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v0.1.0: First Official Release — Decision Engine, Classical ANOVA & Mixed Models

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@PALP31 PALP31 released this 22 Aug 18:43
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v0.1.0
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🌱 agriDesignR v0.1.0: First Official Release

Motor Asistido de Decisión, Diagnóstico y Modelos Mixtos para Ciencias Agronómicas y Biológicas

We are excited to announce the initial official release of agriDesignR (v0.1.0)!

agriDesignR is an end-to-end R package designed to bridge the gap between experimental design planning in the field/greenhouse and rigorous statistical modeling for agronomy, plant biotechnology, and experimental biology.

🌟 Key Highlights & Features in v0.1.0

1. 🎯 Pre-Experimental Planning & Decision Engine (plan_experiment())

  • Rigorous Decision Rules: Provides structured decision criteria to choose between DCA (CRD), DBCA (RCBD), Factorial Designs (1, 2, and 3-way), Split-Plot, Split-Split-Plot, Latin Square, and Repeated Measures.
  • Statistical Power & Replications: Automatically calculates the minimum number of blocks/replications required to guarantee residual error degrees of freedom ($df_{\text{error}} \ge 12$).
  • Methodological Safeguards: Explicitly alerts researchers against common pitfalls (e.g., misusing Split-Plot for factorials that can be fully randomized, pseudoreplication, or unneeded blocking in homogeneous chambers).

2. 🗺️ 2D Spatial Layout & Planting Map Generator (generate_layout())

  • Reproducible Randomization: Generates complete planting schedules with Plot_ID, Block, Whole_Plot, Sub_Plot, and spatial coordinates.
  • Phenotyping CSV Templates: Automatically exports ready-to-fill CSV data sheets for direct use during harvest.
  • Publication-Quality 2D Croquis: Plots clear 2D bench croquis identifying every greenhouse table, pot position (Pos 01 to Pos 10), and treatment tag.

3. 📊 Dual Statistical Framework: Classical ANOVA vs. Mixed Models (suggest_model(), fit_experiment())

  • 🏛️ Classical ANOVA (stats::aov() / stats::lm()): Exact F-tests (Type I, II, III Sums of Squares) and standard Tukey HSD multiple comparisons for balanced designs, fixed greenhouse blocks, and standard thesis tables.
  • 🚀 Linear Mixed-Effects Models (lme4::lmer / nlme::lme / glmmTMB): Restricted Maximum Likelihood (REML), Kenward-Roger / Satterthwaite degrees of freedom approximations, and BLUPs for hierarchical split-plots and unbalanced datasets.
  • Descomposition in Simple Effects (agri_posthoc(..., by = ...)): Slices 2-way and 3-way factorial interactions to compare genotypes within each environmental level.

4. 💊 Automated Model Remedies (remedy())

  • Automatic Box-Cox power transformation ($\lambda$).
  • Heteroscedastic variance weighting (nlme::varIdent).
  • Generalized Linear Mixed Models (GLMM Gamma, Negative Binomial, Poisson).

5. 📈 Design Efficiency & Biological Rankings (calc_design_efficiency(), agri_ranking())

  • Cochran & Cox / Kempthorne Relative Efficiency ($RE%$): Quantifies experimental precision gained by blocking and equivalent replications saved.
  • Biological Ranking & Effect Sizes: Computes standardized Cohen's $d$ and percentage gain against control benchmarks.

6. 🎨 Publication Figures & Markdown Reports (plot_publication(), experiment_report())

  • Vector graphics (PDF/PNG 300 DPI) styled for Nature and Crop Science with Compact Letter Display (CLD) Tukey letters and colorblind-safe palettes (Forest, Okabe-Ito).
  • Complete automated doctoral narrative reports written in Markdown.

7. 🖥️ Interactive Web Dashboard GUI (launch_app())

  • Full modern Bootstrap 5 Shiny dashboard featuring 5 interactive modules (Planning, Model Fitting, Diagnostics & Remedies, Publication Figures, and Markdown Report Download).

📦 Installation

# From GitHub
if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")
remotes::install_github("PALP31/agriDesignR")

# Launch the interactive GUI
library(agriDesignR)
launch_app()

👤 Author & Affiliation

  • Paul Lopez (Estudiante del Doctorado en Biotecnología Vegetal | Profesor Universitario de Aplicaciones Estadísticas, Pontificia Universidad Católica de Chile)
  • GitHub: @PALP31
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