new_ode_model {PKPDsim}

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.

Value

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