{
  "_id": "6a192fdaacfb0bcc41dd0494",
  "Package": "scorematchingad",
  "Title": "Score Matching Estimation by Automatic Differentiation",
  "Version": "0.1.6",
  "Authors@R": "c(person(given = \"Kassel Liam\", family = \"Hingee\", email = \"kassel.hingee@anu.edu.au\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-9894-2407\")),\nperson(\"Janice\", \"Scealy\", role = c(\"aut\"), comment = c(ORCID = \"0000-0002-9718-869X\")),\nperson(\"Bradley M.\", \"Bell\", role = c(\"cph\"))\n)",
  "Description": "Hyvärinen's score matching (Hyvärinen, 2005)\n<https://jmlr.org/papers/v6/hyvarinen05a.html> is a useful\nestimation technique when the normalising constant for a\nprobability distribution is difficult to compute. This package\nimplements score matching estimators using automatic\ndifferentiation in the 'CppAD' library\n<https://github.com/coin-or/CppAD> and is designed for quickly\nimplementing score matching estimators for new models. Also\navailable is general robustification (Windham, 1995)\n<https://www.jstor.org/stable/2346159>. Already in the package\nare estimators for directional distributions (Mardia, Kent and\nLaha, 2016) <doi:10.48550/arXiv.1604.08470> and the flexible\nPolynomially-Tilted Pairwise Interaction model for\ncompositional data. The latter estimators perform well when\nthere are zeros in the compositions (Scealy and Wood, 2023)\n<doi:10.1080/01621459.2021.2016422>, even many zeros (Scealy,\nHingee, Kent, and Wood, 2024) <doi:10.1007/s11222-024-10412-w>.\nA partial interface to CppAD's ADFun objects is also available.",
  "License": "GPL (>=3)",
  "Encoding": "UTF-8",
  "LazyData": "true",
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  "Roxygen": "list(markdown = TRUE)",
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  "URL": "https://github.com/kasselhingee/scorematchingad",
  "BugReports": "https://github.com/kasselhingee/scorematchingad/issues",
  "Config/pak/sysreqs": "cmake",
  "Repository": "https://kasselhingee.r-universe.dev",
  "Date/Publication": "2025-11-30 02:36:34 UTC",
  "RemoteUrl": "https://github.com/kasselhingee/scorematchingad",
  "RemoteRef": "HEAD",
  "RemoteSha": "d508563e8df067807530a0629a3a9f9e76ddf6d9",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-29 06:03:59 UTC",
    "User": "root"
  },
  "Author": "Kassel Liam Hingee [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-9894-2407>),\nJanice Scealy [aut] (ORCID: <https://orcid.org/0000-0002-9718-869X>),\nBradley M. Bell [cph]",
  "Maintainer": "Kassel Liam Hingee <kassel.hingee@anu.edu.au>",
  "MD5sum": "6e9069ce69f1a115a4260f4a97e0eaeb",
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  "_created": "2026-05-29T06:03:59.000Z",
  "_published": "2026-05-29T06:19:06.613Z",
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    "message": "resubmitted to CRAN without extra erroneous file\n",
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    "cppad_closed",
    "cppad_search",
    "dppi",
    "evaltape",
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    "FB",
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    "ppi_fromAstar",
    "ppi_mmmm",
    "ppi_parammats",
    "ppi_paramvec",
    "ppi_robust",
    "ppi_robust_alrgengamma",
    "ppi_smvalues",
    "ppi_toAstar",
    "print",
    "quadratictape_parts",
    "rppi",
    "rppi_egmodel",
    "rsymmetricmatrix",
    "show",
    "smvalues",
    "smvalues_wsum",
    "tape_bdryw",
    "tape_bdryw_inbuilt",
    "tape_gradoffset",
    "tape_Hessian",
    "tape_Jacobian",
    "tape_logJacdet",
    "tape_smd",
    "tape_swap",
    "tape_uld",
    "tape_uld_inbuilt",
    "testquadratic",
    "vMF",
    "vMF_robust",
    "Windham",
    "Windham_populationinverse",
    "Windham_populationinverse_alternative"
  ],
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      "title": "16s Microbiome Data for Soil-Transmitted Helminths",
      "object": "microbiome",
      "class": [
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      ],
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        "Year",
        "Sex",
        "Treatment",
        "Age",
        "ct_Al",
        "ct_Na",
        "ct_Ad",
        "ct_St",
        "micr_Tt",
        "Helminth",
        "Acidobacteria",
        "Actinobacteria",
        "Bacteroidetes",
        "Chloroflexi",
        "Cyanobacteria/Chloroplast",
        "Deinococcus-Thermus",
        "Elusimicrobia",
        "Firmicutes",
        "Fusobacteria",
        "Gemmatimonadetes",
        "Lentisphaerae",
        "Planctomycetes",
        "Proteobacteria",
        "Spirochaetes",
        "Synergistetes",
        "TM7",
        "Tenericutes",
        "Verrucomicrobia",
        "Unclassified_Bacteria",
        "Unclassified_root"
      ],
      "rows": 300,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "scorematchingad-package",
      "title": "scorematchingad: Score Matching Estimation by Automatic Differentiation",
      "topics": [
        "scorematchingad-package",
        "scorematchingad"
      ]
    },
    {
      "page": "avgrange",
      "title": "Average Across Range of a Tape",
      "concept": [
        "tape builders"
      ],
      "topics": [
        "avgrange"
      ]
    },
    {
      "page": "Bingham",
      "title": "Score Matching Estimators for the Bingham Distribution",
      "concept": [
        "directional model estimators"
      ],
      "topics": [
        "Bingham"
      ]
    },
    {
      "page": "cppad_closed",
      "title": "Score Matching Estimator for Quadratic-Form Score Matching Discrepancies",
      "concept": [
        "generic score matching tools"
      ],
      "topics": [
        "cppad_closed"
      ]
    },
    {
      "page": "cppad_search",
      "title": "Iterative Score Matching Estimator Using Conjugate-Gradient Descent",
      "concept": [
        "generic score matching tools"
      ],
      "topics": [
        "cppad_search"
      ]
    },
    {
      "page": "dppi",
      "title": "Improper Log-Density of the PPI Model",
      "concept": [
        "PPI model tools"
      ],
      "topics": [
        "dppi"
      ]
    },
    {
      "page": "evaltape",
      "title": "Evaluate a CppAD Tape Many Times",
      "concept": [
        "tape evaluators"
      ],
      "topics": [
        "evaltape",
        "evaltape_wsum"
      ]
    },
    {
      "page": "FB",
      "title": "Estimate the Fisher-Bingham Distribution",
      "concept": [
        "directional model estimators"
      ],
      "topics": [
        "FB"
      ]
    },
    {
      "page": "fixdynamic",
      "title": "Fix Dynamic Parameters of a Tape",
      "concept": [
        "tape builders"
      ],
      "topics": [
        "fixdynamic"
      ]
    },
    {
      "page": "fixindependent",
      "title": "Fix Independent Arguments of a Tape",
      "concept": [
        "tape builders"
      ],
      "topics": [
        "fixindependent"
      ]
    },
    {
      "page": "keeprange",
      "title": "Reduce Range Dimension of a Tape",
      "concept": [
        "tape builders"
      ],
      "topics": [
        "keeprange"
      ]
    },
    {
      "page": "microbiome",
      "title": "16s Microbiome Data for Soil-Transmitted Helminths",
      "topics": [
        "microbiome"
      ]
    },
    {
      "page": "ppi",
      "title": "Estimation of Polynomially-Tilted Pairwise Interaction (PPI) Model",
      "concept": [
        "PPI model tools"
      ],
      "topics": [
        "ppi",
        "ppi_smvalues"
      ]
    },
    {
      "page": "ppi_cW",
      "title": "Quickly Generate a Vector of Windham Exponents for the PPI Model",
      "topics": [
        "ppi_cW",
        "ppi_cW_auto"
      ]
    },
    {
      "page": "ppi_mmmm",
      "title": "A PPI Score-Matching Marginal Moment Matching Estimator (dimension=3 only)",
      "topics": [
        "ppi_mmmm"
      ]
    },
    {
      "page": "ppi_param_tools",
      "title": "PPI Parameter Tools",
      "concept": [
        "PPI model tools"
      ],
      "topics": [
        "ppi_fromAstar",
        "ppi_parammats",
        "ppi_paramvec",
        "ppi_param_tools",
        "ppi_toAstar"
      ]
    },
    {
      "page": "ppi_robust",
      "title": "Robustly Estimate Parameters of the PPI Distribution",
      "concept": [
        "PPI model tools",
        "Windham robustness functions"
      ],
      "topics": [
        "ppi_robust",
        "ppi_robust_alrgengamma"
      ]
    },
    {
      "page": "print-Rcpp_ADFun",
      "title": "Print or show a summary of an Rcpp_ADFun",
      "topics": [
        "print,Rcpp_ADFun",
        "print,Rcpp_ADFun-method",
        "show,Rcpp_ADFun-method"
      ]
    },
    {
      "page": "quadratictape_parts",
      "title": "Evaluate the Hessian and Gradient Offset of a Taped Quadratic Function",
      "concept": [
        "tape evaluators"
      ],
      "topics": [
        "quadratictape_parts"
      ]
    },
    {
      "page": "Rcpp_ADFun-class",
      "title": "A Class for CppAD Tapes",
      "topics": [
        "ADFun",
        "Rcpp_ADFun",
        "Rcpp_ADFun-class"
      ]
    },
    {
      "page": "rppi",
      "title": "Simulate from a PPI Model",
      "concept": [
        "PPI model tools"
      ],
      "topics": [
        "rppi",
        "rppi_egmodel"
      ]
    },
    {
      "page": "rsymmetricmatrix",
      "title": "Quickly Generate a Symmetric Matrix for Testing and Examples",
      "topics": [
        "rsymmetricmatrix"
      ]
    },
    {
      "page": "scorematchingtheory",
      "title": "Introduction to Score Matching",
      "topics": [
        "scorematchingtheory"
      ]
    },
    {
      "page": "smvalues",
      "title": "Compute Score Matching Discrepancy Value, Gradient, and Hessian",
      "concept": [
        "tape evaluators"
      ],
      "topics": [
        "smvalues",
        "smvalues_wsum"
      ]
    },
    {
      "page": "tape_bdryw",
      "title": "Generate a tape of a custom boundary weight function",
      "concept": [
        "tape builders"
      ],
      "topics": [
        "tape_bdryw",
        "tape_bdryw_inbuilt"
      ]
    },
    {
      "page": "tape_gradoffset",
      "title": "Tape the Gradient Offset of a Quadratic CppAD Tape",
      "concept": [
        "tape builders"
      ],
      "topics": [
        "tape_gradoffset"
      ]
    },
    {
      "page": "tape_Hessian",
      "title": "Tape the Hessian of a CppAD Tape",
      "concept": [
        "tape builders"
      ],
      "topics": [
        "tape_Hessian"
      ]
    },
    {
      "page": "tape_Jacobian",
      "title": "Tape the Jacobian of CppAD Tape",
      "concept": [
        "tape builders"
      ],
      "topics": [
        "tape_Jacobian"
      ]
    },
    {
      "page": "tape_logJacdet",
      "title": "Tape the log of Jacobian determinant of a CppAD Tape",
      "concept": [
        "tape builders"
      ],
      "topics": [
        "tape_logJacdet"
      ]
    },
    {
      "page": "tape_smd",
      "title": "Build CppAD Tapes for Score Matching",
      "concept": [
        "generic score matching tools",
        "tape builders"
      ],
      "topics": [
        "tape_smd"
      ]
    },
    {
      "page": "tape_swap",
      "title": "Switch Dynamic and Independent Values of a Tape",
      "concept": [
        "tape builders"
      ],
      "topics": [
        "tape_swap"
      ]
    },
    {
      "page": "tape_uld",
      "title": "Generate a tape of a custom unnormalised log-density",
      "concept": [
        "tape builders"
      ],
      "topics": [
        "tape_uld",
        "tape_uld_inbuilt"
      ]
    },
    {
      "page": "testquadratic",
      "title": "Test Whether a CppAD Tape is a Quadratic Function",
      "concept": [
        "tape evaluators"
      ],
      "topics": [
        "testquadratic"
      ]
    },
    {
      "page": "vMF",
      "title": "Score Matching Estimator for the von-Mises Fisher Distribution",
      "concept": [
        "directional model estimators"
      ],
      "topics": [
        "vMF"
      ]
    },
    {
      "page": "vMF_robust",
      "title": "Robust Fitting of von Mises Fisher",
      "concept": [
        "Windham robustness functions",
        "directional model estimators"
      ],
      "topics": [
        "vMF_robust"
      ]
    },
    {
      "page": "Windham",
      "title": "Windham Robustification of Point Estimators for Exponential Family Distributions",
      "concept": [
        "Windham robustness functions",
        "generic score matching tools"
      ],
      "topics": [
        "Windham"
      ]
    },
    {
      "page": "Windham_populationinverse",
      "title": "Inverse Transform for the Population Parameters Under Windham Weights",
      "topics": [
        "Windham_populationinverse",
        "Windham_populationinverse_alternative"
      ]
    }
  ],
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