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Calculate urine saturation with the EQUIL-2 V1 algorithm

equil2_v1.Rd

This is a port of the original Mayo Clinic class-based VBA module clsEquil2 ("V1") that predates the form-based BASIC source ported in equil2(). V1 accepts mmol/L (or any molar-convertible unit) inputs, models CO2/bicarbonate chemistry, TRIS buffer, and several ion-pair complexes that V5 omits, and (when chloride is omitted) auto-fills chloride from electroneutrality.

Usage

equil2_v1(
  pH,
  calcium_mmol_L = 0,
  phosphate_mmol_L = 0,
  oxalate_mmol_L = 0,
  sodium_mmol_L = 0,
  potassium_mmol_L = 0,
  magnesium_mmol_L = 0,
  ammonia_mmol_L = 0,
  citrate_mmol_L = 0,
  sulfate_mmol_L = 0,
  urate_mmol_L = 0,
  chloride_mmol_L = NA,
  CO2_mmol_L = 0,
  pyrophosphate_mmol_L = 0,
  TRIS_mmol_L = 0,
  tolerance = 1e-04,
  max_iterations = 500
)

Arguments

pH

The urine pH (unitless).

calcium_mmol_L, phosphate_mmol_L, oxalate_mmol_L, sodium_mmol_L, potassium_mmol_L, magnesium_mmol_L, ammonia_mmol_L, citrate_mmol_L, sulfate_mmol_L, urate_mmol_L

Concentration of each species in mmol/L (or any unit value the units package can convert to mmol/L, e.g. set_units(100, "mg_phosphate/dL")). Defaults to zero.

chloride_mmol_L

Chloride concentration in mmol/L. If NA (the default) chloride is auto-computed via electroneutrality, matching V1's If TCl = 0 Then ... block.

CO2_mmol_L

Total CO2 (CO2 + H2CO3 + HCO3- + CO3^2- + carbonate complexes) in mmol/L.

pyrophosphate_mmol_L, TRIS_mmol_L

Total pyrophosphate and TRIS buffer in mmol/L. Note: the V1 source unconditionally sets TPP = 0 after reading the input, so the pyrophosphate chemistry is effectively disabled in V1 (this port preserves that behavior). TRIS is fully supported.

tolerance, max_iterations

Convergence tolerance and iteration cap. Defaults match V1 (1e-4 on the relative change in Ca/Mg/PO4/Ox/Cit/CO2, 500 max iterations).

Value

A list with elements:

  • supersaturation: a data.frame with columns species, activity_product (mol^2/L^2 or mol^3/L^3 depending on stoichiometry), and RSR (relative saturation ratio; >1 means supersaturated).

  • ionic_strength: scalar.

  • activity_factors: named numeric c(F1, F2, F3, F4) for ions of charge 1/2/3/4 respectively.

  • iterations: number of convergence iterations.

  • chloride_mmol_L: chloride used (input or electroneutrality-derived).

Details

The V1 algorithm computes mass balance over a wider set of species than V5 (carbonate chemistry, TRIS buffer, struvite in the Mg/NH4 balance, urate-cation complexes in the Na/K/NH4 balance). The output reports activity products and relative saturation ratios (RSRs) for the four crystalline phases V1 itself reports — Calcium Oxalate, Brushite (CaHPO4·2H2O), Struvite (MgNH4PO4), and Uric Acid. For Hydroxyapatite, Sodium Urate, and Ammonium Urate supersaturations (which V1 does not output but V5 does), call equil2() instead.

Inputs are accepted in mmol/L. Supplying mass-based unit values via units::set_units() works (and is more chemically explicit than V5's mg/dL mode), but for phosphate_mmol_L and sulfate_mmol_L, note the same caveat as equil2(): the mg_phosphate/dL unit is the mass of PO4 (94.97 g/mol), not the mass of inorganic phosphorus that U.S. clinical labs typically report.

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

See also

equil2() for the V5-based port (with Hydroxyapatite, Sodium Urate, and Ammonium Urate outputs) and vignette("original-source-v1") for the V1 VBA source.

Examples

# Same LabCorp inputs used by equil2()'s example, expressed in mmol/L
equil2_v1(
  pH = 5.5,
  sodium_mmol_L = 45,
  potassium_mmol_L = 55,
  calcium_mmol_L = units::set_units(15, "mg_calcium/dL"),
  magnesium_mmol_L = units::set_units(15, "mg_magnesium/dL"),
  ammonia_mmol_L = units::set_units(10, "ug_ammonia/dL"),
  chloride_mmol_L = 75,
  phosphate_mmol_L = 32.285,
  sulfate_mmol_L = 10,
  oxalate_mmol_L = units::set_units(10, "mg_oxalate/L"),
  citrate_mmol_L = units::set_units(400, "mg_citrate/L"),
  urate_mmol_L = units::set_units(50, "mg_urate/dL")
)
#> $supersaturation
#>           species activity_product          RSR
#> 1 Calcium Oxalate     1.907592e-05 3.096740e+00
#> 2        Brushite     2.981115e-07 7.488357e-01
#> 3        Struvite     3.736751e-19 5.263029e-06
#> 4       Uric Acid     1.230873e-03 4.715988e+00
#> 
#> $ionic_strength
#> [1] 0.1320986
#> 
#> $activity_factors
#>         F1         F2         F3         F4 
#> 0.75941759 0.33260029 0.08400902 0.01223744 
#> 
#> $iterations
#> [1] 14
#> 
#> $chloride_mmol_L
#> [1] 75
#>