{
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  "Title": "Poisson Lognormal Models",
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  "Authors@R": "c(\nperson(\"Julien\", \"Chiquet\", , \"julien.chiquet@inrae.fr\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-3629-3429\")),\nperson(\"Mahendra\", \"Mariadassou\", , \"mahendra.mariadassou@inrae.fr\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-2986-354X\")),\nperson(\"Stéphane\", \"Robin\", , \"stephane.robin@inrae.fr\", role = \"aut\"),\nperson(\"François\", \"Gindraud\", , \"francois.gindraud@gmail.com\", role = \"aut\"),\nperson(\"Julie\", \"Aubert\", , \"julie.aubert@inrae.fr\", role = \"ctb\"),\nperson(\"Bastien\", \"Batardière\", , \"bastien.batardiere@inrae.fr\", role = \"ctb\"),\nperson(\"Giovanni\", \"Poggiato\", , \"giov.poggiato@gmail.com\", role = \"ctb\"),\nperson(\"Cole\", \"Trapnell\", , \"coletrap@uw.edu\", role = \"ctb\"),\nperson(\"Maddy\", \"Duran\", , \"duran@uw.edu\", role = \"ctb\")\n)",
  "Description": "The Poisson-lognormal model and variants (Chiquet,\nMariadassou and Robin, 2021 <doi:10.3389/fevo.2021.588292>) can\nbe used for a variety of multivariate problems when count data\nare at play, including principal component analysis for count\ndata, discriminant analysis, model-based clustering and network\ninference. Implements variational algorithms to fit such models\naccompanied with a set of functions for visualization and\ndiagnostic.",
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  "Repository": "https://pln-team.r-universe.dev",
  "Date/Publication": "2026-04-10 08:17:24 UTC",
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  "Author": "Julien Chiquet [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-3629-3429>),\nMahendra Mariadassou [aut] (ORCID:\n<https://orcid.org/0000-0003-2986-354X>),\nStéphane Robin [aut],\nFrançois Gindraud [aut],\nJulie Aubert [ctb],\nBastien Batardière [ctb],\nGiovanni Poggiato [ctb],\nCole Trapnell [ctb],\nMaddy Duran [ctb]",
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    "PLN",
    "PLN_param",
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    "PLNmixture_param",
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    "PLNnetwork_param",
    "PLNPCA",
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    "predict_cond",
    "prepare_data",
    "rPLN",
    "stability_selection",
    "standard_error",
    "ZIPLN",
    "ZIPLN_param",
    "ZIPLNnetwork",
    "ZIPLNnetwork_param"
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        "Latitude",
        "Longitude",
        "Depth",
        "Temperature",
        "Offset"
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        "sample",
        "site",
        "time",
        "site_time",
        "Offset"
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      "table": false,
      "tojson": true
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      "title": "Mollusk data set",
      "object": "mollusk",
      "class": [
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      ],
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      "table": false,
      "tojson": true
    },
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      "object": "oaks",
      "class": [
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      "fields": [
        "Abundance",
        "Sample",
        "tree",
        "branch",
        "leafNo",
        "distTObase",
        "distTOtrunk",
        "distTOground",
        "pmInfection",
        "orientation",
        "readsTOTfun",
        "readsTOTbac",
        "Offset"
      ],
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      "table": false,
      "tojson": true
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      "title": "Single cell RNA-seq data",
      "object": "scRNA",
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        "cell_line",
        "total_counts"
      ],
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      "table": false,
      "tojson": true
    },
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      "title": "Trichoptera data set",
      "object": "trichoptera",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
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    {
      "page": "barents",
      "title": "Barents fish data set",
      "topics": [
        "barents"
      ]
    },
    {
      "page": "coef.PLNfit",
      "title": "Extract model coefficients",
      "topics": [
        "coef.PLNfit"
      ]
    },
    {
      "page": "coef.PLNLDAfit",
      "title": "Extracts model coefficients from objects returned by 'PLNLDA()'",
      "topics": [
        "coef.PLNLDAfit"
      ]
    },
    {
      "page": "coef.PLNmixturefit",
      "title": "Extract model coefficients",
      "topics": [
        "coef.PLNmixturefit"
      ]
    },
    {
      "page": "coef.ZIPLNfit",
      "title": "Extract model coefficients",
      "topics": [
        "coef.ZIPLNfit"
      ]
    },
    {
      "page": "coefficient_path",
      "title": "Extract the regularization path of a PLNnetwork fit",
      "topics": [
        "coefficient_path"
      ]
    },
    {
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      "title": "Compute offsets from a count data using one of several normalization schemes",
      "topics": [
        "compute_offset"
      ]
    },
    {
      "page": "compute_PLN_starting_point",
      "title": "Helper function for PLN initialization.",
      "topics": [
        "compute_PLN_starting_point"
      ]
    },
    {
      "page": "extract_probs",
      "title": "Extract edge selection frequency in bootstrap subsamples",
      "topics": [
        "extract_probs"
      ]
    },
    {
      "page": "fitted.PLNfit",
      "title": "Extracts model fitted values from objects returned by 'PLN()' and its variants",
      "topics": [
        "fitted.PLNfit"
      ]
    },
    {
      "page": "fitted.PLNmixturefit",
      "title": "Extracts model fitted values from objects returned by 'PLNmixture()' and its variants",
      "topics": [
        "fitted.PLNmixturefit"
      ]
    },
    {
      "page": "fitted.ZIPLNfit",
      "title": "Extracts model fitted values from objects returned by 'ZIPLN()' and its variants",
      "topics": [
        "fitted.ZIPLNfit"
      ]
    },
    {
      "page": "getBestModel",
      "title": "Best model extraction from a collection of models",
      "topics": [
        "getBestModel",
        "getBestModel.Networkfamily",
        "getBestModel.PLNmixturefamily",
        "getBestModel.PLNnetworkfamily",
        "getBestModel.PLNPCAfamily",
        "getBestModel.ZIPLNnetworkfamily"
      ]
    },
    {
      "page": "getModel",
      "title": "Model extraction from a collection of models",
      "topics": [
        "getModel",
        "getModel.Networkfamily",
        "getModel.PLNmixturefamily",
        "getModel.PLNnetworkfamily",
        "getModel.PLNPCAfamily",
        "getModel.ZIPLNnetworkfamily"
      ]
    },
    {
      "page": "microcosm",
      "title": "Cow microbiome data set",
      "topics": [
        "microcosm"
      ]
    },
    {
      "page": "mollusk",
      "title": "Mollusk data set",
      "topics": [
        "mollusk"
      ]
    },
    {
      "page": "Networkfamily",
      "title": "An R6 Class to virtually represent a collection of network fits",
      "topics": [
        "Networkfamily"
      ]
    },
    {
      "page": "oaks",
      "title": "Oaks amplicon data set",
      "topics": [
        "oaks"
      ]
    },
    {
      "page": "PLN",
      "title": "Poisson lognormal model",
      "topics": [
        "PLN"
      ]
    },
    {
      "page": "PLN_param",
      "title": "Control of a PLN fit",
      "topics": [
        "PLN_param"
      ]
    },
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      "page": "PLNfamily",
      "title": "An R6 Class to represent a collection of PLNfit",
      "topics": [
        "PLNfamily"
      ]
    },
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