remove R's pipe operator to allow for further back compatibility

CU-DBMI-Peds · Mar 1, 2024 · 3a1f1b5 · 3a1f1b5
1 parent a61615c
commit 3a1f1b5
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Showing 3 changed files with 18 additions and 10 deletions.
diff --git a/tests/test-phoenix8.R b/tests/test-phoenix8.R
@@ -173,14 +173,16 @@ stopifnot(identical(hepatic$expected_score, hepatic$phoenix_hep))
 
 N <- 1e5
 DF <-
- list(respiratory, cardiovascular, coagulation, neurologic, endocrine, immunolgic, hepatic) |>
- lapply(function(DF) {
- idx <- sample(1:nrow(DF), size = N, replace = TRUE)
- rtn <- DF[idx, ]
+ list(respiratory, cardiovascular, coagulation, neurologic, endocrine, immunolgic, hepatic)
+DF <-
+ lapply(DF,
+ function(x) {
+ idx <- sample(1:nrow(x), size = N, replace = TRUE)
+ rtn <- x[idx, ]
  rtn <- rtn[, -which(names(rtn) == "expected_score")]
  rtn
-  }) |>
-  do.call(cbind, args = _)
+ })
+DF <- do.call(cbind, args = DF)
 
 DF$creatinine <- NA
 DF$phoenix_renal <- NA

diff --git a/vignette-spinners/phoenix.R b/vignette-spinners/phoenix.R
@@ -230,8 +230,11 @@ resp_data <- unique(resp_data)
 resp_data$phoenix_respiratory_score <- factor(phoenix_respiratory(pfr, sfr, imv, o2, data = resp_data))
 
 resp_data$oxygen_support <-
- interaction(resp_data$imv, resp_data$o2) |>
- factor(levels = c("0.0", "0.1", "1.1"), c("No Oxygen Support", "Non-invasive Oxygen Support", "Invasive Oxygen Support"))
+ factor(
+ interaction(resp_data$imv, resp_data$o2),
+ levels = c("0.0", "0.1", "1.1"),
+ labels = c("No Oxygen Support", "Non-invasive Oxygen Support", "Invasive Oxygen Support")
+ )
 
 ggplot2::ggplot(data = resp_data) +
  ggplot2::theme_classic() +

diff --git a/vignettes/phoenix.Rmd b/vignettes/phoenix.Rmd
@@ -234,8 +234,11 @@ resp_data <- unique(resp_data)
 resp_data$phoenix_respiratory_score <- factor(phoenix_respiratory(pfr, sfr, imv, o2, data = resp_data))
 
 resp_data$oxygen_support <-
- interaction(resp_data$imv, resp_data$o2) |>
- factor(levels = c("0.0", "0.1", "1.1"), c("No Oxygen Support", "Non-invasive Oxygen Support", "Invasive Oxygen Support"))
+ factor(
+ interaction(resp_data$imv, resp_data$o2),
+ levels = c("0.0", "0.1", "1.1"),
+ labels = c("No Oxygen Support", "Non-invasive Oxygen Support", "Invasive Oxygen Support")
+ )
 
 ggplot2::ggplot(data = resp_data) +
  ggplot2::theme_classic() +