M17 analysis code
=================

This archive accompanies the manuscript:
"Pleiotropic effects of Rht-B1p, Ppd-D1b and Vrn-B1 on agronomic traits in spring wheat: a multi-environment, multivariate analysis".

Contents
--------
- run_M17_pipeline.R: top-level R entry point.
- R/: data preparation, exploratory analysis, mixed models, interactions, multivariate analysis, GGE, ICC, diagnostics, and output compilation.
- python/: Python multivariate-analysis entry points and core functions.
- generate_html_report.py and report_tools/: optional report generation.

Data and outputs
----------------
The analysis-ready dataset is supplied separately as Additional file 4. Compiled environment-specific and pooled statistical results are supplied as Additional files 2 and 3.

Reproducibility note
--------------------
The submitted analysis package does not include a pinned R/Python environment lockfile. Software and package requirements are described in the Methods section of the manuscript. Paths and input locations may need to be adjusted before execution in a new environment.
