In nlmixr2/rxode2: Facilities for Simulating from ODE-Based Models

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);
  })
}