new_ode_model function

Create new ODE model

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.

Returns

If package name is NULL, returns the model object. Otherwise has no return value.