Fix NAFLD/NASH model + Shiny app errors and improve navbar contrast#7
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mingushin3 wants to merge 2 commits into
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Fix NAFLD/NASH model + Shiny app errors and improve navbar contrast#7mingushin3 wants to merge 2 commits into
mingushin3 wants to merge 2 commits into
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…ontrast mrgsolve model (nafld_mrgsolve_model.R): - Remove compartments from CAPTURE block (mrgsolve >=1.0 rejects them; compartment amounts are returned automatically) Shiny app (nafld_shiny_app.R): - Remove compartments from CAPTURE block - TABLE: use TIME instead of lowercase time (collided with C library time()) - Remove apostrophes from an in-model comment that prematurely closed the single-quoted R model string (caused "unexpected symbol") - Hoist valueBox_shiny() above the ui object (UI called it at build time) - Replace deprecated page_navbar bg= with navbar_options(bg=, theme=) - High-contrast navbar: deep-maroon bar, light tab labels, white-pill active tab, white brand title (via bs_add_rules) Verified: both models parse, compile, and simulate; Shiny UI builds with no errors or warnings. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…el for stability req() error (Scenario Comparison / Endpoint Summary tabs): - mrgsolve exports a req() S3 generic that masks shiny::req() (loaded earlier), so req(input$compare_arms) hit mrgsolve's generic -> "no applicable method for req applied to character". Qualified all four server calls as shiny::req(). Model divergence (placebo grew ~10x/week to ~1e+85): - Root cause: disease pools were not initialized at their own steady state (absolute production terms) and the steatosis->Kupffer->TNFa->IR->DNL->fat positive-feedback loop was unbounded. - Re-calibrated BOTH nafld_mrgsolve_model.R and nafld_shiny_app.R to steady-state-consistent indirect-response (turnover) form (kin = KOUT*baseline) with fold-change-normalized, saturable drivers and loop gain << 1 (Dayneka 1993; Jusko & Ko 1994; Woo 2009; Angeli-Ferrell-Sontag 2004; Maldonado 2022). - LIVER_FAT influx split into DNL + adipose-NEFA(weight); Kupffer drive saturable; ALT injury is now a sum (not product) of normalized drivers; collagen made the slowest pool. INS_RES/BODY_WT/ADIPONECTIN already correct (set-point form). - Remapped the Fibrosis-tab sliders/param() to the new sensitivity names (GTGF_HSC, GHSC_COL, GLIP_KUP, GKUP_TGF) and adjusted ranges. - Added nafld_model_design_brief.md documenting the literature basis. Verified (R, mrgsolve 2.0.1): placebo flat to machine precision for all 11 states over 72 wk; perturbation recovers to baseline; no divergence in any arm; drug directions clinically correct (resmetirom -40% liver fat ~ MAESTRO, semaglutide lowers fat/HOMA-IR/weight & raises adiponectin, OCA lowers fibrosis, triple best); fibrosis-tab live-param path works. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Summary
Fixes a chain of errors that prevented the NAFLD/NASH mrgsolve model and Shiny app from running under current package versions (mrgsolve 2.0.1, bslib 0.11.0), and improves navbar readability.
Changes
nafld_mrgsolve_model.R$CAPTUREblock. mrgsolve ≥1.0 rejects compartments in$CAPTURE(their amounts are already returned automatically). Derived$TABLEvariables are kept.nafld_shiny_app.R$CAPTURE(same rule).$TABLE: useTIMEinstead of lowercasetime, which collided with the C librarytime()function and broke C++ compilation.unexpected symbolparse error).valueBox_shiny()above theuiobject, since the UI calls it at build time (was defined afterui, causingcould not find function).page_navbar(bg=)withnavbar_options(bg=, theme=)(bslib ≥0.9.0).bs_add_rules().Verification
uiobject builds and renders to HTML (Sass compiles) with no errors and no warnings;serveris a valid function.🤖 Generated with Claude Code