RXR-2598: consolidate model compilation & tests #132
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Move shared model compilations from individual test files to setup.R to reduce redundant compilation during test runs. Models are compiled once at test session startup and reused across test files. Models moved include IOV models, multi-observation models, mixture models, time-varying covariate models, and various library models (3cmt, 2cmt oral, MM kinetics). Conditional compilation (NOT_CRAN) preserved for slower models. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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Pull request overview
This PR consolidates model compilations and reorganizes test files to improve test organization and reduce compilation time during testing. Models that were previously compiled separately in individual test files are now compiled once in setup.R, and tests have been reorganized to follow a test_<function> naming convention.
Changes:
- Models consolidated into
setup.Rfor one-time compilation at test session startup - Tests from multiple files (test_iov.R, test_multi_obs.R, test_mixture_model.R, test_compare_results.R, test_cmt_mapping.R, test_timevar_cov.R, test_t_init.R, test_sim_lagtime.R, test_time_rounding_bug.R) moved into test_sim.R
- Tests from test_bioav_def.R moved into test_new_ode_model.R
- Tests from test_advan_with_auc.R and test_advan_with_covariates.R consolidated into test_advan.R
- New test files created for specific functions (test_new_adherence.R, test_check_mixture_model.R, test_calculate_parameters.R, test_pkpdsim_to_nlmixr.R)
- New R implementation file R/new_adherence.R added with adherence simulation functions
Reviewed changes
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Show a summary per file
| File | Description |
|---|---|
| tests/testthat/setup.R | Centralized model compilation with clear organization and comments |
| tests/testthat/test_sim.R | Consolidated tests from multiple files into describe() blocks |
| tests/testthat/test_new_ode_model.R | Added IOV and bioavailability tests from test_bioav_def.R |
| tests/testthat/test_advan.R | Added AUC and covariate tests from separate files |
| tests/testthat/test_new_adherence.R | New test file for adherence functions |
| tests/testthat/test_check_mixture_model.R | New test file extracted from test_mixture_model.R |
| tests/testthat/test_calculate_parameters.R | New test file for parameter calculation |
| tests/testthat/test_pkpdsim_to_nlmixr.R | New test file for nlmixr conversion |
| R/new_adherence.R | New implementation of adherence simulation functions |
| tests/testthat/test_get_var_y.R | Added seed parameters for reproducibility |
| tests/testthat/test_reparametrization.R | Updated to use models from setup.R |
| tests/testthat/test_parameters_table.R | Updated to use models from setup.R |
| tests/testthat/test_calc_ss_analytic.R | Updated to use models from setup.R |
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mccarthy-m-g
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Jan 20, 2026
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lgtm! Nice clean up 🧹
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| ## there is slight difference in how bolus doses are handled. | ||
| ## Analytical equation is perhaps more consistent, so not testing | ||
| ## simulations at dose times. Should look into later. |
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Maybe add a TODO here?
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test_<function>(some where grouped more by topic).No changes to actual code, just tests.