60 for infusion, sc, and im
JordanBrooks33 Jun 6, 2024
92313ae
Update R/new_regimen.R
JordanBrooks33 Jun 6, 2024
5bbf857
Update R/new_regimen.R
JordanBrooks33 Jun 6, 2024
9aceaf8
cleaned up repetitive formatting
JordanBrooks33 Jun 6, 2024
8c43c2d
add contributor; tests for edge cases
jasmineirx Jun 7, 2024
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26 changes: 23 additions & 3 deletions R/new_regimen.R
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Original file line number Diff line number Diff line change
Expand Up @@ -69,9 +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$type=="infusion"] = 1
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} else if (any(is.na(t_inf))) {
t_inf[is.na(t_inf)] <- 1
reg$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[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$t_inf))] <- 0
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}
}
if(ss) {
Expand Down Expand Up @@ -121,7 +141,7 @@ new_regimen <- function(
if(length(reg$type) != length(reg$dose_times)) {
reg$type <- rep(reg$type[1], length(reg$dose_times))
}
if(any(reg$type == "infusion")) {
if(any(reg$type == "infusion" | reg$type == "sc" | reg$type == "im")) {
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if(any(reg$t_inf == 0)) {
reg$t_inf[reg$t_inf == 0] <- 1/60
reg$rate[reg$t_inf == 0] <- 60
Expand Down
27 changes: 27 additions & 0 deletions tests/testthat/test_new_regimen.R
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Expand Up @@ -67,3 +67,30 @@ 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)
)
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))
})

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