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  "Package": "krm",
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  "Version": "2022.10-17",
  "Title": "Kernel Based Regression Models",
  "Authors@R": "c(person(\"Youyi\", \"Fong\", role = \"cre\", email = \"youyifong@gmail.com\"), person(\"Saheli\", \"Datta\", role = \"aut\", email = \"saheli8@gmail.com\"), person(\"Krisztian\", \"Sebestyen\", role = \"aut\", email = \"ksebestyen@gmail.com\"), person(\"Steve\", \"Park\", role = \"ctb\"), person(\"Dave\", \"Geyer\", role = \"ctb\"))",
  "Description": "Implements several methods for testing the variance\ncomponent parameter in regression models that contain\nkernel-based random effects, including a maximum of adjusted\nscores test. Several kernels are supported, including a profile\nhidden Markov model mutual information kernel for protein\nsequence. This package is described in Fong et al. (2015)\n<DOI:10.1093/biostatistics/kxu056>.",
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  "Packaged": {
    "Date": "2026-05-11 08:09:44 UTC",
    "User": "root"
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  "Author": "Youyi Fong [cre], Saheli Datta [aut], Krisztian Sebestyen\n[aut], Steve Park [ctb], Dave Geyer [ctb]",
  "Maintainer": "Youyi Fong <youyifong@gmail.com>",
  "Repository": "https://youyifong.r-universe.dev",
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    "readFastaFile",
    "readPriorFromFile",
    "readSelexAsMatrix",
    "readSelexFile",
    "removeGap",
    "rmdirichlet",
    "selexFile2arabicFile",
    "sim.liu.2007",
    "sim.liu.2008",
    "string2arabic",
    "stringList2arabicFile",
    "writeFastaFile"
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      "title": "Amino Acid Properties",
      "object": "aa.prop.list",
      "class": [
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      ],
      "fields": [
        "Symbol",
        "AA_Name",
        "AA_Symbol",
        "Surface_Area_Chothia",
        "Residue_Volume_Zamayatin",
        "Bulkiness_Jones",
        "Polarity_Jones",
        "Refractivity_Jones",
        "Hydrophobicity_Engleman",
        "Hydrophobicity_Prabha",
        "Hydrophilicity_Hopp",
        "Hydrophilicity_Levitt",
        "RelMutability_Jones"
      ],
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    },
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      "name": "cloud9",
      "title": "9-Component Mixture Dirichlet Prior for Protein Sequences",
      "object": "cloud9",
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        "list"
      ],
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      "table": false,
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      "title": "Amino Acid Properties",
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        "aa.prop.list"
      ]
    },
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      "title": "Functions Related to Sequence Alignment",
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        "alignment2trancount",
        "calcPairwiseIdentity",
        "removeGap"
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      "title": "A Transformation of Chi-squared Random Variable",
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      ]
    },
    {
      "page": "cloud9",
      "title": "9-Component Mixture Dirichlet Prior for Protein Sequences",
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      ]
    },
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        "dmdirichlet",
        "logIntegrateDirichlet",
        "logIntegrateMixDirichlet",
        "modifyDirichlet",
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        "rmdirichlet"
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    },
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        "arabic2fastaFile",
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