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The R/ Directory Layout
Files are grouped into four main categories based on their role in the package architecture:
- Foundation and Utilities:
-
00_utils.R: Shared internal helper functions used across various methods. -
postlink-package.R: The core package-level documentation and namespace directives. -
stanmodels.R: The interface for pre-compiled Stan/C++ models used in Bayesian adjustments.
- Phase 1: Adjustment Constructors (The
01_Prefix): These files contain the user-facing constructor functions that define the linked data and specify the adjustment method.
-
01_adjELE.R,01_adjMixture.R,01_adjMixBayes.R: The core constructor functions. -
01_adjELE_methods.R, etc.: The S3 methods (likeprint,summary) specifically for these adjustment objects.
- Phase 2: Wrapper Models (The
02_Prefix): These files contain the user-facing modeling functions that parse formulas and dispatch the appropriate internal routine based on the provided adjustment object.
-
02_plglm.R,02_plcoxph.R,02_plctable.R,02_plsurvreg.R
- Internal Routines for the Adjustment Methods: The internal computational routines are completely decoupled from the wrappers. They are named using a
[method]_[model]syntax.
- ELE:
ele_glm.R,ele_coxph.R, and their associated*_methods.Rfiles. - Mixture:
mixture_glm.R,mixture_coxph.R,mixture_ctable.R,mixture_helpers.R, etc. - Bayesian Mixture:
mixbayes_glm.R,mixbayes_survreg.R,mixbayes_helpers.R, etc.
- Datasets:
-
lifem.R,brfss.R: Roxygen documentation for the included demo datasets.