{
  "_id": "6a1005ceacfb0bcc41c7dd5c",
  "Package": "paneljudge",
  "Title": "Judge the performance of a panel of genetic markers using\nsimulated data",
  "Version": "0.0.0.9000",
  "Authors@R": "c(\nperson(given = \"Aimee\",\nfamily = \"Taylor\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-2337-8992\"),\nemail = \"ataylor@hsph.harvard.edu\"),\nperson(given = \"Pierre\",\nfamily = \"Jacob\",\ncomment = c(ORCID = \"0000-0002-3126-6966\"),\nrole = \"aut\"))",
  "Description": "An R package to judge the performance of a panel of\ngenetic markers using data simulated for pairs of haploid\ngenotypes. The data are simulated under a hidden Markov model\nof relatedness (described in Taylor, A.R., Jacob, P.E.,\nNeafsey, D.E. and Buckee, C.O., 2019. Estimating relatedness\nbetween malaria parasites. Genetics, 212(4), pp.1337-1351)\nusing allele frequency estimates provided by the user and\ninter-marker distances. The markers are treated as categorical\nrandom variables whose realisations (alleles) are unordered.\nThe effective cardinalities and diversities of the markers can\nbe computed using the input allele frequency estimates. Panel\nperformance can be judged in terms of the root mean square\nerror (RMSE) and confidence interval width of estimated\nrelatedness, where relatedness is estimated under the same\nmodel used to simulate the data. At present, the examples we\nprovide do not consider model misspecification; do not account\nfor uncertainty around input allele frequency estimates; do not\nconsider relatedness between pairs of haploid genotypes\nsimulated using different allele frequencies; do not account\nfor marker drop-out (markers that fail to produce useful data,\ne.g. because they a monomorphic). Otherwise stated, in the\nexamples provided, the performance of a panel is judged in its\nmost favourable light; it will likely perform less well in\nreality.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.1.1",
  "VignetteBuilder": "knitr",
  "Repository": "https://plasmogenepi.r-universe.dev",
  "Date/Publication": "2023-03-01 13:44:31 UTC",
  "RemoteUrl": "https://github.com/aimeertaylor/paneljudge",
  "RemoteRef": "HEAD",
  "RemoteSha": "b489f6ab4669d0d3c6ff6e3bdfa9666375889a31",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-22 07:24:20 UTC",
    "User": "root"
  },
  "Author": "Aimee Taylor [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-2337-8992>),\nPierre Jacob [aut] (ORCID: <https://orcid.org/0000-0002-3126-6966>)",
  "Maintainer": "Aimee Taylor <ataylor@hsph.harvard.edu>",
  "MD5sum": "bf192a4127d843d039b342daa835f2be",
  "_user": "plasmogenepi",
  "_type": "src",
  "_file": "paneljudge_0.0.0.9000.tar.gz",
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  "_created": "2026-05-22T07:24:20.000Z",
  "_published": "2026-05-22T07:29:18.383Z",
  "_distro": "noble",
  "_jobs": [
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    "author": "Aimee Taylor <aimee.r.taylor.85@gmail.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Update email and other small edits",
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    "email": "ataylor@hsph.harvard.edu",
    "orcid": "0000-0002-2337-8992"
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    },
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      "package": "knitr",
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    },
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      "package": "rmarkdown",
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  ],
  "_owner": "aimeertaylor",
  "_selfowned": false,
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  "_tags": [],
  "_stars": 6,
  "_contributors": [
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      "uuid": 19333433
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    "uuid": 140542976,
    "type": "organization",
    "name": "PlasmoGenEpi",
    "description": "We are a network of scientists who have come together since 2018 to address challenges in malaria genomic epidemiology."
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    "extra/citation.html",
    "extra/citation.json",
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  "_cranurl": false,
  "_exports": [
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    "compute_eff_cardinalities",
    "compute_r_and_k_CIs",
    "estimate_r_and_k",
    "simulate_Ys"
  ],
  "_datasets": [
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      "name": "chr_lengths",
      "title": "Data on chromosome lengths.",
      "object": "chr_lengths",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
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      "title": "Data on allele frequencies of the example GTseq panel.",
      "object": "frequencies",
      "class": [
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      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
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      "name": "markers",
      "title": "Data on markers of the example GTseq panel.",
      "object": "markers",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Amplicon_name",
        "Chr",
        "Start",
        "Stop",
        "length",
        "pos",
        "chrom",
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      ],
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  "_help": [
    {
      "page": "chr_lengths",
      "title": "Data on chromosome lengths.",
      "topics": [
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    },
    {
      "page": "compute_diversities",
      "title": "Function to compute marker diversities",
      "topics": [
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      ]
    },
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      "page": "compute_eff_cardinalities",
      "title": "Function to compute marker effective cardinalities",
      "topics": [
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      ]
    },
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      "page": "compute_r_and_k_CIs",
      "title": "Function to compute confidence intervals for relatedness and switch rate parameters",
      "topics": [
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      ]
    },
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      "page": "estimate_r_and_k",
      "title": "Function to estimate relatedness and switch rate parameters",
      "topics": [
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      ]
    },
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      "title": "Data on allele frequencies of the example GTseq panel.",
      "topics": [
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      "title": "Data on markers of the example GTseq panel.",
      "topics": [
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      ]
    },
    {
      "page": "simulate_Ys",
      "title": "Function to simulate genotype calls for a pair of haploid genotypes",
      "topics": [
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      ]
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  ],
  "_readme": "https://github.com/aimeertaylor/paneljudge/raw/HEAD/README.md",
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      "title": "Example panel performance",
      "author": "Aimee R Taylor",
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      "headings": [
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        "References"
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      "created": "2020-04-04 10:41:54",
      "modified": "2021-07-20 21:17:48",
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