Calculate urine saturation with the EQUIL-2 algorithm

Usage

equil2(
  sodium_mEq_L,
  potassium_mEq_L,
  calcium_mg_dL,
  magnesium_mg_dL,
  ammonia_mEq_L,
  chloride_mEq_L,
  phosphate_mg_dL,
  sulfate_mg_dL,
  oxalate_mg_dL,
  citrate_mg_dL,
  pH,
  urate_mg_dL
)

Arguments

sodium_mEq_L, potassium_mEq_L, ammonia_mEq_L, chloride_mEq_L: Concentration of the given species in mEq/L (or a unit value that can be converted to mEq/L)
calcium_mg_dL, magnesium_mg_dL, phosphate_mg_dL, sulfate_mg_dL, oxalate_mg_dL, citrate_mg_dL, urate_mg_dL: Concentration of the given species in mg/dL (or a unit value that can be converted to mg/dL)
pH: The urine pH

Value

A data.frame with three columns:

"species" indicating the chemical species
"super_saturation" is the supersaturation ratio. This is SS as defined in Werness 1985.
"neg_delta_Gibbs" which is the negative of the change in Gibbs free energy of transfer from a supersaturated to a saturated solution (the value is negative for under-saturated solutions, zero for solutions at the solubility product, and positive for supersaturated solutions). This is DG as defined in Werness 1985.

Details

This program is intended for research use, only. The code within is translated from Visual Basic code based on Werness, et al 1985 to R. The Visual Basic code was kindly provided by Dr. John Lieske of the Mayo Clinic.

phosphate_mg_dL is the mass of phosphate (PO4, 94.97 g/mol) per dL, and sulfate_mg_dL is the mass of sulfate (SO4, 96.07 g/mol) per dL. U.S. clinical labs typically report "phosphate" and "sulfate" as the mass of the inorganic element (P or S), so a value of 100 mg/dL on a clinical report corresponds to ~32.3 mmol/L of phosphate (P MW 30.97) or ~31.2 mmol/L of sulfate (S MW 32.06). Supplying inputs in mmol/L (or any molar unit) avoids ambiguity.

References

Werness PG, Brown CM, Smith LH, Finlayson B. Equil2: A Basic Computer Program for the Calculation of Urinary Saturation. Journal of Urology. 1985;134(6):1242-1244. doi:10.1016/S0022-5347(17)47703-2

Examples

# Example values from https://files.labcorp.com/testmenu-d8/sample_reports/306266.pdf
# Phosphate and sulfate inputs are given in mmol/L so the meaning is
# unambiguous: clinical labs often report "phosphate (mg/dL)" as mass of
# inorganic phosphorus (P), but the `mg_phosphate/dL` unit in this package
# is mass of the PO4 ion. See vignette("original-source") for details.
equil2(
  sodium_mEq_L=units::set_units(45, "mmol_sodium/L"),
  potassium_mEq_L=units::set_units(55, "mmol_potassium/L"),
  calcium_mg_dL=units::set_units(15, "mg_calcium/dL"),
  magnesium_mg_dL=units::set_units(15, "mg_magnesium/dL"),
  ammonia_mEq_L=units::set_units(10, "ug_ammonia/dL"),
  chloride_mEq_L=units::set_units(75, "mmol_chloride/L"),
  phosphate_mg_dL=units::set_units(32.285, "mmol_phosphate/L"),
  sulfate_mg_dL=units::set_units(10, "mmol_sulfate/L"),
  oxalate_mg_dL=units::set_units(10, "mg_oxalate/L"),
  citrate_mg_dL=units::set_units(400, "mg_citrate/L"),
  pH=5.5,
  urate_mg_dL=units::set_units(50, "mg_urate/dL")
)
#>           species super_saturation neg_delta_Gibbs
#> 1 Calcium Oxalate     3.096613e+00       1.4620547
#> 2        Brushite     1.259350e+00       0.2982760
#> 3  Hydroxyapatite     3.904189e+04       3.0389279
#> 4       Uric Acid     4.563641e+00       3.9273785
#> 5    Sodium Urate     1.626900e+00       0.6295155
#> 6  Ammonium Urate     1.618179e-04     -11.2910116