Run simulations

Run simulations

Usage

run_sim(
  fit = NULL,
  data = NULL,
  model = NULL,
  id = irxutils::get_random_id("sim_"),
  force = FALSE,
  tool = c("auto", "nonmem", "nlmixr2"),
  n_iterations = 1,
  variables = NULL,
  add_pk_variables = FALSE,
  output_file = "simtab",
  update_table = TRUE,
  seed = 12345,
  verbose = TRUE
)

Arguments

fit

a Pharmpy modelfit object.

data

a NONMEM-format data.frame to use as the simulation dataset. Typically the output of create_sim_dataset(). If NULL, the dataset attached to model is used as-is.

model

either a Pharmpy model object, or a filename (for a model with NONMEM model code). If the latter, run_sim() will attempt to load the model into Pharmpy first.

id

run id, e.g. run1. This will be the folder in which the NONMEM model is run. If no folder is specified, it will create a folder run1 in the current working directory, and will increment the run number for each subsequent run.

force

if run folder (id) exists, should existing results be removed before rerunning NONMEM? Default FALSE.

tool

the tool to run the model in, either nonmem, or nlmixr.

n_iterations

number of iterations of the entire simulation to perform. The dataset for the simulation will stay the same between each iterations.

variables

vector of variables to output. If NULL, will output default variables c("ID", "TIME", "DV", "EVID", "PRED") as well as all variables declared in the NONMEM code.

add_pk_variables

calculate basic PK variables: CMAX_OBS, TMAX_OBS, CMIN_OBS, and (when CL is in the output table) AUC_SS. AUC_SS is derived as the last dose in the simulation dataset divided by CL.

output_file

TODO

update_table

should any existing $TABLE records be removed, and a new simtab be created? This is default. If FALSE, it will leave $TABLEs as specifed in the model. However, in the return object, only the first table is returned back. If FALSE, the add_pk_variables argument will be ignored.

seed

TODO

verbose

verbose output?

Value

data.frame with simulation results