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.
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) { # \dontrun{
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)
} # }