Package index • hyperion

All functions

ModelComments(): Model comments container with cross-validation
OmegaComment(): Omega parameter comment class
SigmaComment(): Sigma parameter comment class
ThetaComment(): Theta parameter comment class
add_parameter_to_lookup(): Add a parameter definition to a lookup file
apply_lookup(): Apply lookup defaults to a ModelComments object
apply_lookup_defaults(): Apply lookup defaults to a parameter comment
are_models_in_lineage(): Check if two models are in a direct lineage
audit_parameter_info(): Audit parameter information sources
`$`(<hyperion_nonmem_model>): Element access for hyperion_nonmem_model objects
check_dataset(): Checks model dataset
check_model(): Checks mod file for nmtran errors
compute_ci(): Compute confidence interval for parameter estimates
compute_cv(): Compute coefficient of variation (CV%) for random effect parameters
compute_rse(): Compute relative standard error (RSE%) for parameter estimates
copy_model(): Copies model file to new model file
from_config_relative(): Convert a config-relative path to an absolute path.
get_comment(): Get a comment by original NONMEM name
get_comment_type(): Get the comment type from pharos.toml config file
get_data_path(): Get data path
get_eps_shrinkage(): Gets EPS shrinkage metrics from .shk file
get_eta_labels(): Get ETA labels from model comments
get_eta_shrinkage(): Gets ETA shrinkage metrics from .shk file
get_final_estimates(): Gets all final estimates from an ext file or vector of ext files
get_gradients(): Gets gradients of pararmeters during modeling
get_model_ancestors(): Get a model's ancestors
get_model_descendants(): Get a model's descendants
get_model_dir(): Get model directory
get_model_lineage(): Get's model lineage
get_model_metadata(): Get model metadata from metadata JSON file
get_model_name(): Get model name
get_model_parameter_info(): Extract all parameter comments from a model as ModelComments object
get_model_summary() deprecated: Gets model run summary
get_parameter_names(): Get parameter names from a model or ModelComments object
get_parameter_transform(): Get parameterization (transform) for parameters by name
get_parameter_unit(): Get unit for parameters by name
get_parameters(): Gets parameter estimates from model run
get_pharos_config(): Gets the pharos.toml configuration as an R object
get_run_info(): Parses lst file for run details and heuristics
get_run_status(): Determine run status for a model path, run directory, or model object.
get_theta_names(): Get all theta names from ModelComments
init(): Initializes pharos
knit_print(<hyperion_model_metadata>): Knit print method for hyperion_model_metadata objects
knit_print(<hyperion_nonmem_dataset>): Knit print method for hyperion_nonmem_dataset objects
knit_print(<hyperion_nonmem_model>): Knit print method for hyperion_nonmem_model objects (for Quarto/R Markdown)
knit_print(<hyperion_nonmem_summary>): Knit print method for hyperion_nonmem_summary objects (for Quarto/R Markdown)
knit_print(<hyperion_nonmem_summary_not_run>): Knit print method for not-run hyperion_nonmem_summary objects
knit_print(<hyperion_nonmem_summary_running>): Knit print method for running hyperion_nonmem_summary objects
knit_print(<hyperion_nonmem_tree>): Knit print method for hyperion_nonmem_tree objects (for Quarto/R Markdown)
knit_print(<parameter_audit>): knit_print method for parameter_audit objects
list_lookup_parameters(): List all parameters in a lookup file
print(<hyperion_model_metadata>): Print method for hyperion_model_metadata objects
print(<hyperion_nonmem_dataset>): Print method for hyperion_nonmem_dataset objects
print(<hyperion_nonmem_model>): Print method for hyperion_nonmem_model objects
print(<hyperion_nonmem_summary>): Print method for hyperion_nonmem_summary objects
print(<hyperion_nonmem_summary_not_run>): Print method for not-run hyperion_nonmem_summary objects
print(<hyperion_nonmem_summary_running>): Print method for running hyperion_nonmem_summary objects
print(<hyperion_nonmem_tree>): Print Method for Hyperion Tree Objects
print(<parameter_audit>): print method for parameter_audit objects
read_ext_file(): Reads ext file
read_model(): Gets model object
remove_parameter_from_lookup(): Remove a parameter definition from a lookup file
set_metadata_file(): Creates a metadata file for a NONMEM model
str(<hyperion_nonmem_model>): Structure method for hyperion_nonmem_model objects
submit_model_to_sge(): Submits a NONMEM model to SGE for execution
submit_model_to_slurm(): Submits a NONMEM model to SLURM for execution
summary(<hyperion_nonmem_model>): Summary method for hyperion_nonmem_model objects
transform_value(): Back-transform a parameter value to the natural scale
update_metadata_file(): Updates a metadatafile
update_param_info(): Update parameter info in a ModelComments object
use_type1_comments(): Set comment type to type1 in pharos.toml