Add adjust_sodium_for_glucose. Update some tests.

NAMESPACE

@@ -2,6 +2,7 @@
 
 export("%>%")
 export(adjust_calcium_for_albumin)
+export(adjust_sodium_for_glucose)
 export(calculate_bmi)
 export(calculate_pulse_pressure)
 export(calculate_qtc)

R/bmi.R

@@ -39,8 +39,8 @@ calculate_bmi <- function(weight, height) {
 #' @export
 #' @seealso [units::set_units()], [units::drop_units()]
 estimate_ibw <- function(height, is_female) {
+  assertthat::assert_that(assertthat::is.number(height) | is.na(height))
   assertthat::assert_that(assertthat::is.flag(is_female))
-  assertthat::assert_that(assertthat::is.number(height))
 
   if(is_female) {
     (45.5 + 0.9 * (height - 152)) %>%

R/bsa.R

@@ -25,17 +25,21 @@ estimate_bsa <- function(weight, height, method = "Monsteller") {
 #' @describeIn estimate_bsa Estimate the body surface area (BSA) according to Monsteller.
 #' @noRd
 estimate_bsa_monsteller <- function(weight, height) {
-  assertthat::assert_that(assertthat::is.number(weight))
-  assertthat::assert_that(assertthat::is.number(height))
+  assertthat::assert_that(assertthat::is.number(weight) |
+                            is.na(weight))
+  assertthat::assert_that(assertthat::is.number(height) |
+                            is.na(height))
   ((weight * height / 3600) ^ (0.5)) %>%
     units::set_units("m-2", mode = "standard")
 }
 
 #' @describeIn estimate_bsa Estimate the body surface area (BSA) according to Du Bois
 #' @noRd
 estimate_bsa_du_bois <- function(weight, height) {
-  assertthat::assert_that(assertthat::is.number(weight))
-  assertthat::assert_that(assertthat::is.number(height))
+  assertthat::assert_that(assertthat::is.number(weight) |
+                            is.na(weight))
+  assertthat::assert_that(assertthat::is.number(height) |
+                            is.na(height))
   (0.007184 * (weight ^ 0.425) * (height ^ 0.725)) %>%
     units::set_units("m-2", mode = "standard")
 }

R/electrolytes.R

@@ -29,3 +29,48 @@ adjust_calcium_for_albumin <-
     (calcium + 0.025 * (normal_albumin - albumin)) %>%
       units::set_units("mmol1 l-1", mode = "standard")
   }
+
+
+#' Adjust sodium for hyperglycaemia
+#'
+#' Hyperglycaemia can lead to hypertonic hyponatriemia. Using observational
+#' data, the following formula predicts sodium levels after correction of
+#' glucose: \eqn{\text{Na}_{predicted} = \text{Na}_\text{measured} + \kappa
+#' \times \frac{\text{glucose} - 5.6}{5.6}}, where \eqn{\kappa} is 1.6 when
+#' derived from the publication by Katz and 2.4 when derived from more recent
+#' work by Hillier (default).
+#'
+#' @references [Katz, M. A. Hyperglycemia-Induced Hyponatremia — Calculation of
+#'   Expected Serum Sodium Depression. N Engl J Med 289, 843–844
+#'   (1973).](https://doi.org/10.1056/NEJM197310182891607) and [Hillier, T. A.,
+#'   Abbott, R. D. & Barrett, E. J. Hyponatremia: evaluating the correction
+#'   factor for hyperglycemia. The American Journal of Medicine 106, 399–403
+#'   (1999).](https://doi.org/10.1016/s0002-9343(99)00055-8).
+#'
+#' @section Caveats: It's just a prediction, and the choice between both
+#'   formulae may result in quite different predictions.
+#'
+#' @param sodium Measured sodium level (mmol/l).
+#' @param glucose Measured glucose level (mmol/l).
+#' @param method Formula. Options are: "Hillier" (default), "Katz".
+#' @return Glucose-adjusted sodium level (mmol/l).
+#' @export
+#' @seealso [units::set_units()], [units::drop_units()]
+adjust_sodium_for_glucose <-
+  function(sodium, glucose, method = "Hillier") {
+    assertthat::assert_that(assertthat::is.number(sodium) |
+                              is.na(sodium))
+    assertthat::assert_that(assertthat::is.number(glucose) |
+                              is.na(glucose))
+    assertthat::assert_that(assertthat::is.string(method))
+
+    xkappa <- switch(
+      method,
+      "Hillier" = 2.4,
+      "Katz" = 1.6,
+      stop("Illegal value for argument method in adjust_sodium_for_glucose().")
+    )
+
+    (sodium + xkappa * ((glucose-5.6)/5.6)) %>%
+      units::set_units("mmol1 l-1", mode = "standard")
+}

R/renal_function.R

@@ -16,10 +16,13 @@
 #' @export
 #' @seealso [units::set_units()], [units::drop_units()]
 estimate_gfr_cockcroft <- function(creatinine, age, is_female, weight) {
-  assertthat::assert_that(assertthat::is.number(creatinine))
-  assertthat::assert_that(assertthat::is.number(age))
+  assertthat::assert_that(assertthat::is.number(creatinine) |
+                            is.na(creatinine))
+  assertthat::assert_that(assertthat::is.number(age) |
+                            is.na(age))
   assertthat::assert_that(assertthat::is.flag(is_female))
-  assertthat::assert_that(assertthat::is.number(weight))
+  assertthat::assert_that(assertthat::is.number(weight) |
+                            is.na(weight))
 
   egfr <- ((140 - age) * weight) / (0.81 * creatinine)
 
@@ -49,8 +52,8 @@ estimate_gfr_cockcroft <- function(creatinine, age, is_female, weight) {
 #' @export
 #' @seealso [units::set_units()], [units::drop_units()]
 estimate_gfr_mdrd <- function(creatinine, age, is_female, is_african_american) {
-  assertthat::assert_that(assertthat::is.number(creatinine))
-  assertthat::assert_that(assertthat::is.number(age))
+  assertthat::assert_that(assertthat::is.number(creatinine) | is.na(creatinine))
+  assertthat::assert_that(assertthat::is.number(age) | is.na(age))
   assertthat::assert_that(assertthat::is.flag(is_female))
   assertthat::assert_that(assertthat::is.flag(is_african_american))
 
@@ -83,8 +86,8 @@ estimate_gfr_mdrd <- function(creatinine, age, is_female, is_african_american) {
 #' @export
 #' @seealso [units::set_units()], [units::drop_units()]
 estimate_gfr_schwartz <- function(creatinine, height) {
-  assertthat::assert_that(assertthat::is.number(creatinine))
-  assertthat::assert_that(assertthat::is.number(height))
+  assertthat::assert_that(assertthat::is.number(creatinine) | is.na(creatinine))
+  assertthat::assert_that(assertthat::is.number(height) | is.na(height))
   (36.2 * height) / creatinine %>%
     units::set_units("ml1 min-1", mode = "standard")
 }
@@ -121,8 +124,8 @@ estimate_gfr_schwartz <- function(creatinine, height) {
 #' @export
 #' @seealso [units::set_units()], [units::drop_units()]
 estimate_gfr_ckdepi <- function(creatinine, age, is_female, is_african_american) {
-  assertthat::assert_that(assertthat::is.number(creatinine))
-  assertthat::assert_that(assertthat::is.number(age))
+  assertthat::assert_that(assertthat::is.number(creatinine) | is.na(creatinine))
+  assertthat::assert_that(assertthat::is.number(age) | is.na(age))
   assertthat::assert_that(assertthat::is.flag(is_female))
   assertthat::assert_that(assertthat::is.flag(is_african_american))
 

README.md

@@ -14,12 +14,14 @@ Help and pull requests are more than welcome.
 - *Anthropometry*
   - Body mass index (BMI, Quetelet index).
   - Body surface area (BSA).
+  - Ideal body weight (IBW).
   - Mean arterial blood pressure (MAP).
   - Pulse pressure.
 - *Cardiology*
   - Corrected QT interval (QTc).
 - *Electrolytes*
-  - Albumin-corrected calcium.
+  - Albumin-adjusted calcium.
+  - Glucose-adjusted sodium.
 - *Infectiology*
   - CURB-65 community-acquired pneumonia severity score.
   - qSOFA score for sepsis.
@@ -66,7 +68,6 @@ remotes::install_github("lc31/clinicalr")
 
 # To do
 * effective osmolality?
-* glucose corrected sodium?
 * anion gap?
 * total body water?
 * fractional excretion of sodium?
@@ -75,3 +76,4 @@ remotes::install_github("lc31/clinicalr")
 * A-a gradient?
 * creatinine clearance (using urine)?
 * Framingham?
+* assertion tests

docs/pkgdown.yml

@@ -2,7 +2,7 @@ pandoc: 2.7.3
 pkgdown: 1.6.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2020-11-04T11:39Z
+last_built: 2020-11-04T21:04Z
 urls:
   reference: https://ls31.github.io/clinicalr//reference
   article: https://ls31.github.io/clinicalr//articles