Package index • aftsplex

Data-generating process

Helpers for the simulation studies used in the manuscript.

f_true(): True dose-response used by the simulation DGP
build_sigma_u(): Build a measurement-error covariance from marginal variances and a correlation
sigma_u_for_reliability(): Build a measurement-error covariance targeting a given reliability
generate_aft_data(): Generate one Monte Carlo replicate of the AFT-spline-SIMEX scenario

Phase 1 — Measurement-error calibration

Multivariate ME model and the GLS combiner.

fit_me_calibration(): Fit the Phase-1 multivariate ME calibration model
gls_combine(): GLS-combine surrogate columns into a single calibrated exposure
extract_surrogate_cols(): Identify surrogate-measurement columns in a data frame

Phase 2 — AFT-spline fitting and SIMEX

The estimator pipeline.

fit_aft_spline(): Fit an AFT model with a natural-cubic-spline exposure
predict_curve(): Predict the centred dose-response curve at a reference covariate setting
simex_aft_spline(): SIMEX-correct the AFT-spline dose-response curve
summary(<simex_aft_spline>): Summarise a SIMEX-corrected AFT-spline fit
plot(<simex_aft_spline>): Plot a SIMEX-corrected AFT-spline fit

Inference — two-stage bootstrap

two_stage_bootstrap(): Two-stage nonparametric bootstrap for the SIMEX-corrected curve
summary(<two_stage_bootstrap>): Summarise a two-stage bootstrap SIMEX dose-response fit

Evaluation and visualisation

compute_ise(): Integrated squared error of a fitted curve against the truth
plot_curves(): Overlay fitted dose-response curves with the truth and an optional CI
stagill_palette(): StaGILL lab palette for this project
method_colors(): Semantic method-to-colour mapping for Naive / Oracle / SIMEX comparisons