Package: aquats 1.2.2

Introduction | Two-Sample Comparison (t-Test and F-Test) | Conceptual Framework | Hypotheses and Variance Assumptions | In-Vignette Data Generation | Visualization Styles | Style A: Publication Boxplot with Jitter | Style B: Faceted / Density-Informed Violin Plot | Style C: Minimalist Point and Mean-CI Error Bars | Model Inspection and Normality Diagnostics | Contingency Analysis and Goodness-of-Fit (Chi-Square Test) | Hypotheses and Effect Sizes | Style A: 100% Stacked Proportion Bar Chart | Style B: Dodged Absolute Count Bar Chart | Model Inspection and Residual Diagnostics | One-Way Analysis of Variance (ANOVA) | Conceptual Framework and Statistical Formulation | Hypotheses and Test Statistics | Style A: Publication Boxplot with Jitter and Mean Marker (Default) | Style B: Grouped Barplot with Standard Error Bars (Mean ± SE) | Style C: Minimalist Point-Range Geometry | Model Inspection and Numerical Summaries | Two-Way Analysis of Variance (ANOVA) | Hypotheses and Variance Partitioning | Style A: Dodged Boxplot with Interaction Letters (Default) | Style B: Faceted Barplot with Standard Error Bars (Mean ± SE) | Style C: Minimalist Point-Range Interaction | Three-Way Analysis of Variance (ANOVA) | Variance Partitioning and Hypotheses | Style A: Faceted Boxplot with Jitter and Means (Default) | Style C: Minimalist Faceted Point-Range Geometry | Analysis of Covariance (ANCOVA) | Homogeneity of Slopes and Adjusted Means | Style A: Single-Panel Parallel Slopes Comparison (Default) | Style B: Faceted Panel View | Multivariate Analysis of Variance (MANOVA) | Hypothesis Testing and Test Statistics | Style A: Faceted Univariate Trait Boxplots (Default) | Style B: Canonical Discriminant Analysis (LDA) Ordination | Parametric & Non-Linear Regression Modeling | Conceptual Framework & Confidence vs. Prediction Bounds | Confidence Interval for the Mean Response | Prediction Interval for Individual Observations | Visualization Styles Across Functional Models | Style A: Allometric Power-Law Model ($W = a \cdot L^b$) with 95% Prediction Interval | Style B: Exponential Growth/Decay ($y = a \cdot e^{kx}$) with 95% Confidence Interval | Style C: Faceted Quadratic Polynomial ($y = \beta_0 + \beta_1 x + \beta_2 x^2$) | Style D: Faceted Cubic Polynomial ($y = \beta_0 + \beta_1 x + \beta_2 x^2 + \beta_3 x^3$) | Model Inspection & Diagnostics | Generalized Linear Models (GLMs) | Poisson and Quasipoisson Regression (Count Dynamics) | Binomial Logistic Regression (Presence / Absence) | Style A: Count Regression Forest Plot (Poisson Model) | Style B: Binary Occurrence Forest Plot (Binomial Model) | Non-metric Multidimensional Scaling (NMDS) | Conceptual Framework and Mathematical Formulation | Stress Evaluation and Quality Criteria | Pre-Ordination Hellinger Transformation | Style A: Community Ordination with 95% Confidence Ellipses | Style B: Community Ordination with Environmental Vector Fitting (envfit) | Permutational Multivariate Analysis of Variance (PERMANOVA) | The Pseudo-$F$ Test Statistic | Statistical Execution and Permutation Testing | Similarity Percentages (SIMPER) Analysis | Average Contribution and Diagnostic Ratios | Style A: Faceted Top Contributing Taxa (Default) | Principal Component Analysis (PCA) Community Biplot | Transformation-Based PCA (tb-PCA) | Style A: Hellinger-Transformed PCA Community Biplot (Default) | Style B: Biplot with Top-Contributing Species Filtered | PCA Correlation Circle for Environmental Parameters | The Unit Circle and $\cos^2$ Metric | Style A: Standard Correlation Circle with $\cos^2$ Gradient (PC1 vs PC2) | Redundancy Analysis (RDA) | Phase 1: Multivariate Multiple Linear Regression | Phase 2: Principal Component Analysis on Fitted Values | Permutation Hypothesis Testing | Style A: Constrained Hellinger RDA Triplot (Default) | Distance-based Redundancy Analysis (db-RDA) | Constrained Regression and Model Permutation | Style A: Bray-Curtis db-RDA Triplot (Default) | Hierarchical Clustering Dendrogram | Agglomerative Linkage Criteria | Style A: Vertical Tree Layout with Cluster Partitioning Line (Default) | Style B: Horizontal Tree Layout | Correlation Heatmaps for Environmental & Morphometric Matrices | Pearson Product-Moment Correlation | Spearman Rank-Order Correlation | Style A: Lower-Triangle Square Heatmap with Coefficients & Asterisks (Default) | Style B: Circle Bubble Heatmap with Significance Asterisks | Integrated Environmental Correlation and Mantel Network Analysis | Mantel Matrix Correlation | Permutation Significance Testing | Style A: Curved Linkage Network Diagram (Default) | Style B: Side-by-Side Correlation Heatmap and Mantel Bars | Ecological Alpha Diversity Indices & Comparative Testing | Shannon-Wiener Diversity Index ($H'$) | Gini-Simpson Index ($1 - D$) | Species Richness Normalizations | Pielou's Equitability Index ($J'$) | Index Calculation and Data Summary | Style A: Single-Factor Diversity Comparison with Kruskal-Wallis Test (Default) | Style B: Two-Factor Factorial Interaction Boxplot with Two-Way ANOVA | Species Accumulation Curves & Sampling Effort Evaluation | The Exact Analytical Expectation (Mao Tau Formulation) | Coleman Rarefaction Formulation | Analytical Variance and Confidence Bounds | Style A: Pooled Whole-Ecosystem Curve with 95% Confidence Band (Default) | Style B: Comparative Multi-Habitat Accumulation Curves | Weighted Arithmetic Water Quality Index (WAWQI) | Unit Weighting Factor ($W_i$) | Quality Rating Scale ($Q_i$) | Overall Index Aggregation and Classification | Calculating Index Scores and Station Summaries | Style A: Status-Filled Bar Chart with Benchmark Bands and 95% CI Whiskers (Default) | Style B: Lollipop Display | Model Inspection and Replicate Data | Heavy Metal Pollution & Ecotoxicological Indices | Contamination Factor ($CF_i$) | Heavy Metal Evaluation Index (HEI) & Contamination Degree ($C_d$) | Pollution Load Index (PLI) | Comprehensive Nemerow Pollution Index ($P_N$) | Heavy Metal Pollution Index (HPI) | Calculating Heavy Metal Indices | Style A: Heavy Metal Pollution Index (HPI) with Critical Threshold (Default) | Style B: Pollution Load Index (PLI) Lollipop Plot | Style C: Degree of Contamination (Cd) | Model Inspection and Replicate Contamination Factors | Descriptive Statistics & Automated Table Summaries | Parametric Estimators of Central Tendency and Dispersion | Non-Parametric Order Statistics | Analytical Execution | Style A: Single-Factor Grouped Summary (Across River Systems) | Style B: Two-Factor Stratified Summary (River x Season Interaction) | Inspection and Formatted Output | Distributional Histograms & Density Curves | Empirical Kernel Density Estimation (KDE) | Theoretical Gaussian Overlay | Central Tendency Reference Lines | Style A: Overall Distribution with Density, Normal Fit & Reference Baselines | Style B: Faceted Distribution Across Habitats | Inspection of Distributional Symmetry | Publication Bar & Lollipop Plots with Grouped Comparisons | Conceptual Framework and Aggregation Mechanics | Frequency Tabulation | Continuous Metric Aggregation | Proportional Stacking (position = "fill") | Style A: Mean Aggregation with Grouped Dodge Layout and Value Labels (Default) | Style B: Proportional 100% Stacked Bar Chart (position = "fill") | Style C: Horizontal Bar Chart for Station Inventories | Style D: Clean Lollipop Plot for Total Catch Aggregations | Style E: Multi-Factor Dodged Lollipop Plot | Inspection of Aggregated Values | Compositional Graphics & Survey Perception Analysis | 3D Depth Pie Charts (plot_pie3d) | Circular Radial Bar Plots (plot_circular_bar) | Hierarchical Nested Donut Charts (plot_donut) | Survey Perception Likert Visualizations (plot_likert) | Ecological Flow and Trophic Visualizations (Sankey Diagram) | Flow Allocation and Stratum Architecture | Style A: Biomass-Weighted Multi-Tier Alluvial | Style B: Unweighted Observation Frequency (Count Flow) | Style C: Two-Tier Catchment-to-Estuary Transition | Customizing and Exporting Diagrams | Temporal Tracking & Multi-Factor Time-Series Analysis | Conceptual Framework & Uncertainty Band Mechanics | Replicate Arithmetic Mean | Standard Error of the Mean (SE Ribbon) | 95% Student's $t$ Confidence Band (CI Ribbon) | Style A: Single-Series Temporal Trajectory with 95% CI Ribbon (Default) | Style B: Two-Factor Comparison with Color-Coded Stations & SE Ribbons | Style C: Three-Factor Factorial Layout (Color + Linetype + Facet) | Summary Table Inspection | Conclusion | Acknowledgements | References | Additional Information & Bug Reporting