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  "Description": "Utility functions for interacting with the 'COMPADRE' and\n'COMADRE' databases of matrix population models. Described in\nJones et al. (2021) <doi:10.1101/2021.04.26.441330>.",
  "License": "GPL-3",
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  "Date/Publication": "2026-05-03 16:28:16 UTC",
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  "Author": "Patrick Barks [aut] (ORCID: <https://orcid.org/0000-0002-5947-8151>),\nDanny Buss [aut],\nRoberto Salguero-Gomez [aut] (ORCID:\n<https://orcid.org/0000-0002-6085-4433>),\nIain Stott [aut] (ORCID: <https://orcid.org/0000-0003-2724-7436>),\nWilliam K. Petry [aut] (ORCID: <https://orcid.org/0000-0002-5230-5987>),\nTamora James [aut] (ORCID: <https://orcid.org/0000-0003-1363-4742>),\nOwen Jones [aut, cre] (ORCID: <https://orcid.org/0000-0001-5720-4686>),\nJulia Jones [aut] (ORCID: <https://orcid.org/0000-0001-9223-1778>),\nGesa Römer [aut] (ORCID: <https://orcid.org/0000-0002-4859-5870>),\nSam Levin [aut] (ORCID: <https://orcid.org/0000-0002-3289-9925>)",
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    "cdb_build_cdb",
    "cdb_check_species",
    "cdb_collapse",
    "cdb_compare",
    "cdb_export_matlab",
    "cdb_fetch",
    "cdb_flag",
    "cdb_flatten",
    "cdb_id",
    "cdb_id_stages",
    "cdb_id_studies",
    "cdb_mean_matF",
    "cdb_metadata",
    "cdb_rbind",
    "cdb_unflatten",
    "cdb_unnest",
    "colnames",
    "CompadreData",
    "DateCreated",
    "mat_elementwise_apply",
    "mat_mean",
    "mat_median",
    "mat_sd",
    "mat_to_string",
    "matA",
    "matC",
    "matF",
    "matrixClass",
    "MatrixClassAuthor",
    "MatrixClassNumber",
    "MatrixClassOrganized",
    "matU",
    "mpm_elementwise_apply",
    "mpm_first_active",
    "mpm_has_active",
    "mpm_has_dorm",
    "mpm_has_prop",
    "mpm_mean",
    "mpm_median",
    "mpm_sd",
    "NumberAcceptedSpecies",
    "NumberMatrices",
    "NumberStudies",
    "string_to_mat",
    "string_to_vec",
    "vec_to_string",
    "Version",
    "VersionData"
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    {
      "name": "Comadre",
      "title": "Subsamples of the COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database for testing and examples",
      "object": "Comadre",
      "class": [
        "CompadreDB"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "Compadre",
      "title": "Subsamples of the COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database for testing and examples",
      "object": "Compadre",
      "class": [
        "CompadreDB"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "CompadreLegacy",
      "title": "Subsample of a legacy version of the COMPADRE Plant Matrix Database for testing and examples",
      "object": "CompadreLegacy",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "as_cdb",
      "title": "Convert legacy COM(P)ADRE database object to CompadreDB",
      "topics": [
        "as_cdb"
      ]
    },
    {
      "page": "cdb_build_cdb",
      "title": "Create a CompadreDB object from user-specified data",
      "concept": [
        "data acquisition"
      ],
      "topics": [
        "cdb_build_cdb"
      ]
    },
    {
      "page": "cdb_check_species",
      "title": "Check whether a COM(P)ADRE database contains one or more species of interest",
      "concept": [
        "data checking"
      ],
      "topics": [
        "cdb_check_species"
      ]
    },
    {
      "page": "cdb_collapse",
      "title": "Collapse a COM(P)ADRE database by averaging matrices over levels of one or more grouping variables",
      "concept": [
        "data checking"
      ],
      "topics": [
        "cdb_collapse"
      ]
    },
    {
      "page": "cdb_compare",
      "title": "Compare two versions or subsets of a COM(P)ADRE database",
      "concept": [
        "data checking"
      ],
      "topics": [
        "cdb_compare"
      ]
    },
    {
      "page": "cdb_export_matlab",
      "title": "Export a COM(P)ADRE database to a Matlab-friendly flat text file",
      "concept": [
        "data management"
      ],
      "topics": [
        "cdb_export_matlab"
      ]
    },
    {
      "page": "cdb_fetch",
      "title": "Fetch the COM(P)ADRE database from compadre-db.org or a local file",
      "concept": [
        "data acquisition"
      ],
      "topics": [
        "cdb_fetch"
      ]
    },
    {
      "page": "cdb_flag",
      "title": "Flag potential issues in matrices of a COM(P)ADRE database",
      "concept": [
        "data checking"
      ],
      "topics": [
        "cdb_flag"
      ]
    },
    {
      "page": "cdb_flatten",
      "title": "Convert a COM(P)ADRE database to a flat data frame with matrices and vectors stored in string representation",
      "concept": [
        "data management"
      ],
      "topics": [
        "cdb_flatten"
      ]
    },
    {
      "page": "cdb_id",
      "title": "Create integer identifiers for a COM(P)ADRE database corresponding to unique combinations of a given set of columns",
      "concept": [
        "data management"
      ],
      "topics": [
        "cdb_id"
      ]
    },
    {
      "page": "cdb_id_stages",
      "title": "Create integer identifiers for a COM(P)ADRE database corresponding to unique combinations of species and matrix stage class definitions",
      "concept": [
        "data management"
      ],
      "topics": [
        "cdb_id_stages"
      ]
    },
    {
      "page": "cdb_id_studies",
      "title": "Create a vector of unique study identifiers from a COM(P)ADRE database",
      "concept": [
        "data management"
      ],
      "topics": [
        "cdb_id_studies"
      ]
    },
    {
      "page": "cdb_mean_matF",
      "title": "Calculate a population-specific mean fecundity matrix for each set of matrices in a COM(P)ADRE database",
      "concept": [
        "data management"
      ],
      "topics": [
        "cdb_mean_matF"
      ]
    },
    {
      "page": "cdb_metadata",
      "title": "Extract metadata from a COM(P)ADRE database",
      "concept": [
        "data acquisition"
      ],
      "topics": [
        "cdb_metadata"
      ]
    },
    {
      "page": "cdb_rbind",
      "title": "Merge COM(P)ADRE databases via row-bind",
      "concept": [
        "data management"
      ],
      "topics": [
        "cdb_rbind"
      ]
    },
    {
      "page": "cdb_unflatten",
      "title": "Reconstitute a flattened COM(P)ADRE database (created by cdb_flatten) as a CompadreDB object",
      "concept": [
        "data management"
      ],
      "topics": [
        "cdb_unflatten"
      ]
    },
    {
      "page": "cdb_unnest",
      "title": "Unnest a COM(P)ADRE database by spreading the components of CompadreMat into separate list-columns",
      "concept": [
        "data management"
      ],
      "topics": [
        "cdb_unnest"
      ]
    },
    {
      "page": "Compadre",
      "title": "Subsamples of the COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database for testing and examples",
      "topics": [
        "Comadre",
        "Compadre"
      ]
    },
    {
      "page": "CompadreDB",
      "title": "CompadreDB Class",
      "topics": [
        "$,CompadreDB-method",
        "$<-,CompadreDB-method",
        "CompadreData",
        "CompadreData,CompadreDB-method",
        "CompadreDB",
        "DateCreated",
        "DateCreated,CompadreDB-method",
        "Version",
        "Version,CompadreDB-method",
        "VersionData",
        "VersionData,CompadreDB-method",
        "[[,CompadreDB,ANY,missing-method",
        "[[<-,CompadreDB,ANY,missing-method"
      ]
    },
    {
      "page": "CompadreDB-Methods",
      "title": "Methods for CompadreDB objects",
      "topics": [
        "as.data.frame.CompadreDB",
        "as_tibble.CompadreDB",
        "cbind.CompadreDB",
        "colnames,CompadreDB-method",
        "CompadreDB-Methods",
        "dim.CompadreDB",
        "droplevels.CompadreDB",
        "head.CompadreDB",
        "merge.CompadreDB",
        "names.CompadreDB",
        "NumberAcceptedSpecies",
        "NumberAcceptedSpecies,CompadreDB-method",
        "NumberMatrices",
        "NumberMatrices,CompadreDB-method",
        "NumberStudies",
        "NumberStudies,CompadreDB-method",
        "print.CompadreDB",
        "rbind.CompadreDB",
        "tail.CompadreDB"
      ]
    },
    {
      "page": "CompadreDB-Subsetting",
      "title": "Subsetting CompadreDB objects",
      "topics": [
        "CompadreDB-Subsetting",
        "subset.CompadreDB",
        "[,CompadreDB-method"
      ]
    },
    {
      "page": "CompadreDB-Tidyverse",
      "title": "Tidyverse methods for CompadreDB objects",
      "topics": [
        "arrange.CompadreDB",
        "CompadreDB-Tidyverse",
        "filter.CompadreDB",
        "fortify.CompadreDB",
        "full_join.CompadreDB",
        "group_by.CompadreDB",
        "inner_join.CompadreDB",
        "left_join.CompadreDB",
        "mutate.CompadreDB",
        "rename.CompadreDB",
        "right_join.CompadreDB",
        "select.CompadreDB",
        "slice.CompadreDB",
        "summarise.CompadreDB",
        "summarize.CompadreDB",
        "ungroup.CompadreDB"
      ]
    },
    {
      "page": "CompadreLegacy",
      "title": "Subsample of a legacy version of the COMPADRE Plant Matrix Database for testing and examples",
      "topics": [
        "CompadreLegacy"
      ]
    },
    {
      "page": "CompadreMatrixMethods",
      "title": "Methods for working with matrices in com(p)adre",
      "topics": [
        "CompadreMatrixMethods",
        "matA",
        "matA,CompadreDB-method",
        "matA,CompadreMat-method",
        "matA,list-method",
        "matC",
        "matC,CompadreDB-method",
        "matC,CompadreMat-method",
        "matC,list-method",
        "matF",
        "matF,CompadreDB-method",
        "matF,CompadreMat-method",
        "matF,list-method",
        "matrixClass",
        "matrixClass,CompadreDB-method",
        "matrixClass,CompadreMat-method",
        "matrixClass,list-method",
        "MatrixClassAuthor",
        "MatrixClassAuthor,CompadreDB-method",
        "MatrixClassAuthor,CompadreMat-method",
        "MatrixClassAuthor,list-method",
        "MatrixClassNumber",
        "MatrixClassNumber,CompadreDB-method",
        "MatrixClassNumber,CompadreMat-method",
        "MatrixClassNumber,list-method",
        "MatrixClassOrganized",
        "MatrixClassOrganized,CompadreDB-method",
        "MatrixClassOrganized,CompadreMat-method",
        "MatrixClassOrganized,list-method",
        "matU",
        "matU,CompadreDB-method",
        "matU,CompadreMat-method",
        "matU,list-method"
      ]
    },
    {
      "page": "mpm_elementwise_apply",
      "title": "Apply a function element-wise to a list of matrices",
      "concept": [
        "data management"
      ],
      "topics": [
        "mat_elementwise_apply",
        "mpm_elementwise_apply"
      ]
    },
    {
      "page": "mpm_mean",
      "title": "Calculate a mean over a list of matrices or CompadreMat objects",
      "concept": [
        "data management"
      ],
      "topics": [
        "mat_mean",
        "mpm_mean"
      ]
    },
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