solve_mcsim: Solve PK Model Through 'GNU MCSim'

In nanhung/rfast99: Global Sensitivity Analysis in Physiologically Based Kinetic Modeling

Solve PK Model Through GNU MCSim

Description

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

Usage

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.

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.

Value

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

Functions

• solve_mcsim(): Numerical analysis for the PK model by GNU MCSim.

• generate_infile(): Generate the GNU MCSim input file.

Examples

## Not run: 
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)

## End(Not run)

nanhung/rfast99 documentation built on Sept. 26, 2022, 5:50 a.m.