From 7c451d815621e46e15752a2e70c21e2146959c2a Mon Sep 17 00:00:00 2001 From: LS31 Date: Wed, 4 Nov 2020 22:06:07 +0100 Subject: [PATCH] Add adjust_sodium_for_glucose. Update some tests. --- NAMESPACE | 1 + R/bmi.R | 2 +- R/bsa.R | 12 +- R/electrolytes.R | 45 ++++ R/renal_function.R | 21 +- README.md | 6 +- docs/index.html | 16 +- docs/pkgdown.yml | 2 +- docs/reference/adjust_sodium_for_glucose.html | 193 ++++++++++++++++++ docs/reference/index.html | 6 + docs/sitemap.xml | 3 + man/adjust_sodium_for_glucose.Rd | 37 ++++ tests/testthat/test-blood_pressure.R | 8 + tests/testthat/test-bmi.R | 13 +- tests/testthat/test-electrolytes.R | 13 ++ 15 files changed, 353 insertions(+), 25 deletions(-) create mode 100644 docs/reference/adjust_sodium_for_glucose.html create mode 100644 man/adjust_sodium_for_glucose.Rd diff --git a/NAMESPACE b/NAMESPACE index ecd66ec..42d8279 100644 --- a/NAMESPACE +++ b/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) diff --git a/R/bmi.R b/R/bmi.R index 94fb559..43d4c07 100644 --- a/R/bmi.R +++ b/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)) %>% diff --git a/R/bsa.R b/R/bsa.R index 5fb8776..27726ce 100644 --- a/R/bsa.R +++ b/R/bsa.R @@ -25,8 +25,10 @@ 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") } @@ -34,8 +36,10 @@ estimate_bsa_monsteller <- function(weight, height) { #' @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") } diff --git a/R/electrolytes.R b/R/electrolytes.R index fc8a363..04eaeab 100644 --- a/R/electrolytes.R +++ b/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") +} diff --git a/R/renal_function.R b/R/renal_function.R index e57fb57..8e865de 100644 --- a/R/renal_function.R +++ b/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)) diff --git a/README.md b/README.md index 39442b9..7a1e93b 100644 --- a/README.md +++ b/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 diff --git a/docs/index.html b/docs/index.html index 8cd8163..70f4853 100644 --- a/docs/index.html +++ b/docs/index.html @@ -87,6 +87,7 @@

@@ -100,7 +101,8 @@

  • Electrolytes
      -
    • Albumin-corrected calcium.
      • +
    • Albumin-adjusted calcium.
      • +
    • Glucose-adjusted sodium.
  • @@ -173,22 +175,21 @@

    How to install

    Clinicalr is not (yet) available on CRAN. Install devtools. Then use devtools to install clinicalr directly from GitHub using the remotes package.

    -
    -install.packages("remotes")
-remotes::install_github("ls31/clinicalr")
    +
    +install.packages("remotes")
+remotes::install_github("ls31/clinicalr")

    How to update

    -
    -remotes::install_github("lc31/clinicalr")
    +
    +remotes::install_github("lc31/clinicalr")

    To do

    • effective osmolality?
      • -
    • glucose corrected sodium?
    • anion gap?
    • total body water?
    • fractional excretion of sodium?
      • @@ -197,6 +198,7 @@

    • A-a gradient?
    • creatinine clearance (using urine)?
    • Framingham?
      • +
    • assertion tests

    diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 46eb26b..473d82e 100644 --- a/docs/pkgdown.yml +++ b/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 diff --git a/docs/reference/adjust_sodium_for_glucose.html b/docs/reference/adjust_sodium_for_glucose.html new file mode 100644 index 0000000..8448912 --- /dev/null +++ b/docs/reference/adjust_sodium_for_glucose.html @@ -0,0 +1,193 @@ + + + + + + + + +Adjust sodium for hyperglycaemia — adjust_sodium_for_glucose • clinicalr + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Adjust sodium for hyperglycaemia

    + Source: R/electrolytes.R + +
    + +
    +

    Hyperglycaemia can lead to hypertonic hyponatriemia. Using observational +data, the following formula predicts sodium levels after correction of +glucose: \(\text{Na}_{predicted} = \text{Na}_\text{measured} + \kappa +\times \frac{\text{glucose} - 5.6}{5.6}\), where \(\kappa\) is 1.6 when +derived from the publication by Katz and 2.4 when derived from more recent +work by Hillier (default).

    +
    + + 
    adjust_sodium_for_glucose(sodium, glucose, method = "Hillier")
    + +

    Arguments

    + + + + + + + + + + + + + + +
    sodium

    Measured sodium level (mmol/l).

    glucose

    Measured glucose level (mmol/l).

    method

    Formula. Options are: "Hillier" (default), "Katz".

    + +

    Value

    + +

    Glucose-adjusted sodium level (mmol/l).

    +

    Caveats

    + +

    It's just a prediction, and the choice between both +formulae may result in quite different predictions.

    +

    References

    + +

    Katz, M. A. Hyperglycemia-Induced Hyponatremia — Calculation of Expected Serum Sodium Depression. N Engl J Med 289, 843–844 (1973). 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)..

    +

    See also

    + +

    units::set_units(), units::drop_units()

    + +
    + +
    + + + +
    + + + + + + + + diff --git a/docs/reference/index.html b/docs/reference/index.html index 874db1f..e024e83 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -141,6 +141,12 @@

    adjust_sodium_for_glucose()

    + +

    Adjust sodium for hyperglycaemia

    + +

    calculate_bmi()

    diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 7b4479b..0ba126b 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -6,6 +6,9 @@ https://ls31.github.io/clinicalr//reference/adjust_calcium_for_albumin.html + + https://ls31.github.io/clinicalr//reference/adjust_sodium_for_glucose.html + https://ls31.github.io/clinicalr//reference/calculate_bmi.html diff --git a/man/adjust_sodium_for_glucose.Rd b/man/adjust_sodium_for_glucose.Rd new file mode 100644 index 0000000..bd37a87 --- /dev/null +++ b/man/adjust_sodium_for_glucose.Rd @@ -0,0 +1,37 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/electrolytes.R +\name{adjust_sodium_for_glucose} +\alias{adjust_sodium_for_glucose} +\title{Adjust sodium for hyperglycaemia} +\usage{ +adjust_sodium_for_glucose(sodium, glucose, method = "Hillier") +} +\arguments{ +\item{sodium}{Measured sodium level (mmol/l).} + +\item{glucose}{Measured glucose level (mmol/l).} + +\item{method}{Formula. Options are: "Hillier" (default), "Katz".} +} +\value{ +Glucose-adjusted sodium level (mmol/l). +} +\description{ +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). +} +\section{Caveats}{ + It's just a prediction, and the choice between both +formulae may result in quite different predictions. +} + +\references{ +\href{https://doi.org/10.1056/NEJM197310182891607}{Katz, M. A. Hyperglycemia-Induced Hyponatremia — Calculation of Expected Serum Sodium Depression. N Engl J Med 289, 843–844 (1973).} and \href{https://doi.org/10.1016/s0002-9343(99)00055-8}{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).}. +} +\seealso{ +\code{\link[units:set_units]{units::set_units()}}, \code{\link[units:drop_units]{units::drop_units()}} +} diff --git a/tests/testthat/test-blood_pressure.R b/tests/testthat/test-blood_pressure.R index 6bd25ac..6ac6732 100644 --- a/tests/testthat/test-blood_pressure.R +++ b/tests/testthat/test-blood_pressure.R @@ -1,5 +1,13 @@ +context("Blood pressure") + test_that("MAP for missing DBP or SBP is missing", { expect_equal(estimate_map(NA, 80), NA_integer_) expect_equal(estimate_map(120, NA), NA_integer_) expect_equal(estimate_map(NA, NA), NA_integer_) }) + +test_that("Pulse pressure for missing DBP or SBP is missing", { + expect_equal(calculate_pulse_pressure(NA, 80), NA_integer_) + expect_equal(calculate_pulse_pressure(120, NA), NA_integer_) + expect_equal(calculate_pulse_pressure(NA, NA), NA_integer_) +}) diff --git a/tests/testthat/test-bmi.R b/tests/testthat/test-bmi.R index d979804..2ca883a 100644 --- a/tests/testthat/test-bmi.R +++ b/tests/testthat/test-bmi.R @@ -1,7 +1,18 @@ -context("BMI") +context("BMI and IBW") test_that("BMI for missing height or weight is missing", { expect_equal(calculate_bmi(NA, 180), NA_integer_) expect_equal(calculate_bmi(80, NA), NA_integer_) expect_equal(calculate_bmi(NA, NA), NA_integer_) }) + +test_that("IBW for missing height is missing", { + expect_equal(estimate_ibw(NA, TRUE), NA_integer_) +}) + + +test_that("IBW for missing sex raises error", { + expect_error(estimate_ibw(180, "bla")) + expect_error(estimate_ibw(180, NA)) + expect_error(estimate_ibw(NA, NA)) +}) diff --git a/tests/testthat/test-electrolytes.R b/tests/testthat/test-electrolytes.R index 95c0fa1..4ce3831 100644 --- a/tests/testthat/test-electrolytes.R +++ b/tests/testthat/test-electrolytes.R @@ -9,3 +9,16 @@ test_that("Albumin-corrected calcium crash on illegal arguments", { expect_error(adjust_calcium_for_albumin("A", 23)) expect_error(adjust_calcium_for_albumin(3, "A")) }) + +test_that("Glucose-corrected sodium for missing values is missing", { + expect_equal(adjust_sodium_for_glucose(120, NA), NA_integer_) + expect_equal(adjust_sodium_for_glucose(NA, 25), NA_integer_) +}) + +test_that("Glucose-corrected sodium crash on illegal arguments", { + expect_error(adjust_sodium_for_glucose("A", 25)) + expect_error(adjust_sodium_for_glucose(120, "A")) + expect_error(adjust_sodium_for_glucose(120, 25, "A")) + expect_error(adjust_sodium_for_glucose(120, 25, NA)) +}) +