solve_mcsim | R Documentation |
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 )
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 |
q.arg |
a list of shape parameters in the sampling distribution ( |
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. |
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
.
The output result is the 4-dimension array with c(model evaluations, replications, time-points, output variables).
solve_mcsim()
: Numerical analysis for the PK model by GNU MCSim.
generate_infile()
: Generate the GNU MCSim input file.
## 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)
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