update O2 formula to convert ml/l to umol/kg

The factor is about 1000/(1000+sigma0) or say 1000/1030 i.e. it yields
about a 0.3 percent reduction in value compared to the formula in
the pilotingapp code.

R/oxygen.R

@@ -5,8 +5,10 @@
 #' \url{https://github.com/DFOglider/pilotingApp}, with minor
 #' modifiations: (1) it has a new name to avoid conflicts, (2) the
 #' calibration coefficients are collected into a single parameter,
-#' `cal`, (3) `oxygenFrequency` is renamed `frequency`, and (4) `unit`
-#' is added, to permit specifying the unit of the return value.
+#' `cal`, (3) `oxygenFrequency` is renamed `frequency`, (3) `unit`
+#' is added, to permit specifying the unit of the return value,
+#' and (5) the conversion to umol/kg takes into account the density,
+#' as indicated in Reference 1.
 #'
 #' @param temperature numeric value holding temperature in degrees C.
 #'
@@ -23,8 +25,9 @@
 #'
 #' @param unit character value indicating the desired unit. The
 #' default is `ml/l` but `umol/kg` is also accepted, the latter being
-#' computed by multiplying the former by 44.6591 (see Reference 1,
-#' which uses the mole fraction stated in Reference 2.)
+#' computed by multiplying the former by `44.6591*1000/(1000+sigma0)`,
+#' where `sigma0` is seawater potential density anomaly in kg/m^3
+#' (see Reference 1, which uses the mole fraction stated in Reference 2).
 #'
 #' @references
 #'
@@ -55,7 +58,11 @@ swOxygenFrequencyToSaturation <- function(temperature,
     if (identical(unit, "ml/l")) {
         mll
     } else if (identical(unit, "umol/kg")) {
-        44.6591 * mll
+        sigma0 <- oce::swSigma0(
+            salinity = salinity,
+            temperature = temperature, pressure = pressure, eos = "unesco"
+        )
+        44.6591 * mll * 1000 / (1000 + sigma0)
     } else {
         stop("unit must be 'ml/l' or 'umol/kg', but it is '", unit, "'")
     }

docs/pkgdown.yml

@@ -4,5 +4,5 @@ pkgdown_sha: ~
 articles:
   oceglider: oceglider.html
   slocum_glider: slocum_glider.html
-last_built: 2024-06-24T19:16Z
+last_built: 2024-06-24T19:39Z
 

tests/testthat/test_oxygen.R

@@ -26,9 +26,9 @@ test_that("oxygen computed against previously-computed values", {
     expect_silent(g <- read.glider.seaexplorer.realtime(directory = directory, yo = 3, progressBar = FALSE))
     g@metadata$oxycalib <- oxycalib
     # consistency check (will fail if dataset is changed or code changes)
-    options(digits = 15)
-    g[["oxygen"]][1:3]
-    expect_equal(g[["oxygen"]][1:3], c(363.265784249780, 363.301998679272, 363.257645877092))
+    # options(digits = 15)
+    # g[["oxygen"]][1:3]
+    expect_equal(g[["oxygen"]][1:3], c(354.508135471242, 354.543025470803, 354.499770611843))
     # test values from the calibration sheet
 })