How rxode2 assigns compartment numbers
rxode2 automatically assigns compartment numbers when parsing. For example, with the Mavoglurant PBPK model the following model may be used:
#> rxode2 3.0.4.9000 using 2 threads (see ?getRxThreads)
#> no cache: create with `rxCreateCache()`
pbpk <- function() {
model({
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 printout, you can see where rxode2 assigned the compartment number(s)
pbpk <- pbpk()
print(pbpk)#> -- rxode2-based free-form 16-cmt ODE model -------------------------------------
#>
#> States ($state or $stateDf):
#> Compartment Number Compartment Name
#> 1 1 Lungs
#> 2 2 Heart
#> 3 3 Brain
#> 4 4 Muscles
#> 5 5 Adipose
#> 6 6 Skin
#> 7 7 Spleen
#> 8 8 Pancreas
#> 9 9 Liver
#> 10 10 Stomach
#> 11 11 Gut
#> 12 12 Bones
#> 13 13 Kidneys
#> 14 14 Arterial_Blood
#> 15 15 Venous_Blood
#> 16 16 Rest_of_Body
#> -- Model (Normalized Syntax): --
#> function() {
#> model({
#> 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)
#> })
#> }You can also see this with the classic rxode2 model. In that case you
use the summary() function:
pbpk <- pbpk$simulationModel#> using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
summary(pbpk)#> rxode2 3.0.4.9000 model named rx_f2eee10822a2b24a0f41e5ed9e55dcb2 model (ready).
#> DLL: /tmp/RtmpNWIsC8/rxode2/rx_f2eee10822a2b24a0f41e5ed9e55dcb2__.rxd/rx_f2eee10822a2b24a0f41e5ed9e55dcb2_.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"
#> -- rxode2 Model Syntax --
#> rxode2({
#> param(lKbBR, lKbMU, lKbAD, lCLint, eta.LClint, lKbBO, lKbRB,
#> WT)
#> 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 rxode2 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 <- function() {
model({
## 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 <- pbpk2()
pbpk2#> -- rxode2-based free-form 16-cmt ODE model -------------------------------------
#>
#> States ($state or $stateDf):
#> Compartment Number Compartment Name
#> 1 1 Venous_Blood
#> 2 2 Skin
#> 3 3 Lungs
#> 4 4 Heart
#> 5 5 Brain
#> 6 6 Muscles
#> 7 7 Adipose
#> 8 8 Spleen
#> 9 9 Pancreas
#> 10 10 Liver
#> 11 11 Stomach
#> 12 12 Gut
#> 13 13 Bones
#> 14 14 Kidneys
#> 15 15 Arterial_Blood
#> 16 16 Rest_of_Body
#> -- Model (Normalized Syntax): --
#> function() {
#> model({
#> cmt(Venous_Blood)
#> cmt(Skin)
#> 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)
#> })
#> }The 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 <- function(){
model({
C2 = center/V
d / dt(depot) = -KA * depot
d/dt(center) = KA * depot - CL*C2
cmt(eff)
})
}
ode.1c.ka <- ode.1c.ka()
print(ode.1c.ka)#> -- rxode2-based free-form 2-cmt ODE model --------------------------------------
#>
#> States ($state or $stateDf):
#> Compartment Number Compartment Name
#> 1 1 depot
#> 2 2 center
#> -- Model (Normalized Syntax): --
#> function() {
#> model({
#> C2 = center/V
#> d/dt(depot) = -KA * depot
#> d/dt(center) = KA * depot - CL * C2
#> cmt(eff)
#> })
#> }You can see this more clearly with the underlying classic
rxode2 model:
ode.1c.ka$simulationModel#> using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’#> rxode2 3.0.4.9000 model named rx_cbb5cd9c9d5675992ba1434d1d05f476 model (ready).
#> x$state: depot, center
#> x$stateExtra: eff
#> x$params: V, KA, CL
#> x$lhs: C2But compartments defined before all the differential equations is not supported; So the model below:
ode.1c.ka <- rxode2({
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.