new_ode_model: Create new ODE model
In PKPDsim: Tools for Performing Pharmacokinetic-Pharmacodynamic Simulations

new_ode_model

R Documentation

Create new ODE model

Description

Create new ODE model

Usage

new_ode_model(
  model = NULL,
  code = NULL,
  pk_code = NULL,
  dose_code = NULL,
  file = NULL,
  func = NULL,
  state_init = NULL,
  parameters = NULL,
  reparametrization = NULL,
  mixture = NULL,
  units = NULL,
  size = NULL,
  lagtime = NULL,
  obs = list(cmt = 1, scale = 1),
  dose = list(cmt = 1),
  covariates = NULL,
  declare_variables = NULL,
  iiv = NULL,
  iov = NULL,
  development = NULL,
  omega_matrix = NULL,
  ruv = NULL,
  ltbs = NULL,
  misc = NULL,
  cmt_mapping = NULL,
  int_step_size = NULL,
  default_parameters = NULL,
  fixed = NULL,
  cpp_show_code = FALSE,
  package = NULL,
  test_file = NULL,
  install = TRUE,
  folder = NULL,
  lib_location = NULL,
  verbose = FALSE,
  as_is = FALSE,
  nonmem = NULL,
  comments = NULL,
  version = "0.1.0",
  quiet = "",
  definition = NULL
)

Arguments

`model`	model name from model library
`code`	C++ code specifying ODE system
`pk_code`	C++ code called at any event
`dose_code`	C++ code called at dose event only
`file`	file containing C++ code
`func`	R function to be used with deSolve library
`state_init`	vector of state init
`parameters`	list or vector of parameter values
`reparametrization`	list of parameters with definitions that reparametrize the linear PK model to a 1-, 2- o4 3-compartment PK with standardized parametrization.
`mixture`	for mixture models, provide a list of the parameter associated with the mixture and it's possible values and probabilities (of the first value), e.g. 'list(CL = list(value = c(10, 20), probability = 0.3)'.
`units`	list or vector of parameter units
`size`	size of state vector for model. Size will be extracted automatically from supplied code, use this argument to override.
`lagtime`	lag time
`obs`	list with "scale": character string with definition for scale, e.g. "V" or "V*(WT/70)". If NULL, scale defaults to 1., and "cmt" the observation compartment
`dose`	specify default dose compartment, e.g. list(cmt = 1)
`covariates`	specify covariates, either as a character vector or a list. if specified as list, it allows use of timevarying covariates (see 'new_covariate()' function for more info)
`declare_variables`	declare variables
`iiv`	inter-individual variability, can optionally be added to library
`iov`	inter-occasion variability, can optionally be added to library
`development`	Information about the model development population, can optionally be added to library
`omega_matrix`	variance-covariance matrix for inter-individual variability, can optionally be added to library
`ruv`	residual variability, can optionally be added to library
`ltbs`	log-transform both sides. Not used in simulations, only for fitting (sets attribute 'ltbs').
`misc`	a list of miscellaneous model metadata
`cmt_mapping`	list indicating which administration routes apply to which compartments. Example: 'list("oral" = 1, "infusion" = 2)'
`int_step_size`	step size for integrator. Can be pre-specified for model, to override default for 'sim_ode()'
`default_parameters`	population or specific patient values, can optionally be added to library
`fixed`	parameters that should not have iiv added.
`cpp_show_code`	show generated C++ code
`package`	package name when saving as package
`test_file`	optional test file to be included with package
`install`	install package after compilation?
`folder`	base folder name to create package in
`lib_location`	install into folder ('–library' argument)
`verbose`	show more output
`as_is`	use C-code as-is, don't substitute line-endings or shift indices
`nonmem`	add nonmem code as attribute to model object
`comments`	comments for model
`version`	number of library
`quiet`	passed on to 'system2' as setting for stderr and stdout; how to output cmd line output. Default ('""') is R console, NULL or FALSE discards. TRUE captures the output and saves as a file.
`definition`	optional, filename for the JSON file the full definition for the model. The definition file will be stored as 'definition.json' in the resulting package.