In RxODE: Facilities for Simulating from ODE-Based Models

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);
})