pharmr (version 1.4.0)

run_amd: run_amd

Description

Run Automatic Model Development (AMD) tool

Usage

run_amd(
  input,
  results = NULL,
  modeltype = "basic_pk",
  administration = "oral",
  strategy = "default",
  cl_init = NULL,
  vc_init = NULL,
  mat_init = NULL,
  b_init = NULL,
  emax_init = NULL,
  ec50_init = NULL,
  met_init = NULL,
  search_space = NULL,
  lloq_method = NULL,
  lloq_limit = NULL,
  allometric_variable = NULL,
  occasion = NULL,
  path = NULL,
  resume = FALSE,
  strictness = "minimization_successful or (rounding_errors and sigdigs>=0.1)",
  dv_types = NULL,
  mechanistic_covariates = NULL,
  retries_strategy = "all_final",
  seed = NULL,
  parameter_uncertainty_method = NULL,
  ignore_datainfo_fallback = FALSE,
  .E = NULL
)

Value

(AMDResults) Results for the run

Arguments

input

(Model or str or data.frame) Starting model or dataset

results

(ModelfitResults (optional)) Reults of input if input is a model

modeltype

(str) Type of model to build. Valid strings are 'basic_pk', 'pkpd', 'drug_metabolite' and 'tmdd'

administration

(str) Route of administration. Either 'iv', 'oral' or 'ivoral'

strategy

(str) Run algorithm for AMD procedure. Valid options are 'default', 'reevaluation', 'SIR', 'SRI', and 'RSI'.

cl_init

(numeric (optional)) Initial estimate for the population clearance

vc_init

(numeric (optional)) Initial estimate for the central compartment population volume

mat_init

(numeric (optional)) Initial estimate for the mean absorption time (not for iv models)

b_init

(numeric (optional)) Initial estimate for the baseline (PKPD model)

emax_init

(numeric (optional)) Initial estimate for E_max (PKPD model)

ec50_init

(numeric (optional)) Initial estimate for EC_50 (PKPD model)

met_init

(numeric (optional)) Initial estimate for mean equilibration time (PKPD model)

search_space

(str (optional)) MFL for search space for structural and covariate model

lloq_method

(str (optional)) Method for how to remove LOQ data. See transform_blq for vector of available methods

lloq_limit

(numeric (optional)) Lower limit of quantification. If NULL LLOQ column from dataset will be used

allometric_variable

(str or Expr (optional)) Variable to use for allometry. This option is deprecated. Please use ALLOMETRY in the mfl instead.

occasion

(str (optional)) Name of occasion column

path

(str (optional)) Path to run AMD in

resume

(logical) Whether to allow resuming previous run

strictness

(str (optional)) Strictness criteria

dv_types

(list(str=numeric) (optional)) Dictionary of DV types for TMDD models with multiple DVs.

mechanistic_covariates

(array(str or list(str)) (optional)) List of covariates or tuple of covariate and parameter combination to run in a separate proioritized covsearch run. For instance c("WT", ("CRCL", "CL")). The effects are extracted from the search space for covsearch.

retries_strategy

(str) Whether or not to run retries tool. Valid options are 'skip', 'all_final' or 'final'. Default is 'final'.

seed

(numeric (optional)) Random number generator or seed to be used.

parameter_uncertainty_method

(str (optional)) Parameter uncertainty method.

ignore_datainfo_fallback

(logical) Ignore using datainfo to get information not given by the user. Default is FALSE

.E

(list(str=numeric or str) (optional)) EXPERIMENTAL FEATURE. Dictionary of different E-values used in mBIC.

See Also

run_iiv

run_tool

Examples

if (FALSE) {
model <- load_example_model("pheno")
results <- load_example_modelfit_results("pheno")
res <- run_amd(model, results=results)
}