Changelog

Source: NEWS.md

hyperion 0.3.2

New features

• Added get_model_metadata() to retrieve model metadata (description, tags, and based_on) directly from a model object.
• Updated documentation for model metadata retrieval and NONMEM comment parsing formats.

hyperion 0.3.1

New features

• updated pharos dependency. When submitting a previously run model, the output directory will be deleted before submission to the grid.
• if NMTRAN is available on head nodes/where models are submitted to the grid from, check_model will be run before submission.

Bug fixes

• fixed issue with error message showing when ext/grd files were attempted to be read for summary(mod) for a running model before ext/grd files existed

hyperion 0.3.0

New Features

Running Model Status Detection

• get_run_status() now returns "running" in addition to "run" and "not_run". Detects active NONMEM execution by checking whether the .ext file contains final estimates.

Summary Support for All Model States

• summary() on NONMEM models now produces distinct output for three states:
  • Completed ("run"): Full parameter table, heuristics, OFV (unchanged).
  • Running ("running"): Recent iterations and gradients from .ext/.grd files. New n_iterations parameter controls how many to show (default 10).
  • Not run ("not_run"): Model metadata (problem statement, dataset path) with submission hints.
• Console and R Markdown/Quarto rendering for running and not-run summaries via print() and knit_print() S3 methods.

New Exported Function: from_config_relative()

• Resolves config-relative paths (stored relative to pharos.toml directory) to absolute paths.

get_model_dir() Gains absolute Parameter

• get_model_dir(mod, absolute = TRUE) returns the absolute path instead of the config-relative path.

hyperion 0.2.0

New Features

Parameter Comment System

• Add a structured parameter metadata system built on S7 classes:
  • ThetaComment, OmegaComment, SigmaComment store per-parameter fields like name, display, description, unit, parameterization, and associated_theta (OMEGA only).
  • ModelComments is a container for all parameters and validates cross-links (e.g., OMEGA associated_theta names).
• New entry point get_model_parameter_info() reads comments from a model or run output and returns a ModelComments object for inspection and reporting.
  • Lookup enrichment: apply_lookup() / apply_lookup_defaults() fill missing fields from a TOML lookup file and track provenance.
  • Update helpers: update_param_info() edits names/display/description/unit/ parameterization with source tracking.
  • Audit helpers: audit_parameter_info() reports where each field came from (model, lookup, or default).

Comment Parsing Modes

• Support for two comment parsing modes controlled via pharos.toml:
  • type1: Structured comment format with explicit field delimiters. Set type = "type1" in the [nonmem.comments] section of pharos.toml.
  • raw (default): Flexible parsing from raw comment text when no type is specified or type is set to any other value.
• New use_type1_comments() helper to configure pharos.toml for type1 comment parsing.
• Query helpers for reporting and labeling:
  • get_parameter_names() returns a NONMEM→user name/display mapping.
  • get_parameter_transform() and get_parameter_unit() retrieve per-parameter transforms/units.
  • get_theta_names() and get_eta_labels() generate labels for tables/plots.
• Add parameter transform calculations for post-processing estimates:
  • compute_cv() and compute_rse() compute CV% and RSE% with transform-aware formulas.
  • compute_ci() returns confidence intervals (with back-transform where appropriate).
  • transform_value() back-transforms estimates to the natural scale.
  • All functions support vector inputs with strict length checks and length-1 recycling.
• Add model lineage helpers and expanded model summary/tree output.
• Expand NONMEM example data bundled with the package.
• Refresh documentation, man pages, and vignettes to cover new APIs and examples.

Model Utilities

• New model accessor functions:
  • get_model_name() - Get the model name (filename without extension)
  • get_model_dir() - Get the model directory path (relative to pharos.toml)
  • get_data_path() - Get the dataset path from the model
• check_dataset() now automatically derives the model directory from the model_source attribute, removing the need for the model_dir argument.

Breaking Changes

• get_model_summary() has been removed; use summary(mod).
• Parameter data frame column renamed: value is now estimate.
• Test data relocated from vignettes/test_data/ to inst/extdata/.
• check_dataset() no longer accepts a model_dir argument; the directory is now derived automatically from the model’s model_source attribute.

Dependencies

• Added S7 to Imports for parameter comment classes.
• Added fs to Imports for path manipulation.
• Added testthat (>= 3.3.2) to Suggests for snapshot testing.
• Moved tomledit from Suggests to Imports.