Solve PK Model Through GNU MCSim — solve

Solve the differential equations of time-dependent quantity/concentration in different tissues/compartments through GNU MCSim.

solve_mcsim(
  x,
  mName,
  infile.name = NULL,
  outfile.name = NULL,
  setpoint.name = NULL,
  params = NULL,
  vars = NULL,
  times = NULL,
  condition = NULL,
  generate.infile = T,
  tell = T,
  rtol = 1e-06,
  atol = 1e-06,
  monte_carlo = NULL,
  dist = NULL,
  q.arg = NULL,
  parallel = 1
)

generate_infile(
  mod = NULL,
  infile.name = NULL,
  outfile.name = NULL,
  params = NULL,
  vars,
  times,
  condition,
  rtol = 1e-06,
  atol = 1e-06,
  monte_carlo = NULL,
  dist = NULL,
  q.arg = NULL
)

Arguments

x: a list of storing information in the defined sensitivity function.
mName: a string giving the name of the model or C file (without extension).
infile.name: a character to assign the name of input file.
outfile.name: a character to assign the name of output file.
setpoint.name: a character to assign the name of file for parameter matrix.
params: a character to assign the testing parameters.
vars: a character or a vector to assign the selected output(s).
times: a numeric vector to define the given time point(s).
condition: a character to set the specific parameter value in the input file.
generate.infile: a logical value to automatically generate the input file.
tell: a logical value to automatically combine the result y to decoupling simulation x.
rtol: an argument passed to the integrator (default 1e-6).
atol: an argument passed to the integrator (default 1e-6).
monte_carlo: a numeric value to define the sample size in Monte Carlo simulation.
dist: a vector of distribution names corresponding to <distribution-name> in GNU MCSim.
q.arg: a list of shape parameters in the sampling distribution (dist).
parallel: a numeric value to assign the number of cores in parallel computing (default is set to 1).
mod: a list of model and parameters information that is used in solving differential equation.

Value

The output result is the 4-dimension array with c(model evaluations, replications, time-points, output variables).

Details

This function allows users to use external data file that assigned in setpoint.name as parameter matrix. If you want to use it, be sure to define n and setpoint.name.

Functions

solve_mcsim(): Numerical analysis for the PK model by GNU MCSim.
generate_infile(): Generate the GNU MCSim input file.

Examples


if (FALSE) {
pbtk1cpt_model()
mName <- "pbtk1cpt"
compile_model(mName)

q <- "qunif"
q.arg <- list(list(min = 0.4, max = 1.1),
              list(min = 0.1, max = 0.4),
              list(min = 1.0, max = 3.0))

params <- c("vdist", "ke", "kgutabs")

set.seed(1234)
x <- rfast99(params = params, n = 200, q = q, q.arg = q.arg, rep = 20)

infile.name <- "example.in"
outfile.name <- "example.csv"
vars <- "Ccompartment"

t <- seq(from = 0.25, to = 12.25, by = 0.5)

y <- solve_mcsim(x, mName = mName, infile.name = infile.name,
                 setpoint.name = "setpoint.dat",
                 outfile.name = outfile.name, params = params, vars = vars, time = t,
                 condition = "Agutlument = 10")
pksim(y)
}