Merge branch 'main' of https://github.com/wardeiling/Master-Thesis

Author: wardeiling

README.md

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+# From Multilevel Modeling to GEE: Revisiting the Within- and Between-Person Debate with Binary Predictors and Outcomes
+
+This repository contains all materials associated with the manuscript:
+**"From Multilevel Modeling to GEE: Revisiting the Within- and Between-Person Debate with Binary Predictors and Outcomes"**
+It includes code, supplementary documentation, and simulation results to ensure full transparency and reproducibility of the study.
+
+## Repository Structure
+
+### `scripts/`
+
+Contains all core scripts for running and analyzing the simulation study.
+
+* **`main-simulation-function-future-simul.R`**
+  Modularized main script that executes the simulation across various design conditions.
+
+* **`results-plotting.R`**
+  Scripts used to produce the plots featured in the Results section of the manuscript.
+
+* **`helper-functions/`** (subfolder with modular components):
+
+  * `data-generation-centeredX.R`: Data-generating mechanisms based on the hybrid model.
+  * `data-generation-mundlak.R`: Data-generating mechanisms based on Mundlak’s contextual model (the model used in the main manuscript).
+  * `model-fitting.R`: Model-fitting procedures for both GLMMs and GEEs.
+  * `result-formatting.R`: Functions to clean and format simulation output.
+
+### `data_exploration/`
+
+Contains interactive and rendered documents to explore the simulation designs.
+
+* **`data-exploration.qmd`**: Allows users to explore all four data-generating mechanisms (DGMs) considered in the study.
+* **`data-exploration.html`**: Rendered HTML version for direct inspection.
+
+### `supplementary_materials/`
+
+Supplementary materials accompanying the manuscript.
+
+* **`supplementary_materials.qmd`**: Quarto document with:
+
+  1. A comparison between the hybrid and Mundlak's contextual model.
+  2. Discussion of boundary/extreme estimates in GEEs and how they were handled.
+* **`supplementary_materials.html`**: Rendered HTML version for direct inspection.
+
+### `simulation_results/`
+
+Contains raw and processed simulation outputs, organized into subfolders corresponding to different simulation runs:
+
+* **`April10_fullsimulation/`**: Part 1, covering DGMs 2–4.
+* **`April17_fullsimulation_contxy/`**: Part 2, covering DGM 1.
+* **`April18_fullsimulation_combined/figures/`**: Final figures used in the manuscript.
+
+Each run folder contains:
+
+* `i.RDS`: Raw output for each design/scenario `i`.
+* `settings.RDS`: Simulation settings used for that batch.
+* `log.txt`: Logs containing warnings and errors during simulation.
+* `summary-results-bias.RDS` & `.csv`: Summary files quantifying bias in the estimates.
+
+---