Transforms mod #36
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Transforms mod #36
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…es. get_model_summary -> summary(mod)
update hyperion_nonmem_model generics and cleaned up token/token_rang…
mduncans
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Jan 28, 2026
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PR Review: Transforms Mod (v0.2.0)
Summary
This PR introduces a comprehensive parameter comment and metadata system for NONMEM models
What This PR Does
1. Parameter Comment System (S7 Classes)
Introduces a structured metadata system built on S7 classes:
ThetaComment,OmegaComment,SigmaComment: Per-parameter containers storingname,display,description,unit(THETA/SIGMA),parameterization, andassociated_theta(OMEGA only)ModelComments: Aggregate container that validates cross-references (e.g., OMEGAassociated_thetanames must exist in theta)- Source tracking: Each field tracks its provenance (model file, lookup file, user-supplied, or default)
2. Comment Parsing Infrastructure
Two parsing modes controlled via pharos.toml:
- type1 mode: pharos supported type1 comments
- raw mode (default): Flexible parsing from free-form comment text
Entry point is get_model_parameter_info() which returns a ModelComments object.
3. TOML Lookup Enrichment
apply_lookup()/apply_lookup_defaults()fill missing fields of a ModelComments object from external TOML file- Case-insensitive matching by parameter name or NONMEM name
- Provenance tracking records which lookup file provided each value
4. Pharos Parameter Transform Calculations
New functions in src/rust/nonmem/src/output_files/transforms.rs:
compute_cv(): Coefficient of variation with transform-aware formulascompute_rse(): Relative standard error percentagecompute_ci(): Confidence intervals with optional back-transformationtransform_value(): Back-transform estimates to natural scale
All support vectorized inputs with length-1 recycling semantics.
5. Query Helpers
get_parameter_names(): NONMEM → user name/display mappingget_parameter_transform()/get_parameter_unit(): Per-parameter metadata retrievalget_theta_names()/get_eta_labels(): Label generation for tables/plots
6. Model Method Improvements
summary.hyperion_nonmem_model()added as S3 methodstr.hyperion_nonmem_model()hides verbose token fields$and[[accessors prevent direct access to internal token fields- Improved print formatting with
build_model_display_parts()refactor
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