run_amd {pharmr} | R Documentation |
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
)
Arguments
input |
(Model or str) Read model object/Path to a 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'. Default is 'default' |
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 |
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 |
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 |
Value
(Model) Reference to the same model object
See Also
run_iiv
run_tool
Examples
## Not run:
model <- load_example_model("pheno")
results <- load_example_modelfit_results("pheno")
run_amd(model, results=results)
## End(Not run)