{
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  "Package": "nexus",
  "Title": "Sourcing Archaeological Materials by Chemical Composition",
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  "Authors@R": "c(\nperson(\"Nicolas\", \"Frerebeau\", , \"nicolas.frerebeau@u-bordeaux-montaigne.fr\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-5759-4944\")),\nperson(\"Anne\", \"Philippe\", , \"anne.philippe@univ-nantes.fr\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-5331-5087\")),\nperson(\"Brice\", \"Lebrun\", role = \"art\",\ncomment = c(ORCID = \"0000-0001-7503-8685\", \"Logo designer\")),\nperson(\"Université Bordeaux Montaigne\", role = \"fnd\",\ncomment = c(ROR = \"03pbgwk21\")),\nperson(\"CNRS\", role = \"fnd\",\ncomment = c(ROR = \"02feahw73\"))\n)",
  "Maintainer": "Nicolas Frerebeau\n<nicolas.frerebeau@u-bordeaux-montaigne.fr>",
  "Description": "Exploration and analysis of compositional data in the\nframework of Aitchison (1986, ISBN: 978-94-010-8324-9). This\npackage provides tools for chemical fingerprinting and source\ntracking of ancient materials.",
  "License": "GPL (>= 3)",
  "URL": "https://codeberg.org/tesselle/nexus,\nhttps://packages.tesselle.org/nexus/,\nhttps://tesselle.r-universe.dev/nexus",
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  "Repository": "https://tesselle.r-universe.dev",
  "Date/Publication": "2026-05-04 12:19:04 UTC",
  "RemoteUrl": "https://codeberg.org/tesselle/nexus",
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  "NeedsCompilation": "no",
  "Packaged": {
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    "User": "root"
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  "Author": "Nicolas Frerebeau [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-5759-4944>),\nAnne Philippe [aut] (ORCID: <https://orcid.org/0000-0002-5331-5087>),\nBrice Lebrun [art] (ORCID: <https://orcid.org/0000-0001-7503-8685>,\nLogo designer),\nUniversité Bordeaux Montaigne [fnd] (ROR: <https://ror.org/03pbgwk21>),\nCNRS [fnd] (ROR: <https://ror.org/02feahw73>)",
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    "archaeological-science",
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    "%power%",
    "aggregate",
    "all_assigned",
    "any_assigned",
    "as_amounts",
    "as_composition",
    "as_graph",
    "barplot",
    "boxplot",
    "closure",
    "color",
    "condense",
    "covariance",
    "describe",
    "detect_outlier",
    "dist",
    "group",
    "group_factor",
    "group_indices",
    "group_levels",
    "group_n",
    "group_names",
    "group_rows",
    "group_size",
    "group_split",
    "group_subset",
    "hist",
    "is_assigned",
    "is_composition",
    "is_element_major",
    "is_element_minor",
    "is_element_trace",
    "is_grouped",
    "is_logratio",
    "is_outlier",
    "is_oxide",
    "labels",
    "mahalanobis",
    "margin",
    "mean",
    "mix",
    "pairs",
    "palette_color_continuous",
    "palette_color_discrete",
    "palette_color_picker",
    "palette_line",
    "palette_shape",
    "palette_size_diverging",
    "palette_size_sequential",
    "pca",
    "perturbation",
    "pip",
    "powering",
    "quantile",
    "rbind2",
    "remove_NA",
    "remove_zero",
    "replace_NA",
    "replace_zero",
    "scalar",
    "scale",
    "split",
    "t",
    "totals",
    "totals<-",
    "transform_alr",
    "transform_clr",
    "transform_ilr",
    "transform_inverse",
    "transform_lr",
    "transform_plr",
    "ungroup",
    "univariate_ilr",
    "variance",
    "variance_total",
    "variation",
    "weights"
  ],
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      "name": "arctic",
      "title": "Arctic Lake",
      "object": "arctic",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sand",
        "silt",
        "clay",
        "depth"
      ],
      "rows": 39,
      "table": true,
      "tojson": true
    },
    {
      "name": "boxite",
      "title": "Boxite Mineralogy",
      "object": "boxite",
      "class": [
        "data.frame"
      ],
      "fields": [
        "A",
        "B",
        "C",
        "D",
        "E",
        "depth"
      ],
      "rows": 25,
      "table": true,
      "tojson": true
    },
    {
      "name": "coxite",
      "title": "Coxite Mineralogy",
      "object": "coxite",
      "class": [
        "data.frame"
      ],
      "fields": [
        "A",
        "B",
        "C",
        "D",
        "E",
        "depth",
        "porosity"
      ],
      "rows": 25,
      "table": true,
      "tojson": true
    },
    {
      "name": "hongite",
      "title": "Hongite Mineralogy",
      "object": "hongite",
      "class": [
        "data.frame"
      ],
      "fields": [
        "A",
        "B",
        "C",
        "D",
        "E"
      ],
      "rows": 25,
      "table": true,
      "tojson": true
    },
    {
      "name": "kongite",
      "title": "Kongite Mineralogy",
      "object": "kongite",
      "class": [
        "data.frame"
      ],
      "fields": [
        "A",
        "B",
        "C",
        "D",
        "E"
      ],
      "rows": 25,
      "table": true,
      "tojson": true
    },
    {
      "name": "lava",
      "title": "Skye Lavas Compositions",
      "object": "lava",
      "class": [
        "data.frame"
      ],
      "fields": [
        "A",
        "F",
        "M"
      ],
      "rows": 23,
      "table": true,
      "tojson": true
    },
    {
      "name": "predator",
      "title": "Predator-Prey Compositions",
      "object": "predator",
      "class": [
        "data.frame"
      ],
      "fields": [
        "P",
        "Q",
        "R"
      ],
      "rows": 25,
      "table": true,
      "tojson": true
    },
    {
      "name": "slides",
      "title": "Thin Sections Compositions",
      "object": "slides",
      "class": [
        "data.frame"
      ],
      "fields": [
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        "slide",
        "quartz",
        "microcline",
        "plagioclass",
        "biotite",
        "muscovite",
        "opaques",
        "nonopaques"
      ],
      "rows": 25,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "aggregate",
      "title": "Compute Summary Statistics of Data Subsets",
      "concept": [
        "statistics"
      ],
      "topics": [
        "aggregate",
        "aggregate,CompositionMatrix-method",
        "aggregate,GroupedComposition-method"
      ]
    },
    {
      "page": "arctic",
      "title": "Arctic Lake",
      "concept": [
        "datasets"
      ],
      "topics": [
        "arctic"
      ]
    },
    {
      "page": "arithmetic",
      "title": "Operations in the Simplex",
      "concept": [
        "operations in the simplex"
      ],
      "topics": [
        "%perturbe%",
        "%perturbe%,CompositionMatrix,CompositionMatrix-method",
        "%power%",
        "%power%,CompositionMatrix,numeric-method",
        "%power%,numeric,CompositionMatrix-method",
        "arithmetic",
        "`%perturbe%`,CompositionMatrix,CompositionMatrix-method",
        "`%perturbe%`-method",
        "`%power%`,CompositionMatrix,numeric-method",
        "`%power%`,numeric,CompositionMatrix-method",
        "`%power%`-method"
      ]
    },
    {
      "page": "as_amounts",
      "title": "Coerce to Amounts",
      "concept": [
        "compositional data tools"
      ],
      "topics": [
        "as_amounts",
        "as_amounts,CompositionMatrix-method",
        "as_amounts-method"
      ]
    },
    {
      "page": "as_composition",
      "title": "Coerce to a Closed Compositional Matrix",
      "concept": [
        "compositional data tools"
      ],
      "topics": [
        "as_composition",
        "as_composition,data.frame-method",
        "as_composition,matrix-method",
        "as_composition,numeric-method",
        "as_composition-method"
      ]
    },
    {
      "page": "as_graph",
      "title": "Graph of Log-ratios",
      "concept": [
        "plot methods"
      ],
      "topics": [
        "as_graph",
        "as_graph,ALR-method",
        "as_graph,ILR-method",
        "as_graph,LR-method",
        "as_graph-method"
      ]
    },
    {
      "page": "as.data.frame",
      "title": "Coerce to a Data Frame",
      "concept": [
        "mutators"
      ],
      "topics": [
        "as.data.frame",
        "as.data.frame,CompositionMatrix-method",
        "as.data.frame,LogRatio-method",
        "as.data.frame,OutlierIndex-method"
      ]
    },
    {
      "page": "barplot",
      "title": "Barplot of Compositional Data",
      "concept": [
        "plot methods"
      ],
      "topics": [
        "barplot",
        "barplot,CompositionMatrix-method"
      ]
    },
    {
      "page": "bind",
      "title": "Combine Two Composition Matrices",
      "concept": [
        "subsetting methods"
      ],
      "topics": [
        "bind",
        "rbind2,CompositionMatrix,CompositionMatrix-method",
        "rbind2,GroupedComposition,GroupedComposition-method"
      ]
    },
    {
      "page": "boxite",
      "title": "Boxite Mineralogy",
      "concept": [
        "datasets"
      ],
      "topics": [
        "boxite"
      ]
    },
    {
      "page": "boxplot",
      "title": "Boxplot of Log-Ratios",
      "concept": [
        "plot methods"
      ],
      "topics": [
        "boxplot",
        "boxplot,GroupedLogRatio-method",
        "boxplot,LogRatio-method"
      ]
    },
    {
      "page": "chemistry",
      "title": "Chemical Elements and Oxides",
      "concept": [
        "tools"
      ],
      "topics": [
        "chemistry",
        "is_element_major",
        "is_element_major,CompositionMatrix-method",
        "is_element_major-method",
        "is_element_minor",
        "is_element_minor,CompositionMatrix-method",
        "is_element_minor-method",
        "is_element_trace",
        "is_element_trace,CompositionMatrix-method",
        "is_element_trace-method",
        "is_oxide",
        "is_oxide,character-method",
        "is_oxide,CompositionMatrix-method",
        "is_oxide-method"
      ]
    },
    {
      "page": "closure",
      "title": "Closure Operation",
      "concept": [
        "operations in the simplex"
      ],
      "topics": [
        "closure",
        "closure,matrix-method",
        "closure,numeric-method",
        "closure-method"
      ]
    },
    {
      "page": "condense",
      "title": "Compositional Mean of Data Subsets",
      "concept": [
        "statistics"
      ],
      "topics": [
        "condense",
        "condense,CompositionMatrix-method",
        "condense,GroupedComposition-method",
        "condense-method"
      ]
    },
    {
      "page": "covariance",
      "title": "Covariance Matrix",
      "concept": [
        "statistics"
      ],
      "topics": [
        "covariance",
        "covariance,ALR-method",
        "covariance,CLR-method",
        "covariance,CompositionMatrix-method",
        "covariance-method"
      ]
    },
    {
      "page": "coxite",
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      "concept": [
        "datasets"
      ],
      "topics": [
        "coxite"
      ]
    },
    {
      "page": "describe",
      "title": "Data Description",
      "concept": [
        "data summaries"
      ],
      "topics": [
        "describe",
        "describe,CompositionMatrix-method",
        "describe,GroupedComposition-method"
      ]
    },
    {
      "page": "detect_outlier",
      "title": "Outlier Detection",
      "concept": [
        "outlier detection methods"
      ],
      "topics": [
        "detect_outlier",
        "detect_outlier,CompositionMatrix,CompositionMatrix-method",
        "detect_outlier,CompositionMatrix,missing-method",
        "detect_outlier-method",
        "is_outlier",
        "is_outlier,OutlierIndex-method",
        "is_outlier-method"
      ]
    },
    {
      "page": "dist",
      "title": "Distances",
      "concept": [
        "statistics"
      ],
      "topics": [
        "dist",
        "dist,CompositionMatrix-method"
      ]
    },
    {
      "page": "group",
      "title": "Group by One or More Variables",
      "concept": [
        "grouping methods"
      ],
      "topics": [
        "group",
        "group,CompositionMatrix-method",
        "group,GroupedComposition-method",
        "group-method",
        "ungroup",
        "ungroup,GroupedALR-method",
        "ungroup,GroupedCLR-method",
        "ungroup,GroupedComposition-method",
        "ungroup,GroupedILR-method",
        "ungroup,GroupedLR-method",
        "ungroup,GroupedPLR-method"
      ]
    },
    {
      "page": "group_names",
      "title": "Grouping Metadata",
      "concept": [
        "grouping methods"
      ],
      "topics": [
        "group_factor",
        "group_factor,ReferenceGroups-method",
        "group_factor-method",
        "group_indices",
        "group_indices,ReferenceGroups-method",
        "group_indices-method",
        "group_levels",
        "group_levels,ReferenceGroups-method",
        "group_levels-method",
        "group_n",
        "group_n,ReferenceGroups-method",
        "group_n-method",
        "group_names",
        "group_names,ReferenceGroups-method",
        "group_names-method",
        "group_rows",
        "group_rows,ReferenceGroups-method",
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