Improved support for NA. Added testing for renal function.

R/blood_pressure.R

@@ -9,12 +9,16 @@
 #'
 #' @param sbp Systolic blood pressure (mmHg).
 #' @param dbp Diastolic blood pressure (mmHg).
-#' @return MAP (mmHg).
+#' @return MAP (mmHg), or `NA` if any parameters are `NA`.
 #' @export
 #' @seealso \code{\link[units]{set_units}}, \code{\link[units]{drop_units}}
 estimate_map <- function(sbp, dbp) {
-  assertthat::assert_that(assertthat::is.number(sbp) | is.na(sbp))
-  assertthat::assert_that(assertthat::is.number(dbp) | is.na(dbp))
+  if (anyNA(c(sbp, dbp))) {
+    return(NA)
+  }
+  assertthat::assert_that(assertthat::is.number(sbp))
+  assertthat::assert_that(assertthat::is.number(dbp))
+
   (dbp + (1/3 * (sbp - dbp))) %>%
     units::set_units("mmHg", mode = "standard")
 }
@@ -30,12 +34,15 @@ estimate_map <- function(sbp, dbp) {
 #'
 #' @param sbp Systolic blood pressure (mmHg).
 #' @param dbp Diastolic blood pressure (mmHg).
-#' @return Pulse pressure (mmHg).
+#' @return Pulse pressure (mmHg), or `NA` if any parameters are `NA`.
 #' @export
 #' @seealso \code{\link[units]{set_units}}, \code{\link[units]{drop_units}}
 calculate_pulse_pressure <- function(sbp, dbp) {
-  assertthat::assert_that(assertthat::is.number(sbp) | is.na(sbp))
-  assertthat::assert_that(assertthat::is.number(dbp) | is.na(dbp))
+  if (anyNA(c(sbp, dbp))) {
+    return(NA)
+  }
+  assertthat::assert_that(assertthat::is.number(sbp))
+  assertthat::assert_that(assertthat::is.number(dbp))
   (sbp - dbp) %>%
     units::set_units("mmHg", mode = "standard")
 }

R/bmi.R

@@ -9,14 +9,18 @@
 #'
 #' @param weight Weight (kg).
 #' @param height Height (cm).
-#' @return BMI (\eqn{\text{kg} m^{-2}}).
+#' @return BMI (\eqn{\text{kg} m^{-2}}), or `NA` if any parameters are `NA`.
 #' @export
 #' @seealso [units::set_units()], [units::drop_units()]
 calculate_bmi <- function(weight, height) {
+  if (anyNA(c(weight, height))) {
+    return(NA)
+  }
   assertthat::assert_that(assertthat::is.number(weight) |
                             is.na(weight))
   assertthat::assert_that(assertthat::is.number(height) |
                             is.na(height))
+
   (weight / ((height / 100) ^ 2)) %>%
     units::set_units("kg1 m-2", mode = "standard")
 }
@@ -35,11 +39,14 @@ calculate_bmi <- function(weight, height) {
 #' @param height Height (cm).
 #' @param is_female `TRUE` if patient is female, `FALSE` if patient is
 #'   male.
-#' @return IBW (kg).
+#' @return IBW (kg), or `NA` if any parameters are `NA`.
 #' @export
 #' @seealso [units::set_units()], [units::drop_units()]
 estimate_ibw <- function(height, is_female) {
-  assertthat::assert_that(assertthat::is.number(height) | is.na(height))
+  if (anyNA(c(height, is_female))) {
+    return(NA)
+  }
+  assertthat::assert_that(assertthat::is.number(height))
   assertthat::assert_that(assertthat::is.flag(is_female))
 
   if(is_female) {

R/bsa.R

@@ -10,7 +10,7 @@
 #' @param height Height (cm).
 #' @param method Formula to estimate BSA. Options are: "Monsteller" (default),
 #'   "Du Bois".
-#' @return BSA (\eqn{m^2}).
+#' @return BSA (\eqn{m^2}), or `NA` if any parameters are `NA`.
 #' @export
 #' @seealso [units::set_units()], [units::drop_units()]
 estimate_bsa <- function(weight, height, method = "Monsteller") {
@@ -25,21 +25,29 @@ 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) {
+  if (anyNA(c(weight, height))) {
+    return(NA)
+  }
   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) {
+  if (anyNA(c(weight, height))) {
+    return(NA)
+  }
   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

@@ -16,15 +16,16 @@
 #' @param calcium Measured total calcium level (mmol/l).
 #' @param albumin Measured albumin level (g/l).
 #' @param normal_albumin Normal value of albumin (g/l) (40 by default).
-#' @return Albumin-adjusted calcium level (mmol/l).
+#' @return Albumin-adjusted calcium level (mmol/l), or `NA` if any parameters are `NA`.
 #' @export
 #' @seealso [units::set_units()], [units::drop_units()]
 adjust_calcium_for_albumin <-
   function(calcium, albumin, normal_albumin = 40) {
-    assertthat::assert_that(assertthat::is.number(calcium) |
-                              is.na(calcium))
-    assertthat::assert_that(assertthat::is.number(albumin) |
-                              is.na(albumin))
+    if (anyNA(c(calcium, albumin, normal_albumin))) {
+      return(NA)
+    }
+    assertthat::assert_that(assertthat::is.number(calcium))
+    assertthat::assert_that(assertthat::is.number(albumin))
 
     (calcium + 0.025 * (normal_albumin - albumin)) %>%
       units::set_units("mmol1 l-1", mode = "standard")
@@ -53,22 +54,23 @@ adjust_calcium_for_albumin <-
 #' @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).
+#' @return Glucose-adjusted sodium level (mmol/l), or `NA` if any parameters are `NA`.
 #' @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))
+    if (anyNA(c(sodium, glucose, method))) {
+      return(NA)
+    }
+    assertthat::assert_that(assertthat::is.number(sodium))
+    assertthat::assert_that(assertthat::is.number(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().")
+      stop(paste0("Error: `method` must be `Hillier` or `Katz`.\n You've supplied method `", method, "`."))
     )
 
     (sodium + xkappa * ((glucose-5.6)/5.6)) %>%

R/metabolic_syndrome.R

@@ -44,7 +44,7 @@
 #' @param has_glucose_drug `TRUE` if patient is on drug treatment for
 #'   elevated glucose, otherwise `FALSE` (default).
 #' @return `TRUE` if patient has the metabolic syndrome, `FALSE` is
-#'   not, `NA` if indetermined.
+#'   not, `NA` if indetermined or `is_female` was `NA`.
 #' @export
 has_metabolic_syndrome_atpiii <- function(is_female,
                                   waist_circumference = NA,
@@ -57,6 +57,10 @@ has_metabolic_syndrome_atpiii <- function(is_female,
                                   has_antihypertensive_drug = FALSE,
                                   has_lipid_drug = FALSE,
                                   has_glucose_drug = FALSE) {
+  if(is.na(is_female)) {
+    warning("Warning: `is_female` was `NA`, therefore presence of the metabolic syndrome could not be determined. `NA` was returned.")
+    return(NA)
+  }
   assertthat::assert_that(assertthat::is.flag(is_female))
   assertthat::assert_that(assertthat::is.number(waist_circumference) | is.na(waist_circumference))
   assertthat::assert_that(assertthat::is.number(sbp) | is.na(sbp))

R/pneumonia.R

@@ -13,15 +13,19 @@
 #' @param sbp Systolic blood pressure (mmHg).
 #' @param dbp Diastolic blood pressure (mmHg).
 #' @param age Age (years).
-#' @return CURB-65 score (points).
+#' @return CURB-65 score (points), or `NA` if any parameters are `NA`.
 #' @export
 score_curb65 <- function(confusion,
                          urea,
                          respiratory_rate,
                          sbp,
                          dbp,
                          age) {
+  if(anyNA(c(confusion, urea, respiratory_rate, sbp, dbp, age))){
+    return(NA)
+  }
   assertthat::assert_that(assertthat::is.flag(confusion))
+  assertthat::assert_that(assertthat::is.number(urea))
   assertthat::assert_that(assertthat::is.number(respiratory_rate))
   assertthat::assert_that(assertthat::is.number(sbp))
   assertthat::assert_that(assertthat::is.number(dbp))

R/qtc.R

@@ -7,7 +7,7 @@
 #' @param heart_rate Heart rate (/min).
 #' @param method Formula for QTc. Options are: "Fridericia" (default),
 #'   "Bazzett".
-#' @return QTc (ms).
+#' @return QTc (ms), or `NA` if any parameters are `NA`.
 #' @export
 #' @seealso [units::set_units()], [units::drop_units()]
 calculate_qtc <- function(qt, heart_rate, method = "Fridericia") {
@@ -20,8 +20,12 @@ calculate_qtc <- function(qt, heart_rate, method = "Fridericia") {
 #' @describeIn calculate_qtc QTc according to Bazett.
 #' @noRd
 calculate_qtc_bazett <- function(qt, heart_rate) {
-  assertthat::assert_that(assertthat::is.number(qt) | is.na(qt))
-  assertthat::assert_that(assertthat::is.number(heart_rate) | is.na(heart_rate))
+  if (anyNA(c(qt, heart_rate))) {
+    return(NA)
+  }
+  assertthat::assert_that(assertthat::is.number(qt))
+  assertthat::assert_that(assertthat::is.number(heart_rate))
+
   qt <- qt / 1000
   rr <- 60 / heart_rate
   (qt / (rr ^ (1 / 2)) * 1000) %>%
@@ -31,8 +35,12 @@ calculate_qtc_bazett <- function(qt, heart_rate) {
 #' @describeIn calculate_qtc QTc according to Fridericia.
 #' @noRd
 calculate_qtc_fridericia <- function(qt, heart_rate) {
-  assertthat::assert_that(assertthat::is.number(qt) | is.na(qt))
-  assertthat::assert_that(assertthat::is.number(heart_rate) | is.na(heart_rate))
+  if (anyNA(c(qt, heart_rate))) {
+    return(NA)
+  }
+  assertthat::assert_that(assertthat::is.number(qt))
+  assertthat::assert_that(assertthat::is.number(heart_rate))
+
   qt <- qt / 1000
   rr <- 60 / heart_rate
   (qt / (rr ^ (1 / 3)) * 1000) %>%