Below are the original Visual Basic source code used for the translation to R. It is included to allow users to inspect the fidelity of the code translation.
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.
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
The code below is the basis of the equil2()
function.
VERSION 5.00
Begin VB.Form Form1
Caption = "Form1"
ClientHeight = 8355
ClientLeft = 60
ClientTop = 345
ClientWidth = 5100
LinkTopic = "Form1"
ScaleHeight = 8355
ScaleWidth = 5100
StartUpPosition = 3 'Windows Default
Begin VB.TextBox Text15
Height = 375
Left = 1680
TabIndex = 2
Top = 480
Width = 3375
End
Begin VB.TextBox Text14
Height = 375
Left = 1680
TabIndex = 1
Top = 0
Width = 3375
End
Begin VB.TextBox Text11
Height = 375
Left = 1680
TabIndex = 13
Top = 6840
Width = 1215
End
Begin VB.TextBox Text10
Height = 375
Left = 1680
TabIndex = 12
Top = 6360
Width = 1215
End
Begin VB.TextBox Text9
Height = 375
Left = 1680
TabIndex = 11
Top = 5880
Width = 1215
End
Begin VB.TextBox Text8
Height = 375
Left = 1680
TabIndex = 10
Top = 5400
Width = 1215
End
Begin VB.TextBox Text7
Height = 375
Left = 1680
TabIndex = 9
Top = 4920
Width = 1215
End
Begin VB.TextBox Text6
Height = 375
Left = 1680
TabIndex = 8
Top = 4440
Width = 1215
End
Begin VB.TextBox Text5
Height = 375
Left = 1680
TabIndex = 7
Top = 3960
Width = 1215
End
Begin VB.TextBox Text4
Height = 375
Left = 1680
TabIndex = 6
Top = 3480
Width = 1215
End
Begin VB.TextBox Text3
Height = 375
Left = 1680
TabIndex = 5
Top = 3000
Width = 1215
End
Begin VB.TextBox Text2
Height = 375
Left = 1680
TabIndex = 4
Top = 2520
Width = 1215
End
Begin VB.TextBox Text1
Height = 375
Left = 1680
TabIndex = 3
Top = 2040
Width = 1215
End
Begin VB.CommandButton Command1
Caption = "Calculate now"
Height = 615
Left = 3240
TabIndex = 0
Top = 7800
Width = 1935
End
Begin VB.Label Label1
Caption = "Enter Collection Date, Time"
Height = 375
Index = 14
Left = 120
TabIndex = 26
Top = 480
Width = 1455
End
Begin VB.Label Label1
Caption = "Enter Patient Name, Clinic Number"
Height = 495
Index = 13
Left = 120
TabIndex = 25
Top = 0
Width = 1455
End
Begin VB.Label Label1
Caption = "pH"
Height = 255
Index = 11
Left = 0
TabIndex = 24
Top = 6480
Width = 1455
End
Begin VB.Label Label1
Caption = "Uric Acid (mg/dl)"
Height = 375
Index = 10
Left = 0
TabIndex = 23
Top = 6840
Width = 1455
End
Begin VB.Label Label1
Caption = "Citrate (mg/dl)"
Height = 375
Index = 9
Left = 0
TabIndex = 22
Top = 5520
Width = 1455
End
Begin VB.Label Label1
Caption = "Oxalate (mg/dl)"
Height = 375
Index = 8
Left = 0
TabIndex = 21
Top = 6000
Width = 1455
End
Begin VB.Label Label1
Caption = "Phosphate (mg/dl)"
Height = 375
Index = 7
Left = 0
TabIndex = 20
Top = 4560
Width = 1455
End
Begin VB.Label Label1
Caption = "Sulfate (mg/dl)"
Height = 375
Index = 6
Left = 0
TabIndex = 19
Top = 5040
Width = 1455
End
Begin VB.Label Label1
Caption = "Chloride (Meq/L)"
Height = 375
Index = 5
Left = 0
TabIndex = 18
Top = 4080
Width = 1455
End
Begin VB.Label Label1
Caption = "Sodium (Meq/L)"
Height = 375
Index = 3
Left = 0
TabIndex = 17
Top = 2160
Width = 1455
End
Begin VB.Label Label1
Caption = "Potassium (Meq/L)"
Height = 375
Index = 2
Left = 0
TabIndex = 16
Top = 2640
Width = 1455
End
Begin VB.Label Label1
Caption = "Magnesium (mg/dl)"
Height = 375
Index = 1
Left = 0
TabIndex = 15
Top = 3600
Width = 1455
End
Begin VB.Label Label1
Caption = "Calcium (mg/dl)"
Height = 375
Index = 0
Left = 0
TabIndex = 14
Top = 3120
Width = 1455
End
End
Attribute VB_Name = "Form1"
Attribute VB_GlobalNameSpace = False
Attribute VB_Creatable = False
Attribute VB_PredeclaredId = True
Attribute VB_Exposed = False
Dim p As String
Dim q As String
Dim a(120) As Double
Sub Command1_Click()
Call calc
End Sub
Sub Form_Load()
Debug.Print "hello"
End Sub
Sub calc()
Rem Open "ssinput.txt" For Input As #1
Debug.Print "Now in calc routine."
10 Dim S(65)
20 S(1) = 1730000000000#
30 S(2) = 14900000#
40 S(3) = 162
50 S(4) = 145.5
60 S(5) = 20750
70 S(6) = 2640000!
80 S(7) = 55210!
90 S(8) = 1247
100 S(9) = 278000!
110 S(10) = 12.9
120 S(11) = 5.433
130 S(12) = 13.4
140 S(13) = 8.5
150 S(14) = 216
160 S(15) = 33.1
170 S(16) = 251.2
180 S(17) = 10
190 S(18) = 8.831001
200 S(19) = 13.4
210 S(20) = 12.6
220 S(21) = 143
230 S(22) = 3597000!
240 S(23) = 685
250 S(24) = 31.3
260 S(25) = 229.6
270 S(26) = 2746
280 S(27) = 17.3
290 S(28) = 71.4
300 S(29) = 60000!
310 S(30) = 505.2
320 S(31) = 12.5
330 S(32) = 3460000!
340 S(33) = 1014
350 S(34) = 31.9
360 S(35) = 188.4
370 S(36) = 4020
380 S(37) = 4.75
390 S(38) = 5.93
400 S(39) = 69900!
410 S(40) = 316.7
420 S(41) = 5
430 S(42) = 10
440 S(43) = 12.9
450 S(44) = 13
460 S(45) = 8.5
470 S(46) = 58800000#
480 S(47) = 2440000000#
490 S(48) = 4970000!
500 S(49) = 171
510 S(50) = 7.05
520 S(51) = 562000!
530 S(52) = 5500
540 S(53) = 794000000#
550 S(54) = 23.1
560 S(55) = 380.19
570 S(56) = 19770000#
580 S(57) = 1995000000#
590 S(58) = 55.6
600 S(59) = 1940000!
610 S(60) = 16600000000#
620 S(61) = 0.00123
630 S(62) = 18.6
640 S(63) = 1.03
650 S(64) = 1897
660 S(65) = 946
670 Rem Dim a(120)
680 Dim T(11)
690 Rem Open "LPT1:" For Output As #1
691 Rem CLS: Key OFF: Color 7, 1, 0
695 Rem Input #1, z$
697 Rem Input #1, z$
700 Rem Input #1, a(120)
701 a(1) = a(1) / 1000
702 Rem Print "K";: Input #1, a(120)
703 a(2) = a(2) / 1000
704 Rem Print "CA";: Input #1, a(120)
705 a(3) = a(3) / 4008
706 Rem Print "MG";: Input #1, a(120)
707 a(4) = a(4) / 2431
708 Rem Print "PYRO";: Input #1, a(11)
709 Rem a(11)=a(11)/2431
710 Rem Print "NH4";: Input #1, a(120)
711 a(5) = a(5) / 1000
712 Rem Print "CL";: Input #1, a(120)
713 a(91) = a(91) / 1000
714 Rem Print "CO2";: Input #1, a(120)
715 Rem a(31)=a(31)/4401
716 Rem Print "P";: Input #1, a(120)
717 a(6) = a(6) / 3097
718 Rem Print "S";: Input #1, a(120)
719 a(7) = a(7) / 3206
720 Rem Print "CIT";: Input #1, a(120)
721 a(9) = a(9) / 19212
722 Rem Print "OX";: Input #1, a(120)
723 a(8) = a(8) / 8802
724 Rem Print "PH";: Input #1, a(120)
726 Rem Print "UR";: Input #1, a(120)
727 a(10) = a(10) / 16800
800 Rem Close #1
820 a(26) = 10 ^ (-a(24))
850 F1 = 0.7
860 F2 = 0.3
870 F3 = 0.1
880 F4 = 0.02
890 O0 = 0
900 O1 = 0
910 O2 = 0
920 O3 = 0
930 O4 = 0
940 For I = 1 To 10
950 a(12 + I) = 0.1 * a(I)
960 Next I
970 a(12) = 0.1 * a(11)
980 a(23) = 0.01 * a(12)
990 For I = 1 To 50
1000 a(25) = 10 ^ (-13.593 + a(24))
1010 a(27) = S(1) * a(26) * a(18) * F3 / F2
1020 a(28) = S(2) * a(26) * a(27) * F2 / F1
1030 a(29) = S(3) * a(26) * a(28) * F1
1040 a(30) = S(61) * a(31) * S(58)
1050 a(32) = a(30) / (a(26) * S(59) * F1)
1060 a(33) = a(32) * F1 / (a(26) * S(60) * F2)
1070 a(34) = S(62) * a(13) * a(33) * F2
1080 a(35) = S(63) * a(13) * a(34) * F1 * F1
1090 a(36) = S(64) * a(15) * a(33) * F2 * F2
1100 a(37) = S(65) * a(16) * a(33) * F2 * F2
1110 a(38) = S(4) * a(26) * a(19) * F2 / F1
1120 a(39) = S(5) * a(26) * a(20) * F2 / F1
1130 a(40) = S(6) * a(26) * a(21) * F3 / F2
1140 a(41) = S(7) * a(26) * a(40) * F2 / F1
1150 a(42) = S(8) * a(26) * a(41) * F1
1160 a(43) = S(9) * a(26) * a(22) * F1
1170 a(44) = S(10) * a(13) * a(27) * F2
1180 a(45) = S(11) * a(13) * a(19) * F2
1190 a(46) = S(12) * a(13) * a(20) * F2
1200 a(47) = S(13) * a(13) * a(21) * F3 * F1 / F2
1210 a(48) = S(14) * a(13) * a(12) * F1 * F4 / F3
1220 a(49) = S(16) * a(13) * a(48) * F1 * F3 / F2
1230 a(50) = S(15) * a(13) * a(23) * F1 * F3 / F2
1240 a(51) = S(17) * a(14) * a(27) * F2
1250 a(52) = S(18) * a(14) * a(19) * F2
1260 a(53) = S(19) * a(14) * a(20) * F2
1270 a(54) = S(20) * a(14) * a(21) * F3 * F1 / F2
1280 a(55) = S(21) * a(14) * a(12) * F1 * F4 / F3
1290 a(56) = S(22) * a(15) * a(18) * F3 * F2 / F1
1300 a(57) = S(23) * a(15) * a(27) * F2 * F2
1310 a(58) = S(24) * a(15) * a(28) * F2
1320 a(59) = S(25) * a(15) * a(19) * F2 * F2
1330 a(60) = S(26) * a(15) * a(20) * F2 * F2
1340 a(61) = S(28) * a(15) * a(60)
1350 a(62) = S(27) * a(60) * a(20)
1360 a(63) = S(29) * a(15) * a(21) * F3 * F2 / F1
1370 a(64) = S(30) * a(15) * a(40) * F2 * F2
1380 a(65) = S(31) * a(15) * a(41) * F2
1390 a(66) = S(32) * a(16) * a(18) * F3 * F2 / F1
1400 a(67) = S(33) * a(16) * a(27) * F2 * F2
1410 a(68) = S(34) * a(16) * a(28) * F2
1420 a(69) = S(35) * a(16) * a(19) * F2 * F2
1430 a(70) = S(36) * a(16) * a(20) * F2 * F2
1440 a(71) = S(37) * a(16) * a(70)
1450 a(72) = S(38) * a(70) * a(20)
1460 a(73) = S(39) * a(16) * a(21) * F3 * F2 / F1
1470 a(74) = S(40) * a(16) * a(40) * F2 * F2
1480 a(75) = S(41) * a(16) * a(41) * F2
1490 a(76) = S(42) * a(17) * a(27) * F2
1500 a(77) = S(43) * a(17) * a(19) * F2
1510 a(78) = S(44) * a(17) * a(20) * F2
1520 a(79) = S(45) * a(17) * a(21) * F3 * F1 / F2
1540 a(23) = S(47) * a(26) * a(12) * F4 / F3
1550 a(81) = S(48) * a(26) * a(23) * F3 / F2
1560 a(82) = S(49) * a(26) * a(81) * F2 / F1
1570 a(83) = S(50) * a(26) * a(82) * F1
1580 a(84) = S(51) * a(15) * a(12) * F4
1590 a(85) = S(52) * a(15) * a(23) * F2 * F3 / F1
1600 a(86) = S(53) * a(15) * a(25) * a(12) * F4 * F2 / F3
1610 a(87) = S(54) * a(15) * a(25) * F2 / F1
1620 a(88) = S(55) * a(16) * a(25) * F2 / F1
1630 a(89) = S(56) * a(16) * a(12) * F4
1640 a(90) = S(57) * a(16) * a(25) * a(12) * F2 * F4 / F3
1650 T(0) = a(13) + a(44) + a(45) + a(46) + a(47) + a(48) + 2 * a(49) + a(50) + a(34) + 2 * a(35)
1660 T(1) = a(14) + a(51) + a(52) + a(53) + a(54) + a(55)
1670 T(2) = a(17) + a(76) + a(77) + a(78) + a(79)
1680 T(3) = a(15) + a(56) + a(57) + a(58) + a(59) + a(60) + 2 * a(61) + a(63) + a(64) + a(62) + a(65) + a(36) + a(85) + a(84) + a(86) + a(87)
1690 T(4) = a(16) + a(66) + a(67) + a(68) + a(69) + a(70) + 2 * a(71) + a(73) + a(74) + a(75) + a(72) + a(37) + a(88) + a(89) + a(90)
1700 T(5) = a(18) + a(27) + a(28) + a(29) + a(44) + a(51) + a(56) + a(57) + a(58) + a(66) + a(67) + a(68) + a(76)
1710 T(6) = a(19) + a(38) + a(45) + a(52) + a(59) + a(69) + a(77)
1720 T(7) = a(20) + a(39) + a(60) + a(61) + a(70) + a(71) + a(46) + a(53) + a(78) + 2 * a(62) + 2 * a(72)
1730 T(8) = a(21) + a(40) + a(41) + a(42) + a(47) + a(54) + a(79) + a(63) + a(64) + a(65) + a(73) + a(74) + a(75)
1740 T(9) = a(12) + a(23) + a(81) + a(82) + a(83) + a(84) + a(85) + a(86) + a(89) + a(90) + a(48) + a(49) + a(50) + a(55)
1750 T(10) = a(22) + a(43)
1760 T(11) = a(33) + a(32) + a(30) + a(34) + a(35) + a(36) + a(37)
1770 For I1 = O To 11
1780 If T(I1) = 0 Then T(I1) = 1E-20
1790 Next I1
1800 a(13) = a(1) * a(13) / T(0)
1810 a(14) = a(2) * a(14) / T(1)
1820 a(15) = a(3) * a(15) / T(3)
1830 a(16) = a(4) * a(16) / T(4)
1840 a(17) = a(5) * a(17) / T(2)
1850 a(18) = a(6) * a(18) / T(5)
1860 a(19) = a(7) * a(19) / T(6)
1870 a(20) = a(8) * a(20) / T(7)
1880 a(21) = a(9) * a(21) / T(8)
1890 a(22) = a(10) * a(22) / T(10)
1900 a(12) = a(11) * a(12) / T(9)
1910 a(33) = a(31) * a(33) / T(11)
1920 S1 = (a(25) + a(26)) / F1 + a(13) + a(14) + a(17) + a(22) + a(91) + a(44) + a(45) + a(46) + a(34) + a(51) + a(52) + a(53) + a(76) + a(77)
1930 S1 = S1 + a(78) + a(56) + a(58) + a(63) + a(65) + a(85) + a(87) + a(28) + a(32) + a(38) + a(39) + a(41) + a(82) + a(66) + a(68) + a(73) + a(75) + a(88)
1940 S2 = 4 * (a(15) + a(16) + a(19) + a(20) + a(33) + a(47) + a(49) + a(54) + a(79) + a(84) + a(50) + a(89) + a(27) + a(40) + a(81) + a(61) + a(71) + a(62) + a(72))
1950 S3 = 9 * (a(18) + a(21) + a(48) + a(55) + a(23) + a(86) + a(90))
1960 S4 = 16 * a(12)
1970 S5 = (S1 + S2 + S3 + S4) / 2
1980 If S5 > 1 Then S5 = 1
1990 If S5 < 0.000001 Then S5 = 0.000001
2000 S6 = Sqr(S5)
2010 F1 = Exp(-1.20218 * ((S6 / (1 + S6)) - 0.285 * S5))
2020 F2 = F1 ^ 4
2030 F3 = F1 ^ 9
2040 F4 = F1 ^ 16
2050 If a(15) = 0 Then GoTo 2070
2060 If Abs((a(15) - O0) / a(15)) > 0.0001 Then GoTo 2160
2070 If a(16) = 0 Then GoTo 2090
2080 If Abs((a(16) - O1) / a(16)) > 0.0001 Then GoTo 2160
2090 If a(18) = 0 Then GoTo 2110
2100 If Abs((a(18) - O2) / a(18)) > 0.0001 Then GoTo 2160
2110 If a(20) = 0 Then GoTo 2130
2120 If Abs((a(20) - O3) / a(20)) > 0.0001 Then GoTo 2160
2130 If a(21) = 0 Then GoTo 2150
2140 If Abs((a(21) - O4) / a(21)) > 0.0001 Then GoTo 2160
2150 GoTo 2230
2160 O0 = a(15)
2170 O1 = a(16)
2180 O2 = a(18)
2190 O3 = a(20)
2200 O4 = a(21)
2210 Next I
2220 Print "50 CYCLES WITHOUT CONVERGE"
2230 a(92) = I
2231 a(93) = S5
2232 a(94) = F1
2234 a(95) = F2
2236 a(96) = F3
2238 a(97) = F4
2250 Open "ssout.txt" For Output As #1
2257 Print #1, "Patient: "; Tab(30); p$
2258 Print #1, "Analysis Date :"; Tab(30); Date$
2259 Print #1, "Collection Date and Time:"; Tab(30); q$: Print #1,
2260 Print #1, "Sodium", a(1) * 1000
2261 Rem Tab(43); "[NAHPP]"; Tab(57); A(50)
2270 Print #1, "Potassium", a(2) * 1000
2271 Rem Tab(43); "[KHPO4]"; Tab(57); A(51)
2280 Print #1, "Calcium", a(3) * 4008
2281 Rem Tab(43); "[KSO4]"; Tab(57); A(52)
2290 Print #1, "Magnesium", a(4) * 2431
2291 Rem Tab(43); "[KOX]"; Tab(57); A(53)
2300 Print #1, "Ammonia", a(5) * 1000
2301 Rem Tab(43); "[KCIT]"; Tab(57); A(54)
2302 Print #1, "Chloride", a(91) * 1000
2310 Print #1, "Phosphate", a(6) * 3097
2311 Rem Tab(43); "[KPP]"; Tab(57); A(55)
2320 Print #1, "Sulfate", a(7) * 3206
2321 Rem Tab(43); "[CAPO4]"; Tab(57); A(56)
2330 Print #1, "Oxalate", a(8) * 8802
2331 Rem Tab(43); "[CAHPO4]"; Tab(57); A(57)
2340 Print #1, "Citrate", a(9) * 19212
2341 Rem Tab(43); "[CAH2P04]"; Tab(57); A(58)
2342 Print #1, "pH", a(24)
2350 Print #1, "Urate", a(10) * 16800
2351 Rem Tab(43); "[CASO4]"; Tab(57); A(59)
2360 Rem Print #1, "PP", A(11)
2361 Rem Tab(43); "[CAOX]"; Tab(57); A(60)
2370 Rem Print #1, "[PP]", A(12), Tab(43); "[CA2OX]"; Tab(57); A(61)
2380 Rem Print #1, "[NA]", A(13), Tab(43); "[CAOX2]"; Tab(57); A(62)
2390 Rem Print #1, "[K]", A(14), Tab(43); "[CACIT]"; Tab(57); A(63)
2400 Rem Print #1, "[CA]", A(15), Tab(43); "[CAHCIT]"; Tab(57); A(64)
2410 Rem Print #1, "[MG]", A(16), Tab(43); "[CAH2CIT]"; Tab(57); A(65)
2420 Rem Print #1, "[NH4]", A(17), Tab(43); "[MGPO4]"; Tab(57); A(66)
2430 Rem Print #1, "[PO4]", A(18), Tab(43); "[MGHPO4]"; Tab(57); A(67)
2440 Rem Print #1, "[SO4]", A(19), Tab(43); "[MGH2PO4]"; Tab(57); A(68)
2450 Rem Print #1, "[OX]", A(20), Tab(43); "[MGSO4]"; Tab(57); A(69)
2460 Rem Print #1, "[CIT]", A(21), Tab(43); "[MGOX]"; Tab(57); A(70)
2470 Rem Print #1, "[HU]", A(22), Tab(43); "[MG2OX]"; Tab(57); A(71)
2480 Rem Print #1, "[HPP]", A(23), Tab(43); "[MGOX2]", Tab(57); A(72)
2490 Rem Print #1, "PH", A(24), Tab(43); "[MGCIT]"; Tab(57); A(73)
2500 Rem Print #1, "(OH)", A(25), Tab(43); "[MGHCIT]"; Tab(57); A(74)
2510 Rem Print #1, "(H)", A(26), Tab(43); "[MGH2CIT]"; Tab(57); A(75)
2520 Rem Print #1, "[HPO4]", A(27), Tab(43); "[NH4HPO4]"; Tab(57); A(76)
2530 Rem Print #1, "[H2PO4]", A(28), Tab(43); "[NH4SO4]"; Tab(57); A(77)
2540 Rem Print #1, "[H3PO4]", A(29), Tab(43); "[NH4OX]"; Tab(57); A(78)
2550 Rem Print #1, "[H2CO3]", A(30), Tab(43); "[NH4CIT]"; Tab(57); A(79)
2560 Rem Print #1, "CO2", A(31)
2570 Rem Print #1, "[HCO3]", A(32), Tab(43); "[H2PP]"; Tab(57); A(81)
2580 Rem Print #1, "[CO3]", A(33), Tab(43); "[H3PP]"; Tab(57); A(82)
2590 Rem Print #1, "[NACO3]", A(34), Tab(43); "[H4PP]"; Tab(57); A(83)
2600 Rem Print #1, "[NA2CO3]", A(35), Tab(43); "[CAPP]"; Tab(57); A(84)
2610 Rem Print #1, "[CACO3]", A(36), Tab(43); "[CAHPP]"; Tab(57); A(85)
2620 Rem Print #1, "[MGCO3]", A(37), Tab(43); "[CAOHPP]"; Tab(57); A(86)
2630 Rem Print #1, "[HSO4]", A(38), Tab(43); "[CAOH]"; Tab(57); A(87)
2640 Rem Print #1, "[HOX]", A(39), Tab(43); "[MGOH]"; Tab(57); A(88)
2650 Rem Print #1, "[HCIT]", A(40), Tab(43); "[MGPP]"; Tab(57); A(89)
2660 Rem Print #1, "[H2CIT]", A(41), Tab(43); "[MGOHPP]"; Tab(57); A(90)
2670 Rem Print #1, "[H3CIT]", A(42), Tab(43); "[CL]"; Tab(57); A(91)
2680 Rem Print #1, "[H2U]", A(43), Tab(43); "CYCLES"; Tab(57); A(92)
2690 Rem Print #1, "[NAHPO4]", A(44), Tab(43); "I.S."; Tab(57); A(93)
2700 Rem Print #1, "[NASO4]", A(45), Tab(43); "F1"; Tab(57); A(94)
2710 Rem Print #1, "[NAOX]", A(46), Tab(43); "F2"; Tab(57); A(95)
2720 Rem Print #1, "[NACIT]", A(47), Tab(43); "F3"; Tab(57); A(96)
2730 Rem Print #1, "[NAPP]", A(48), Tab(43); "F4"; Tab(57); A(97)
2740 Rem Print #1, "[NA2PP]", A(49)
2750 Print #1, "Cycles", a(92)
2760 Print #1,
2770 Print #1, Tab(20); "SS", Tab(43); "DG"
2780 a(100) = a(60) / 0.00000616
2790 a(101) = a(15) * a(27) * F2 * F2 / 0.000000237
2800 X1 = F2 * a(15) * 1000
2810 X2 = F3 * a(18) * 10000000000#
2820 a(102) = (X1 ^ 5) * (X2 ^ 3) * a(25) / 1.45E-14
2830 a(103) = F1 * F2 * F3 * a(16) * a(17) * a(18) / 0.000000000000115
2840 a(104) = a(43) / 0.000261
2850 a(105) = F1 * F1 * a(22) * a(13) / 0.0000279
2860 a(106) = F1 * F1 * a(22) * a(17) / 0.000036
2870 a(107) = F1 * F1 * a(22) * a(14) / 0.0000963
2875 If a(100) <= 0 Then a(108) = 0: GoTo 2885
2880 a(108) = 1.2935 * Log(a(100))
2885 If a(101) <= 0 Then a(109) = 0: GoTo 2895
2890 a(109) = 1.2935 * Log(a(101))
2895 If a(102) <= 0 Then a(110) = 0: GoTo 2905
2900 a(110) = 0.28744 * Log(a(102))
2905 If a(103) <= 0 Then a(111) = 0: GoTo 2915
2910 a(111) = 0.8623 * Log(a(103))
2915 If a(104) <= 0 Then a(112) = 0: GoTo 2925
2920 a(112) = 2.587 * Log(a(104))
2925 If a(105) <= 0 Then a(113) = 0: GoTo 2935
2930 a(113) = 1.2935 * Log(a(105))
2935 If a(106) <= 0 Then a(114) = 0: GoTo 2945
2940 a(114) = 1.2935 * Log(a(106))
2945 If a(107) <= 0 Then a(115) = 0: GoTo 3000
2950 a(115) = 1.2935 * Log(a(107))
3000 Print #1, "Calcium Oxalate"; Tab(20); Format(a(100), "###0.00"), Tab(43); Format(a(108), "###0.00")
3010 Print #1, "Brushite"; Tab(20); Format(a(101), "###0.00"), Tab(43); Format(a(109), "###0.00")
3020 Print #1, "Hydroxyapatite"; Tab(20); Format(a(102), "###0.00"), Tab(43); Format(a(110), "###0.00")
3030 Rem Print #1, "STRU", Format(A(103), "###0.00"), Tab(43); Format(A(111), "###0.00")
3040 Print #1, "Uric Acid"; Tab(20); Format(a(104), "###0.00"), Tab(43); Format(a(112), "###0.00")
3050 Print #1, "Sodium Urate"; Tab(20); Format(a(105), "###0.00"), Tab(43); Format(a(113), "###0.00")
3060 Print #1, "Ammonium Urate"; Tab(20); Format(a(106), "###0.00"), Tab(43); Format(a(114), "###0.00")
3070 Rem Print #1, "KU", Format(A(100), "###0.00"), Tab(43); Format(A(115), "###0.00")
3080 Print #1,: Print #1,: Print #1,: Print #1,
3100 Close #1
3240 Close
3250 End
End Sub
Sub Text1_Change()
a(1) = Val(Text1.Text)
End Sub
Sub Text10_Change()
a(24) = Val(Text10.Text)
End Sub
Sub Text11_Change()
a(10) = Val(Text11.Text)
End Sub
Private Sub Text14_Change()
p = Text14.Text
End Sub
Private Sub Text15_Change()
q = Text15.Text
End Sub
Sub Text2_Change()
a(2) = Val(Text2.Text)
End Sub
Sub Text3_Change()
a(3) = Val(Text3.Text)
End Sub
Sub Text4_Change()
a(4) = Val(Text4.Text)
End Sub
Sub Text5_Change()
a(91) = Val(Text5.Text)
End Sub
Sub Text6_Change()
a(6) = Val(Text6.Text)
End Sub
Sub Text7_Change()
a(7) = Val(Text7.Text)
End Sub
Sub Text8_Change()
a(9) = Val(Text8.Text)
End Sub
Sub Text9_Change()
a(8) = Val(Text9.Text)
End SubLines 717 and 719 of the V5 source above
divide the “Phosphate (mg/dl)” and “Sulfate (mg/dl)” inputs by
3097 and 3206 respectively:
717 a(6) = a(6) / 3097
719 a(7) = a(7) / 3206These factors are the atomic weights of inorganic phosphorus (P, 30.97 g/mol) and sulfur (S, 32.06 g/mol) multiplied by 100 to convert mg/dL to mol/L. They do not correspond to the molecular weights of the phosphate ion (PO₄³⁻, 94.97 g/mol) or the sulfate ion (SO₄²⁻, 96.07 g/mol). In other words, the V5 algorithm expects “Phosphate (mg/dl)” to be the mass of inorganic phosphorus and “Sulfate (mg/dl)” to be the mass of sulfur — which is consistent with how U.S. clinical labs report those species, but conflicts with the chemical names of the inputs.
This mismatch was reported in issue #2 by Lea
Lerose, who demonstrated that the R port’s unit-aware inputs (e.g.
set_units(32, "mmol_phosphate/L")) were being inflated by a
factor of roughly 94.97 / 30.97 ≈ 3.07 because the units
package converts the input value via the true PO₄ molecular
weight while the algorithm then divides by the P-based factor.
In the R port, this has been resolved by replacing the V5 factors with the true polyatomic-ion factors:
| V5 source line | V5 value | R port value | Reason |
|---|---|---|---|
a(6) = a(6) / 3097 |
3097 | 9497 | 94.97 g/mol × 100 dL/L — actual PO₄ ion mass |
a(7) = a(7) / 3206 |
3206 | 9607 | 96.07 g/mol × 100 dL/L — actual SO₄ ion mass |
output a(6) * 3097 |
3097 | 9497 | mirror of the input factor |
output a(7) * 3206 |
3206 | 9607 | mirror of the input factor |
Users with legacy clinical data recorded as “phosphate (mg/dL)” meaning mass of P should convert by multiplying by ≈ 3.066 (= 94.97 / 30.97) to get mass of PO₄, or — more simply — supply the value in mmol/L, where 1 mmol of P = 1 mmol of PO₄. Same logic applies to sulfate with the ratio 96.07 / 32.06 ≈ 3.00.
Cross-validation. The R port has been
cross-validated against the V5 BASIC source itself by transcribing the
calc() Sub above (with the same /9497 and
/9607 fix applied) into LibreOffice 26.2.4 Basic and
running it with the LabCorp inputs in mmol_phosphate/L /
mmol_sulfate/L form. R and V5 BASIC agree on ionic strength
to about 2 parts per billion and on all six supersaturation values
(Calcium Oxalate, Brushite, Hydroxyapatite, Uric Acid, Sodium Urate,
Ammonium Urate) plus their ΔGibbs energies to better than 1 part per
million. Residual differences are floating-point ordering noise.
The R port is based on the V5 (form-based BASIC) source shown above.
The original Mayo Clinic class module clsEquil2 (“V1”) is a
richer implementation that is provided in issue #2 as an attached
.txt file. Below is a brief summary of the differences,
included so users can decide whether they need V1’s additional
capabilities.
Inputs. V1 takes all species in mmol per collection
volume (plus a Vol parameter) and then converts to mol/L by
dividing by Vol × 1000. This means V1 has no per-species
atomic-weight factors at all, and the phosphate/sulfate confusion above
does not arise — the V1 approach is unambiguous by construction.
Additional chemistry in V1. V1 models several pathways that V5 (and therefore the R port) does not:
Stability constants. V1 and V5 share the same
constants for the core CaOx / brushite / hydroxyapatite / uric-acid /
Na-urate / NH₄-urate pathways. The constants that differ are
concentrated in the CO₂, PP, and HU pathways — pathways V5 does not use
anyway. For example, V1 uses P7 = 0.00229 for CO₂
dissociation while V5 uses S(61) = 0.00123; V1 uses
7.943 × 10¹⁰ for HU formation while V5 uses
S(9) = 278000.
Outputs. V1 reports activity products
(APCaOx, APBr, APStru,
APUA, APNaU) and relative saturation ratios
(RSR) for calcium oxalate, brushite, struvite, and uric acid only. V5
(and the R port) additionally reports supersaturation for
hydroxyapatite, sodium urate, and ammonium urate, plus negative ΔGibbs
energies for all six.
Convergence. V1 caps iteration at 500 and treats non-convergence as an error. V5 (and the R port) caps at 50 and warns.
Bottom line. The R port is a faithful translation of V5. The only true bug it inherited from V5 is the phosphate/sulfate unit confusion fixed in this release. The other items above are V5-vs-V1 scope gaps, not translation errors. A more complete port that adopts V1’s structure is feasible but is out of scope for the current release.