R Notebook

## Description ####
# 1-compartment model with 1st-order absorption rate and 
# linear elimination 
#
# Date: 06-02-2019
# 
# Units: 
# - time in hr
# - volumes in L
# - masses of substances in mg
# - concentrations of substances in mg/L

## States ####
States = { 
  A_gut,      # Amount in the gut (mg)
  A_central,  # Amount in central compartment (mg)
  A_elim,     # Amount elimination (mg)
  }     

## Outputs ####
Outputs = {
  BW,         # Body weight (kg)
  C_central,  # Concentration in central compartment (mg/L)
  A_total,    # Total quantity for mass balance (Cumulative intake dose)
  }    

## Inputs ####
Inputs = { Dose } # Oral dose (mg) 

## Parameters ####

# Dosing
Dose = 1.0;   # Oral dose (mg/kg)
TChng = 0.05;   # Infusion duration (hr)

# Chemical-specific parameters
Ka = 0.1;             # Gut absorption rate constant (1/h)
Ke = 0.1;             # Elimination rate constant (1/h)
Pct_M_central = 0.05; # % body weight

## Dynamics ####
Dynamics {
  
  t1 = t / 24.0; # time in day
  
  # Body weight (kg) 
  BW = (t1 < 1 ? 60 : 
          (t1 < 2 ? 61 :
             (t1 < 3 ? 62 :
                (t1 < 4 ? 63 :
                   (t1 < 5 ? 64 :
                      65)))));
  
  V_central = BW * Pct_M_central; 
  
  # Infusion rate (/h)
  kDose = Dose / TChng; 
  
  # Rate of amount change in the gut (mg/h)
  dt (A_gut) = kDose - Ka * A_gut;
  dt (A_elim) = Ke * A_central;
  dt (A_central) = Ka * A_gut - dt(A_elim);
  
  C_central = A_central / V_central;
}

## CalcOutputs ####
CalcOutputs { 
  BW = BW;
  C_central = C_central;
  A_total = A_gut + A_central + A_elim;
}

End.

# ./mcsim.1cpt.model.R.exe 1cpt.in.R
Ka      = 1.9;  
Pct_M_central = 1;

Simulation { # Intake 1, 2, 3, 4, 5 mg at 1, 2,3, 4, 5 day 
  Dose = NDoses(10, 1, 0, 2, 0, 3, 0, 4, 0, 5, 0, 
                0, 0.05, 24, 24.05, 48, 48.05, 72, 72.05, 96,   96.05 ); 
  #BW = 60;
  PrintStep (BW, Dose, A_central, A_elim, A_total, C_central, 0, 120, 24);
}

End.

y <- mcsim("1cpt.model.R","1cpt.in.R")

Execute: ./mcsim.1cpt.model.R.exe modeling/1cpt.in.R

________________________________________

MCSim v6.1.0

Copyright (c) 1993-2019 Free Software Foundation, Inc.

MCSim comes with ABSOLUTELY NO WARRANTY;
This is free software, and you are welcome to redistribute it
under certain conditions; see the GNU General Public License.

* Using `modeling/1cpt.model.R' model in file "1cpt.model.R.c" created by ./MCSim/mod.exe v6.1.0

Reading experiment 1.

Doing analysis - 1 normal experiment 
 1
Wrote output file "sim.out"
Done.

y

Body_burden <- y$Dose / y$BW
Body_burden

[1] 0.01666667 0.03278689 0.04838710 0.06349206 0.07812500 0.00000000

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