Merge pull request #65 from InsightRX/RXR-2295_cefepime-neurotoxicity

RXR-2295 Add `calc_cefepime_neurotoxicity()` function

DESCRIPTION

@@ -7,8 +7,10 @@ Authors@R: c(person("Ron", "Keizer", email = "ron@insight-rx.com", role
         = c("aut",  "cre")), 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("InsightRX", role = c("cph", "fnd")))
+        person("Kara", "Woo", email = "kara@insight-rx.com", role = c("aut")), 
+        person("Michael", "McCarthy", email = "michael.mccarthy@insight-rx.com", 
+        role = "aut"),
+        person("InsightRX", role = c("cph", "fnd")))
 Description: Provides equations commonly used in clinical
         pharmacokinetics and clinical pharmacology, such as equations
         for dose individualization, compartmental pharmacokinetics,
@@ -20,6 +22,6 @@ URL: https://github.com/InsightRX/clinPK,
         https://insightrx.github.io/clinPK/
 License: MIT + file LICENSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Suggests: testthat (>= 3.0.0)
 Config/testthat/edition: 3

NAMESPACE

@@ -13,6 +13,7 @@ export(calc_baseline_scr)
 export(calc_bmi)
 export(calc_bsa)
 export(calc_carboplatin_calvert)
+export(calc_cefepime_neurotoxicity)
 export(calc_creat)
 export(calc_creat_neo)
 export(calc_dosing_weight)

R/calc_cefepime_neurotoxicity.R

@@ -0,0 +1,25 @@
+#' Calculate Cefepime-associated Neurotoxicity
+#' 
+#' Calculate probability of cefepime-associated neurotoxicity as a function of
+#' cefepime plasma trough concentrations. This model was based on a data set
+#' of adult patients receiving thrice-daily cefepime and may not correspond to
+#' other dosing intervals or patient populations.
+#' 
+#' @note
+#' The intercept and slope used in this function match Figure 2 in the cited
+#' paper, but differ slightly from the values provided in the text. This 
+#' interpretation was confirmed via correspondence with the authors.
+#' 
+#' @param trough_concentration Cefepime plasma trough concentration (mg/L).
+#' @references \href{https://doi.org/10.1016/j.cmi.2019.06.028}{
+#' Boschung-Pasquier et al., Clinical Microbiology and Infection (2020)}
+#' 
+#' @return Probability of cefepime-associated neurotoxicity.
+#' @examples
+#' calc_cefepime_neurotoxicity(trough_concentration = c(13.7, 17.8))
+#' @export
+calc_cefepime_neurotoxicity <- function(trough_concentration) {
+  b0 <- -4.7777798
+  b1 <- 0.2684747
+  stats::plogis(b0 + b1*trough_concentration)
+}

R/calc_creat.R

@@ -21,7 +21,7 @@
 #' @param digits number of digits to round to
 #' @examples
 #' calc_creat(sex = "male", age = 40)
-#' calc_creat(sex = "male", age = 40, wt = 100, ht = 175, method="brooks)
+#' calc_creat(sex = "male", age = 40, weight = 100, height = 175, adult_method = "brooks")
 #' calc_creat(sex = "male", age = c(10, 17, 60))
 #' @export
 calc_creat <- function (

R/clinPK-package.R

@@ -2,10 +2,9 @@
 #'
 #' Equations and tool for clinical pharmacokinetics
 #'
-#' @docType package
 #' @name clinPK-package
 #' @author Ron Keizer \email{ronkeizer@@gmail.com}
 #' @importFrom stats coef lm
 #' @importFrom utils read.table tail
 #' @keywords internal
-NULL
+"_PACKAGE"

_pkgdown.yml

@@ -100,6 +100,7 @@ reference:
       - egfr_cov_reqs
       - check_covs_available
       - calc_carboplatin_calvert
+      - calc_cefepime_neurotoxicity
       - calc_kel_single_tdm
       - calc_kel_double_tdm
       - calc_t12

tests/testthat/test-calc_cefepime_neurotoxicity.R

@@ -0,0 +1,4 @@
+test_that("cefepime neurotoxicity calculation is correct", {
+  expect_equal(signif(calc_cefepime_neurotoxicity(13.7), 2), .25)
+  expect_equal(signif(calc_cefepime_neurotoxicity(17.8), 2), .50)
+})