How RxODE assigns compartment numbers
RxODE automatically assigns compartment numbers when parsing. For example, with the Mavoglurant PBPK model the following model may be used:
#> RxODE 1.1.1 using 1 threads (see ?getRxThreads)
#> no cache: create with `rxCreateCache()`
pbpk <- RxODE({
KbBR = exp(lKbBR)
KbMU = exp(lKbMU)
KbAD = exp(lKbAD)
CLint= exp(lCLint + eta.LClint)
KbBO = exp(lKbBO)
KbRB = exp(lKbRB)
## Regional blood flows
# Cardiac output (L/h) from White et al (1968)
CO = (187.00*WT^0.81)*60/1000;
QHT = 4.0 *CO/100;
QBR = 12.0*CO/100;
QMU = 17.0*CO/100;
QAD = 5.0 *CO/100;
QSK = 5.0 *CO/100;
QSP = 3.0 *CO/100;
QPA = 1.0 *CO/100;
QLI = 25.5*CO/100;
QST = 1.0 *CO/100;
QGU = 14.0*CO/100;
# Hepatic artery blood flow
QHA = QLI - (QSP + QPA + QST + QGU);
QBO = 5.0 *CO/100;
QKI = 19.0*CO/100;
QRB = CO - (QHT + QBR + QMU + QAD + QSK + QLI + QBO + QKI);
QLU = QHT + QBR + QMU + QAD + QSK + QLI + QBO + QKI + QRB;
## Organs' volumes = organs' weights / organs' density
VLU = (0.76 *WT/100)/1.051;
VHT = (0.47 *WT/100)/1.030;
VBR = (2.00 *WT/100)/1.036;
VMU = (40.00*WT/100)/1.041;
VAD = (21.42*WT/100)/0.916;
VSK = (3.71 *WT/100)/1.116;
VSP = (0.26 *WT/100)/1.054;
VPA = (0.14 *WT/100)/1.045;
VLI = (2.57 *WT/100)/1.040;
VST = (0.21 *WT/100)/1.050;
VGU = (1.44 *WT/100)/1.043;
VBO = (14.29*WT/100)/1.990;
VKI = (0.44 *WT/100)/1.050;
VAB = (2.81 *WT/100)/1.040;
VVB = (5.62 *WT/100)/1.040;
VRB = (3.86 *WT/100)/1.040;
## Fixed parameters
BP = 0.61; # Blood:plasma partition coefficient
fup = 0.028; # Fraction unbound in plasma
fub = fup/BP; # Fraction unbound in blood
KbLU = exp(0.8334);
KbHT = exp(1.1205);
KbSK = exp(-.5238);
KbSP = exp(0.3224);
KbPA = exp(0.3224);
KbLI = exp(1.7604);
KbST = exp(0.3224);
KbGU = exp(1.2026);
KbKI = exp(1.3171);
##-----------------------------------------
S15 = VVB*BP/1000;
C15 = Venous_Blood/S15
##-----------------------------------------
d/dt(Lungs) = QLU*(Venous_Blood/VVB - Lungs/KbLU/VLU);
d/dt(Heart) = QHT*(Arterial_Blood/VAB - Heart/KbHT/VHT);
d/dt(Brain) = QBR*(Arterial_Blood/VAB - Brain/KbBR/VBR);
d/dt(Muscles) = QMU*(Arterial_Blood/VAB - Muscles/KbMU/VMU);
d/dt(Adipose) = QAD*(Arterial_Blood/VAB - Adipose/KbAD/VAD);
d/dt(Skin) = QSK*(Arterial_Blood/VAB - Skin/KbSK/VSK);
d/dt(Spleen) = QSP*(Arterial_Blood/VAB - Spleen/KbSP/VSP);
d/dt(Pancreas) = QPA*(Arterial_Blood/VAB - Pancreas/KbPA/VPA);
d/dt(Liver) = QHA*Arterial_Blood/VAB + QSP*Spleen/KbSP/VSP +
QPA*Pancreas/KbPA/VPA + QST*Stomach/KbST/VST +
QGU*Gut/KbGU/VGU - CLint*fub*Liver/KbLI/VLI - QLI*Liver/KbLI/VLI;
d/dt(Stomach) = QST*(Arterial_Blood/VAB - Stomach/KbST/VST);
d/dt(Gut) = QGU*(Arterial_Blood/VAB - Gut/KbGU/VGU);
d/dt(Bones) = QBO*(Arterial_Blood/VAB - Bones/KbBO/VBO);
d/dt(Kidneys) = QKI*(Arterial_Blood/VAB - Kidneys/KbKI/VKI);
d/dt(Arterial_Blood) = QLU*(Lungs/KbLU/VLU - Arterial_Blood/VAB);
d/dt(Venous_Blood) = QHT*Heart/KbHT/VHT + QBR*Brain/KbBR/VBR +
QMU*Muscles/KbMU/VMU + QAD*Adipose/KbAD/VAD + QSK*Skin/KbSK/VSK +
QLI*Liver/KbLI/VLI + QBO*Bones/KbBO/VBO + QKI*Kidneys/KbKI/VKI +
QRB*Rest_of_Body/KbRB/VRB - QLU*Venous_Blood/VVB;
d/dt(Rest_of_Body) = QRB*(Arterial_Blood/VAB - Rest_of_Body/KbRB/VRB);
})If you look at the summary, you can see where RxODE assigned the compartment number(s)
summary(pbpk)#> RxODE 1.1.1 model named rx_da652f665a4b8c80ed5c5c7ce618e36c model (ready).
#> DLL: /tmp/RtmpogyZre/RxODE/rx_da652f665a4b8c80ed5c5c7ce618e36c__.rxd/rx_da652f665a4b8c80ed5c5c7ce618e36c_.so
#> NULL
#>
#> Calculated Variables:
#> [1] "KbBR" "KbMU" "KbAD" "CLint" "KbBO" "KbRB" "CO" "QHT" "QBR"
#> [10] "QMU" "QAD" "QSK" "QSP" "QPA" "QLI" "QST" "QGU" "QHA"
#> [19] "QBO" "QKI" "QRB" "QLU" "VLU" "VHT" "VBR" "VMU" "VAD"
#> [28] "VSK" "VSP" "VPA" "VLI" "VST" "VGU" "VBO" "VKI" "VAB"
#> [37] "VVB" "VRB" "fub" "KbLU" "KbHT" "KbSK" "KbSP" "KbPA" "KbLI"
#> [46] "KbST" "KbGU" "KbKI" "S15" "C15"
#> ______________________________ RxODE Model Syntax ______________________________
#> RxODE({
#> KbBR = exp(lKbBR)
#> KbMU = exp(lKbMU)
#> KbAD = exp(lKbAD)
#> CLint = exp(lCLint + eta.LClint)
#> KbBO = exp(lKbBO)
#> KbRB = exp(lKbRB)
#> CO = (187 * WT^0.81) * 60/1000
#> QHT = 4 * CO/100
#> QBR = 12 * CO/100
#> QMU = 17 * CO/100
#> QAD = 5 * CO/100
#> QSK = 5 * CO/100
#> QSP = 3 * CO/100
#> QPA = 1 * CO/100
#> QLI = 25.5 * CO/100
#> QST = 1 * CO/100
#> QGU = 14 * CO/100
#> QHA = QLI - (QSP + QPA + QST + QGU)
#> QBO = 5 * CO/100
#> QKI = 19 * CO/100
#> QRB = CO - (QHT + QBR + QMU + QAD + QSK + QLI + QBO + QKI)
#> QLU = QHT + QBR + QMU + QAD + QSK + QLI + QBO + QKI + QRB
#> VLU = (0.76 * WT/100)/1.051
#> VHT = (0.47 * WT/100)/1.03
#> VBR = (2 * WT/100)/1.036
#> VMU = (40 * WT/100)/1.041
#> VAD = (21.42 * WT/100)/0.916
#> VSK = (3.71 * WT/100)/1.116
#> VSP = (0.26 * WT/100)/1.054
#> VPA = (0.14 * WT/100)/1.045
#> VLI = (2.57 * WT/100)/1.04
#> VST = (0.21 * WT/100)/1.05
#> VGU = (1.44 * WT/100)/1.043
#> VBO = (14.29 * WT/100)/1.99
#> VKI = (0.44 * WT/100)/1.05
#> VAB = (2.81 * WT/100)/1.04
#> VVB = (5.62 * WT/100)/1.04
#> VRB = (3.86 * WT/100)/1.04
#> BP = 0.61
#> fup = 0.028
#> fub = fup/BP
#> KbLU = exp(0.8334)
#> KbHT = exp(1.1205)
#> KbSK = exp(-0.5238)
#> KbSP = exp(0.3224)
#> KbPA = exp(0.3224)
#> KbLI = exp(1.7604)
#> KbST = exp(0.3224)
#> KbGU = exp(1.2026)
#> KbKI = exp(1.3171)
#> S15 = VVB * BP/1000
#> C15 = Venous_Blood/S15
#> d/dt(Lungs) = QLU * (Venous_Blood/VVB - Lungs/KbLU/VLU)
#> d/dt(Heart) = QHT * (Arterial_Blood/VAB - Heart/KbHT/VHT)
#> d/dt(Brain) = QBR * (Arterial_Blood/VAB - Brain/KbBR/VBR)
#> d/dt(Muscles) = QMU * (Arterial_Blood/VAB - Muscles/KbMU/VMU)
#> d/dt(Adipose) = QAD * (Arterial_Blood/VAB - Adipose/KbAD/VAD)
#> d/dt(Skin) = QSK * (Arterial_Blood/VAB - Skin/KbSK/VSK)
#> d/dt(Spleen) = QSP * (Arterial_Blood/VAB - Spleen/KbSP/VSP)
#> d/dt(Pancreas) = QPA * (Arterial_Blood/VAB - Pancreas/KbPA/VPA)
#> d/dt(Liver) = QHA * Arterial_Blood/VAB + QSP * Spleen/KbSP/VSP +
#> QPA * Pancreas/KbPA/VPA + QST * Stomach/KbST/VST + QGU *
#> Gut/KbGU/VGU - CLint * fub * Liver/KbLI/VLI - QLI * Liver/KbLI/VLI
#> d/dt(Stomach) = QST * (Arterial_Blood/VAB - Stomach/KbST/VST)
#> d/dt(Gut) = QGU * (Arterial_Blood/VAB - Gut/KbGU/VGU)
#> d/dt(Bones) = QBO * (Arterial_Blood/VAB - Bones/KbBO/VBO)
#> d/dt(Kidneys) = QKI * (Arterial_Blood/VAB - Kidneys/KbKI/VKI)
#> d/dt(Arterial_Blood) = QLU * (Lungs/KbLU/VLU - Arterial_Blood/VAB)
#> d/dt(Venous_Blood) = QHT * Heart/KbHT/VHT + QBR * Brain/KbBR/VBR +
#> QMU * Muscles/KbMU/VMU + QAD * Adipose/KbAD/VAD + QSK *
#> Skin/KbSK/VSK + QLI * Liver/KbLI/VLI + QBO * Bones/KbBO/VBO +
#> QKI * Kidneys/KbKI/VKI + QRB * Rest_of_Body/KbRB/VRB -
#> QLU * Venous_Blood/VVB
#> d/dt(Rest_of_Body) = QRB * (Arterial_Blood/VAB - Rest_of_Body/KbRB/VRB)
#> })
#> ________________________________________________________________________________In this case, Venous_Blood is assigned to compartment 15. Figuring this out can be inconvenient and also lead to re-numbering compartment in simulation or estimation datasets. While it is easy and probably clearer to specify the compartment by name, other tools only support compartment numbers. Therefore, having a way to number compartment easily can lead to less data modification between multiple tools.
Changing compartment numbers by pre-declaring the compartments
To add the compartments to the RxODE model in the order you desire you simply need to pre-declare the compartments with cmt. For example specifying is Venous_Blood and Skin to be the 1st and 2nd compartments, respectively, is simple:
pbpk2 <- RxODE({
## Now this is the first compartment, ie cmt=1
cmt(Venous_Blood)
## Skin may be a compartment you wish to dose to as well,
## so it is now cmt=2
cmt(Skin)
KbBR = exp(lKbBR)
KbMU = exp(lKbMU)
KbAD = exp(lKbAD)
CLint= exp(lCLint + eta.LClint)
KbBO = exp(lKbBO)
KbRB = exp(lKbRB)
## Regional blood flows
# Cardiac output (L/h) from White et al (1968)m
CO = (187.00*WT^0.81)*60/1000;
QHT = 4.0 *CO/100;
QBR = 12.0*CO/100;
QMU = 17.0*CO/100;
QAD = 5.0 *CO/100;
QSK = 5.0 *CO/100;
QSP = 3.0 *CO/100;
QPA = 1.0 *CO/100;
QLI = 25.5*CO/100;
QST = 1.0 *CO/100;
QGU = 14.0*CO/100;
QHA = QLI - (QSP + QPA + QST + QGU); # Hepatic artery blood flow
QBO = 5.0 *CO/100;
QKI = 19.0*CO/100;
QRB = CO - (QHT + QBR + QMU + QAD + QSK + QLI + QBO + QKI);
QLU = QHT + QBR + QMU + QAD + QSK + QLI + QBO + QKI + QRB;
## Organs' volumes = organs' weights / organs' density
VLU = (0.76 *WT/100)/1.051;
VHT = (0.47 *WT/100)/1.030;
VBR = (2.00 *WT/100)/1.036;
VMU = (40.00*WT/100)/1.041;
VAD = (21.42*WT/100)/0.916;
VSK = (3.71 *WT/100)/1.116;
VSP = (0.26 *WT/100)/1.054;
VPA = (0.14 *WT/100)/1.045;
VLI = (2.57 *WT/100)/1.040;
VST = (0.21 *WT/100)/1.050;
VGU = (1.44 *WT/100)/1.043;
VBO = (14.29*WT/100)/1.990;
VKI = (0.44 *WT/100)/1.050;
VAB = (2.81 *WT/100)/1.040;
VVB = (5.62 *WT/100)/1.040;
VRB = (3.86 *WT/100)/1.040;
## Fixed parameters
BP = 0.61; # Blood:plasma partition coefficient
fup = 0.028; # Fraction unbound in plasma
fub = fup/BP; # Fraction unbound in blood
KbLU = exp(0.8334);
KbHT = exp(1.1205);
KbSK = exp(-.5238);
KbSP = exp(0.3224);
KbPA = exp(0.3224);
KbLI = exp(1.7604);
KbST = exp(0.3224);
KbGU = exp(1.2026);
KbKI = exp(1.3171);
##-----------------------------------------
S15 = VVB*BP/1000;
C15 = Venous_Blood/S15
##-----------------------------------------
d/dt(Lungs) = QLU*(Venous_Blood/VVB - Lungs/KbLU/VLU);
d/dt(Heart) = QHT*(Arterial_Blood/VAB - Heart/KbHT/VHT);
d/dt(Brain) = QBR*(Arterial_Blood/VAB - Brain/KbBR/VBR);
d/dt(Muscles) = QMU*(Arterial_Blood/VAB - Muscles/KbMU/VMU);
d/dt(Adipose) = QAD*(Arterial_Blood/VAB - Adipose/KbAD/VAD);
d/dt(Skin) = QSK*(Arterial_Blood/VAB - Skin/KbSK/VSK);
d/dt(Spleen) = QSP*(Arterial_Blood/VAB - Spleen/KbSP/VSP);
d/dt(Pancreas) = QPA*(Arterial_Blood/VAB - Pancreas/KbPA/VPA);
d/dt(Liver) = QHA*Arterial_Blood/VAB + QSP*Spleen/KbSP/VSP +
QPA*Pancreas/KbPA/VPA + QST*Stomach/KbST/VST + QGU*Gut/KbGU/VGU -
CLint*fub*Liver/KbLI/VLI - QLI*Liver/KbLI/VLI;
d/dt(Stomach) = QST*(Arterial_Blood/VAB - Stomach/KbST/VST);
d/dt(Gut) = QGU*(Arterial_Blood/VAB - Gut/KbGU/VGU);
d/dt(Bones) = QBO*(Arterial_Blood/VAB - Bones/KbBO/VBO);
d/dt(Kidneys) = QKI*(Arterial_Blood/VAB - Kidneys/KbKI/VKI);
d/dt(Arterial_Blood) = QLU*(Lungs/KbLU/VLU - Arterial_Blood/VAB);
d/dt(Venous_Blood) = QHT*Heart/KbHT/VHT + QBR*Brain/KbBR/VBR +
QMU*Muscles/KbMU/VMU + QAD*Adipose/KbAD/VAD + QSK*Skin/KbSK/VSK +
QLI*Liver/KbLI/VLI + QBO*Bones/KbBO/VBO + QKI*Kidneys/KbKI/VKI +
QRB*Rest_of_Body/KbRB/VRB - QLU*Venous_Blood/VVB;
d/dt(Rest_of_Body) = QRB*(Arterial_Blood/VAB - Rest_of_Body/KbRB/VRB);
})You can see this change in the simple printout
pbpk2#> RxODE 1.1.1 model named rx_61aa0ce42b7116dad49bbee2a53ecf50 model (ready).
#> x$state: Venous_Blood, Skin, Lungs, Heart, Brain, Muscles, Adipose, Spleen, Pancreas, Liver, Stomach, Gut, Bones, Kidneys, Arterial_Blood, Rest_of_Body
#> x$params: lKbBR, lKbMU, lKbAD, lCLint, eta.LClint, lKbBO, lKbRB, WT, BP, fup
#> x$lhs: KbBR, KbMU, KbAD, CLint, KbBO, KbRB, CO, QHT, QBR, QMU, QAD, QSK, QSP, QPA, QLI, QST, QGU, QHA, QBO, QKI, QRB, QLU, VLU, VHT, VBR, VMU, VAD, VSK, VSP, VPA, VLI, VST, VGU, VBO, VKI, VAB, VVB, VRB, fub, KbLU, KbHT, KbSK, KbSP, KbPA, KbLI, KbST, KbGU, KbKI, S15, C15The first two compartments are Venous_Blood followed by Skin.
Appending compartments to the model
You can also append “compartments” to the model. Because of the ODE solving internals, you cannot add fake compartments to the model until after all the differential equations are defined.
For example this is legal:
ode.1c.ka <- RxODE({
C2 = center/V;
d / dt(depot) = -KA * depot
d/dt(center) = KA * depot - CL*C2
cmt(eff);
})
print(ode.1c.ka)#> RxODE 1.1.1 model named rx_0c56901bc2fe74980e24263c457e21b5 model (ready).
#> $state: depot, center
#> $stateExtra: eff
#> $params: V, KA, CL
#> $lhs: C2But compartments defined before all the differential equations is not supported; So the model below:
ode.1c.ka <- RxODE({
cmt(eff);
C2 = center/V;
d / dt(depot) = -KA * depot
d/dt(center) = KA * depot - CL*C2
})will give an error:
Error in rxModelVars_(obj) :
Evaluation error: Compartment 'eff' needs differential equations defined.