Use pharmpy create_basic_pk_model() as default instead of templates#59
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roninsightrx merged 3 commits intomainfrom Apr 3, 2026
Merged
Use pharmpy create_basic_pk_model() as default instead of templates#59roninsightrx merged 3 commits intomainfrom
roninsightrx merged 3 commits intomainfrom
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Switch create_model() to use pharmr::create_basic_pk_model() by default (use_template=FALSE) instead of reading from built-in NONMEM template files. This fixes the issue where create_basic_pk_model() returned JSON instead of NONMEM code by converting to NONMEM format early in the pipeline. Key changes: - Add use_template parameter (default FALSE) to create_model() - Convert generic pharmpy model to NONMEM format immediately after creation - Add parameter name mapping (V→VC, V1→VC, V2→VP1, Q→QP1, CL→CLMM) in set_iiv(), set_initial_estimates(), and find_pk_parameter() - Fix blank line handling in create_pharmpy_model_from_list() - Update all affected tests to use new parameter naming conventions - Tests requiring ADVAN-specific features use use_template=TRUE explicitly Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
CI doesn't have devtools installed — tests are loaded automatically by testthat. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Summary
create_model()to usepharmr::create_basic_pk_model()by default (use_template=FALSE) instead of reading from built-in NONMEM template filesV→VC,Q→QP1,V2→VP1) inset_iiv(),set_initial_estimates(), andfind_pk_parameter()create_basic_pk_model()returning JSON instead of NONMEM code by converting to NONMEM format early in the pipelineTest plan
get_pharmpy_confordering failure unrelated to changes)create_model()produces valid NONMEM control streams for iv, oral, and multi-compartment modelsuse_template=TRUEstill works as before for backward compatibility🤖 Generated with Claude Code