{
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  "Title": "Robust Ecological and Fisheries Data Analysis and Visualization",
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  "Authors@R": "c(\nperson(\ngiven = \"Ataher\",\nfamily = \"Ali\",\nemail = \"ataher.cu.ms@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0008-8780-0903\")\n),\nperson(\ngiven = c(\"Mohammed\", \"Shahidul\"),\nfamily = \"Alam\",\nemail = \"alamms@cu.ac.bd\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0003-2740-5908\")\n)\n)",
  "Description": "A comprehensive statistical and visualization toolkit\ntailored for observational data in fisheries science and\naquatic ecology. Provides streamlined workflows for univariate\nand factorial analysis of variance (ANOVA), analysis of\ncovariance (ANCOVA), multivariate analysis of variance\n(MANOVA), permutational multivariate analysis of variance\n(PERMANOVA), similarity percentages (SIMPER), generalized\nlinear models, non-linear morphometric regressions, two-group\nhypothesis testing, and chi-square tests. Features multivariate\nordination methods including non-metric multidimensional\nscaling (NMDS), principal component analysis (PCA), redundancy\nanalysis (RDA), distance-based redundancy analysis (db-RDA),\nand hierarchical cluster dendrograms. Computes alpha diversity\nmetrics, species accumulation curves, water quality index (WQI)\nvalues, heavy metal ecotoxicological contamination indices,\ncorrelation heatmaps, and Mantel test network linkages. Offers\nspecialized environmental visualizations including Sankey\ndiagrams, Likert plots, circular bar charts, and longitudinal\ntime-series with uncertainty ribbons. Methodological\nformulations for multivariate permutation tests follow Anderson\n(2001) <doi:10.1111/j.1442-9993.2001.01070.pp.x>. Ecological\ncommunity dissimilarity transformations follow Legendre and\nGallagher (2001) <doi:10.1007/s004420100716>, and\necotoxicological contamination index models follow Tomlinson et\nal. (1980) <doi:10.1007/BF02414780>.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/Ataher76/aquats,\nhttps://doi.org/10.5281/zenodo.22885025",
  "BugReports": "https://github.com/Ataher76/aquats/issues",
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  "Date/Publication": "2026-10-22 17:35:57 UTC",
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  "_created": "2026-10-22T19:28:49.000Z",
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        "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",
        "Simple Mantel Matrix Correlation",
        "Partial Mantel Correlation Under Environmental Collinearity",
        "Permutation Significance and Multiple-Testing Correction",
        "Style A: Lower-Triangular Tile Network with Significance Stars",
        "Style B: Proportional Circle Network with Partial Mantel and FDR Correction",
        "Style C: Side-by-Side Correlation Heatmap and Faceted 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"
      ],
      "created": "2026-09-21 23:51:56",
      "modified": "2026-10-22 17:35:57",
      "commits": 5
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