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simcrc_chile v1.0.0
simcrc_chile
SimCRC model adapted for Chilean CRC screening policy analysis. Implements BayCANN-based Bayesian calibration of the SimCRC microsimulation model to Chilean epidemiological data, cost-effectiveness analysis of CRC screening strategies under Chilean cost and life-table assumptions, and Quarto-based presentation of results.
simcrc_chile v1.0.0
Initial release. Delivers the full calibration pipeline (BayCANN v0.13.0, Adenoma Female), cost-effectiveness analysis with three cost versions reflecting evolving Chilean estimates, Chile vs USA model comparisons, and presentation slides with v2-vs-v3 cost impact analysis. The updated 2026 costs (v3) reveal that higher Chilean procedure prices shift the efficient frontier toward cheaper screening modalities like FIT.
Sub-issues are shown in chronological order of merge with the Dev branch.
Issues related to "release prep", "CHANGELOG update", or "version milestone
tracking" are excluded.
#1 - Add simcrc targets CSV data file
Description:
Added Chilean CRC calibration target data as the foundation for the entire calibration effort. Includes both numerical targets (CRC incidence by age, adenoma prevalence by lesion count) and categorical targets (stage distribution, size distribution by location). These targets drive all subsequent LHS design, ANN training, and posterior validation steps.
Files Changed:
data-raw/true_target_simcrcRvCH.csv,data-raw/true_target_simcrcRvCH.rda,data-raw/true_target_simcrcRvCH.xlsx- Chilean calibration target data in CSV, RDA, and Excel formats
analysis/01_wrangle_targets.R- Script to wrangle and plot target data, comparing Chile vs USA
#5 - Add calibration infrastructure
Description:
Built the complete BayCANN calibration pipeline for the Chilean SimCRC model. This is the core of the project: LHS parameter space design, coverage analysis, ANN emulator training via keras3/TensorFlow, Bayesian posterior sampling with Stan, posterior validation against targets, and best parameter set selection. Multiple calibration runs were executed across v0.12.x and v0.13.0, with iterative prior tightening based on results.
Files Changed:
R/(8 files)- Model input functions, calibration functions, BayCANN setup, calibration targets, and validation functions
analysis/01_calibration_setup.Rthroughanalysis/20_SimCRC_calibration_all.R- Numbered pipeline scripts covering the full calibration workflow
outputs/BayCANN_versions/Chile/andoutputs/BayCANN_versions/USA/- Versioned calibration outputs across multiple runs (v0.12.x, v0.13.0)
#9 - Calibration SimCRC v0.12.1
Description:
Initial calibration runs using SimCRC v0.12.1, establishing the baseline Chilean calibration. Included iterative prior adjustments, Stan sampler diagnostics, and chain selection filtering. Results from these runs informed the prior tightening for the subsequent v0.13.0 calibration.
Files Changed:
outputs/BayCANN_versions/Chile/Adenoma/F/v0.12.1/- Multiple calibration run outputs with priors, posteriors, and validation plots
#11 - Implement screening
Description:
Implemented cost-effectiveness analysis for CRC screening strategies in Chile. Includes strategy definitions, cost inputs (screening and CRC care), life tables, utility weights, and ICER computation. Both single-thread and parallel versions of the CEA script were developed. The ceacrc and dampack packages drive the CEA computations and frontier plotting.
Files Changed:
analysis/cea_analysis_chile.R,analysis/cea_analysis_chile_parallel.R- CEA scripts evaluating all screening strategies and FIT-only subsets
data-raw/cea_inputs/- Screening costs (v1, v2), CRC care costs, utility weights, strategy definitions
ce_results/- ICER tables, CE frontier plots, process logs, and model run data
#18 - Add updated Chilean treatment costs for CEA
Description:
Updated screening costs to 2026 Chilean values (v3). FIT increased 51%, colonoscopies 49%, and polypectomy/complications nearly tripled (+196%). The higher costs shift the efficient frontier: NoScreening and FIT re-enter the non-dominated set, demonstrating that cheaper screening modalities become more competitive under realistic Chilean pricing. Added side-by-side v2 vs v3 comparison slides for presentation.
Files Changed:
data-raw/cea_inputs/screen_costs_v3.csv- New cost input file with 2026 Chilean screening costs
ce_results/df_icer_*_v2.csv,ce_results/plot_ce_*_v2.svg- Baseline v2 CEA outputs preserved for comparison
ce_results/df_icer_*.csv,ce_results/plot_ce_*.svg- Updated v3 CEA results showing shifted frontier
SimCRC slides/calibration_results_Adenoma_F_v0.13.0.qmd- Added cost comparison table and 2x2 v2-vs-v3 CEA comparison slides
Number of total issues resolved in simcrc_chile v1.0.0: 5 issues.
Full Changelog: v0.0.0...v1.0.0