{
  "_id": "6ad49a25dc7ca4d810c6d622",
  "Package": "aphid",
  "Type": "Package",
  "Title": "Analysis with Profile Hidden Markov Models",
  "Version": "1.3.6",
  "Authors@R": "person(\"Shaun\", \"Wilkinson\", email = \"shaunpwilkinson@gmail.com\",\nrole = c(\"aut\", \"cre\"))",
  "Author": "Shaun Wilkinson [aut, cre]",
  "Maintainer": "Shaun Wilkinson <shaunpwilkinson@gmail.com>",
  "Description": "Designed for the development and application of hidden\nMarkov models and profile HMMs for biological sequence\nanalysis. Contains functions for multiple and pairwise sequence\nalignment, model construction and parameter optimization, file\nimport/export, implementation of the forward, backward and\nViterbi algorithms for conditional sequence probabilities,\ntree-based sequence weighting, and sequence simulation.\nFeatures a wide variety of potential applications including\ndatabase searching, gene-finding and annotation, phylogenetic\nanalysis and sequence classification. Based on the models and\nalgorithms described in Durbin et al (1998, ISBN:\n9780521629713).",
  "License": "GPL-3",
  "URL": "https://github.com/shaunpwilkinson/aphid",
  "BugReports": "https://github.com/shaunpwilkinson/aphid/issues",
  "LazyData": "TRUE",
  "Encoding": "UTF-8",
  "SystemRequirements": "GNU make",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.1",
  "Config/pak/sysreqs": "make libjpeg-dev libssl-dev",
  "Repository": "https://shaunpwilkinson.r-universe.dev",
  "Date/Publication": "2026-01-23 02:04:50 UTC",
  "RemoteUrl": "https://github.com/shaunpwilkinson/aphid",
  "RemoteRef": "HEAD",
  "RemoteSha": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-18 09:58:16 UTC",
    "User": "root"
  },
  "_user": "shaunpwilkinson",
  "_type": "src",
  "_file": "aphid_1.3.6.tar.gz",
  "_fileid": "https://r2.ropensci.org/62e92b91767bedeb5a5bc16545ee25f2baa2f84bc2c3af395d0a2d19956af83d",
  "_filesize": 609921,
  "_sha256": "62e92b91767bedeb5a5bc16545ee25f2baa2f84bc2c3af395d0a2d19956af83d",
  "_expires": "2027-01-26T10:06:27.000Z",
  "_created": "2026-10-18T09:58:16.000Z",
  "_published": "2026-10-18T10:06:29.756Z",
  "_buildurl": "https://github.com/r-universe/shaunpwilkinson/actions/runs/39117226126",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 117645993972,
      "time": 119,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12132703543"
    },
    {
      "job": 117645993926,
      "time": 137,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12132793342"
    },
    {
      "job": 117645993965,
      "time": 160,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12133092035"
    },
    {
      "job": 117645993912,
      "time": 148,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12132289960"
    },
    {
      "job": 117645993885,
      "time": 143,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12133037294"
    },
    {
      "job": 117645993938,
      "time": 265,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12133086311"
    },
    {
      "job": 117645993906,
      "time": 122,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12133420216"
    },
    {
      "job": 117645993905,
      "time": 323,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12133175944"
    },
    {
      "job": 117645414091,
      "time": 193,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12133095916"
    },
    {
      "job": 117645993978,
      "time": 104,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12132803204"
    },
    {
      "job": 117645993952,
      "time": 439,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12133226131"
    },
    {
      "job": 117645993916,
      "time": 172,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12132618858"
    },
    {
      "job": 117645993899,
      "time": 126,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12132858095"
    },
    {
      "job": 117645993976,
      "time": 371,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12132574279"
    },
    {
      "job": 117645994072,
      "time": 91,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12133410229"
    }
  ],
  "_upstream": "https://github.com/shaunpwilkinson/aphid",
  "_commit": {
    "id": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873",
    "author": "Shaun Wilkinson <shaunpwilkinson@gmail.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Delete aphid.Rproj",
    "time": 1769133890
  },
  "_maintainer": {
    "name": "Shaun Wilkinson",
    "email": "shaunpwilkinson@gmail.com",
    "login": "shaunpwilkinson",
    "description": "Managing Director at Wilderlab",
    "uuid": 10361217
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "openssl",
      "role": "Imports"
    },
    {
      "package": "kmer",
      "version": ">= 1.0.0",
      "role": "Imports"
    },
    {
      "package": "qpdf",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.12.5",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "ape",
      "version": ">= 4.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "shaunpwilkinson",
  "_selfowned": true,
  "_usedby": 3,
  "_updates": [
    {
      "week": "2026-03",
      "n": 2
    },
    {
      "week": "2026-04",
      "n": 6
    }
  ],
  "_tags": [],
  "_stars": 22,
  "_contributors": [
    {
      "user": "shaunpwilkinson",
      "count": 216,
      "uuid": 10361217
    }
  ],
  "_userbio": {
    "uuid": 10361217,
    "type": "user",
    "name": "Shaun Wilkinson",
    "followers": 37,
    "description": "Managing Director at Wilderlab"
  },
  "_downloads": {
    "count": 629,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/aphid"
  },
  "_devurl": "https://github.com/shaunpwilkinson/aphid",
  "_searchresults": 48,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/aphid.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/shaunpwilkinson/aphid",
  "_realowner": "shaunpwilkinson",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2017-06-24"
    },
    {
      "version": "1.0.1",
      "date": "2017-07-07"
    },
    {
      "version": "1.1.0",
      "date": "2018-03-16"
    },
    {
      "version": "1.2.0",
      "date": "2018-08-14"
    },
    {
      "version": "1.3.0",
      "date": "2018-10-09"
    },
    {
      "version": "1.3.1",
      "date": "2018-11-10"
    },
    {
      "version": "1.3.2",
      "date": "2019-03-15"
    },
    {
      "version": "1.3.3",
      "date": "2019-05-08"
    },
    {
      "version": "1.3.5",
      "date": "2022-12-05"
    },
    {
      "version": "1.3.6",
      "date": "2026-01-23"
    }
  ],
  "_exports": [
    "align",
    "align.AAbin",
    "align.default",
    "align.DNAbin",
    "align.list",
    "backward",
    "backward.HMM",
    "backward.PHMM",
    "deriveHMM",
    "derivePHMM",
    "derivePHMM.AAbin",
    "derivePHMM.default",
    "derivePHMM.DNAbin",
    "derivePHMM.list",
    "forward",
    "forward.HMM",
    "forward.PHMM",
    "generate",
    "generate.HMM",
    "generate.PHMM",
    "logsum",
    "map",
    "plot.HMM",
    "plot.PHMM",
    "posterior",
    "posterior.HMM",
    "posterior.PHMM",
    "print.DPA",
    "print.HMM",
    "print.PHMM",
    "readPHMM",
    "train",
    "train.HMM",
    "train.PHMM",
    "unalign",
    "Viterbi",
    "Viterbi.default",
    "Viterbi.HMM",
    "Viterbi.PHMM",
    "weight",
    "weight.AAbin",
    "weight.default",
    "weight.dendrogram",
    "weight.DNAbin",
    "weight.list",
    "writePHMM"
  ],
  "_datasets": [
    {
      "name": "casino",
      "title": "Dishonest casino.",
      "object": "casino",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "globins",
      "title": "Globin protein alignment.",
      "object": "globins",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [],
      "rows": 7,
      "table": true,
      "tojson": true
    },
    {
      "name": "substitution",
      "title": "Substitution matrices.",
      "object": "substitution",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "align",
      "title": "Multiple sequence alignment in R.",
      "topics": [
        "align",
        "align.AAbin",
        "align.default",
        "align.DNAbin",
        "align.list"
      ]
    },
    {
      "page": "aphid",
      "title": "The 'aphid' package for analysis with profile hidden Markov models.",
      "topics": [
        "aphid-package",
        "aphid"
      ]
    },
    {
      "page": "backward",
      "title": "The backward algorithm.",
      "topics": [
        "backward",
        "backward.HMM",
        "backward.PHMM"
      ]
    },
    {
      "page": "casino",
      "title": "Dishonest casino.",
      "topics": [
        "casino"
      ]
    },
    {
      "page": "deriveHMM",
      "title": "Derive a standard hidden Markov model from a set of sequences.",
      "topics": [
        "deriveHMM"
      ]
    },
    {
      "page": "derivePHMM",
      "title": "Derive a profile hidden Markov model from sequences.",
      "topics": [
        "derivePHMM",
        "derivePHMM.AAbin",
        "derivePHMM.default",
        "derivePHMM.DNAbin",
        "derivePHMM.list"
      ]
    },
    {
      "page": "forward",
      "title": "The forward algorithm.",
      "topics": [
        "forward",
        "forward.HMM",
        "forward.PHMM"
      ]
    },
    {
      "page": "generate",
      "title": "Generate random sequences from a model.",
      "topics": [
        "generate",
        "generate.HMM",
        "generate.PHMM"
      ]
    },
    {
      "page": "globins",
      "title": "Globin protein alignment.",
      "topics": [
        "globins"
      ]
    },
    {
      "page": "logsum",
      "title": "Sum of logged probabilities.",
      "topics": [
        "logsum"
      ]
    },
    {
      "page": "map",
      "title": "Optimized profile HMM construction.",
      "topics": [
        "map"
      ]
    },
    {
      "page": "plot.HMM",
      "title": "Plot standard hidden Markov models.",
      "topics": [
        "plot.HMM"
      ]
    },
    {
      "page": "plot.PHMM",
      "title": "Plot profile hidden Markov models.",
      "topics": [
        "plot.PHMM"
      ]
    },
    {
      "page": "posterior",
      "title": "Posterior decoding.",
      "topics": [
        "posterior",
        "posterior.HMM",
        "posterior.PHMM"
      ]
    },
    {
      "page": "print",
      "title": "Print summary methods.",
      "topics": [
        "print",
        "print.DPA",
        "print.HMM",
        "print.PHMM"
      ]
    },
    {
      "page": "readPHMM",
      "title": "Import profile hidden Markov models into R.",
      "topics": [
        "readPHMM"
      ]
    },
    {
      "page": "substitution",
      "title": "Substitution matrices.",
      "topics": [
        "substitution"
      ]
    },
    {
      "page": "train",
      "title": "Iterative model refinement.",
      "topics": [
        "train",
        "train.HMM",
        "train.PHMM"
      ]
    },
    {
      "page": "unalign",
      "title": "Deconstruct an alignment.",
      "topics": [
        "unalign"
      ]
    },
    {
      "page": "Viterbi",
      "title": "The Viterbi algorithm.",
      "topics": [
        "Viterbi",
        "Viterbi.default",
        "Viterbi.HMM",
        "Viterbi.PHMM"
      ]
    },
    {
      "page": "weight",
      "title": "Sequence weighting.",
      "topics": [
        "weight",
        "weight.AAbin",
        "weight.default",
        "weight.dendrogram",
        "weight.DNAbin",
        "weight.list"
      ]
    },
    {
      "page": "writePHMM",
      "title": "Export profile hidden Markov models as text.",
      "topics": [
        "writePHMM"
      ]
    }
  ],
  "_readme": "https://github.com/shaunpwilkinson/aphid/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "askpass",
    "curl",
    "digest",
    "kmer",
    "lattice",
    "nlme",
    "openssl",
    "phylogram",
    "qpdf",
    "Rcpp",
    "sys"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "aphid-vignette.Rmd",
      "filename": "aphid-vignette.html",
      "title": "The 'aphid' package for analysis with profile hidden Markov models",
      "author": "Shaun Wilkinson",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Abstract",
        "Introduction",
        "The 'aphid' package",
        "Hidden Markov Models",
        "Deriving HMMs from sequence data",
        "Profile Hidden Markov Models",
        "File I/O",
        "Sequence Simulation",
        "Model Training",
        "Sequence Alignment",
        "Further Reading",
        "Acknowledgements",
        "References"
      ],
      "created": "2017-03-21 07:11:42",
      "modified": "2026-01-22 08:11:53",
      "commits": 15
    }
  ],
  "_score": 6.977906427637118,
  "_indexed": true,
  "_nocasepkg": "aphid",
  "_universes": [
    "shaunpwilkinson"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.3.6",
      "date": "2026-10-18T10:00:07.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873",
      "fileid": "https://r2.ropensci.org/e80c956e3c5378fefa011865e3236bd92270036fc67ee48b6f346471b6080b6f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/shaunpwilkinson/actions/runs/39117226126"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.3.6",
      "date": "2026-10-18T10:00:27.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873",
      "fileid": "https://r2.ropensci.org/0d8e75ea6812822a1bec6b3677ef84378c58e699fdf120986394f5be16664fbb",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/shaunpwilkinson/actions/runs/39117226126"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.3.6",
      "date": "2026-10-18T10:00:54.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873",
      "fileid": "https://r2.ropensci.org/34a53639c9dc5129628f6359e16bd78211b58c4d31a7f4fa1d70fcb05436ca10",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/shaunpwilkinson/actions/runs/39117226126"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.3.6",
      "date": "2026-10-18T10:00:34.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873",
      "fileid": "https://r2.ropensci.org/6017121331e30577bf7e470ed42e6f54994036df9e08d3f61af8cdc323f4c934",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/shaunpwilkinson/actions/runs/39117226126"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.3.6",
      "date": "2026-10-18T10:00:29.000Z",
      "arch": "aarch64",
      "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873",
      "fileid": "https://r2.ropensci.org/ba4729dbff917ee706406035f9b67892f42483591f9dee78d70f45de55e1b2b1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/shaunpwilkinson/actions/runs/39117226126"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.3.6",
      "date": "2026-10-18T10:01:22.000Z",
      "arch": "x86_64",
      "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873",
      "fileid": "https://r2.ropensci.org/1d78d2470a57ba705ae7b349f2bc8aab4a123e1caf64828c11a62349f6863aec",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/shaunpwilkinson/actions/runs/39117226126"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.3.6",
      "date": "2026-10-18T10:00:15.000Z",
      "arch": "aarch64",
      "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873",
      "fileid": "https://r2.ropensci.org/88f88cb164a2e1f7d6244cbc1d0d1d7e1539bbe741eef08c41bc93b8aa2c8374",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/shaunpwilkinson/actions/runs/39117226126"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.3.6",
      "date": "2026-10-18T10:02:07.000Z",
      "arch": "x86_64",
      "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873",
      "fileid": "https://r2.ropensci.org/748a4ab9b28c4b09efae1219ab01ef503a044246e16bad9dc018bdd41fc5a859",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/shaunpwilkinson/actions/runs/39117226126"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.3.6",
      "date": "2026-10-18T10:00:29.000Z",
      "arch": "emscripten",
      "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873",
      "fileid": "https://r2.ropensci.org/d06eceb7054d813854d7780790778fc81a841075fe00a51f7c566a98a38db58e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/shaunpwilkinson/actions/runs/39117226126"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.3.6",
      "date": "2026-10-18T10:04:40.000Z",
      "arch": "aarch64",
      "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873",
      "fileid": "https://r2.ropensci.org/ca4c12371c53408b6a70ff7e03c004ffc3071a419b8af8b6bc2d5e578d1f47ae",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/shaunpwilkinson/actions/runs/39117226126"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.3.6",
      "date": "2026-10-18T09:59:36.000Z",
      "arch": "x86_64",
      "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873",
      "fileid": "https://r2.ropensci.org/1c28be11cd19fd708f440c6ace9e19659183a4d609760dd59962f046c87cf449",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/shaunpwilkinson/actions/runs/39117226126"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.3.6",
      "date": "2026-10-18T09:59:38.000Z",
      "arch": "x86_64",
      "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873",
      "fileid": "https://r2.ropensci.org/76cf562faaa0ea981945d842882d7daeba14386c5603642e82d6ff88c9428a0a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/shaunpwilkinson/actions/runs/39117226126"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.3.6",
      "date": "2026-10-18T10:03:25.000Z",
      "arch": "aarch64",
      "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873",
      "fileid": "https://r2.ropensci.org/1c5be7f73af8fc3eef8178cd9c8f9add6bce792bea62de84c85d99216083690a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/shaunpwilkinson/actions/runs/39117226126"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.3.6",
      "date": "2026-10-18T09:59:32.000Z",
      "arch": "x86_64",
      "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873",
      "fileid": "https://r2.ropensci.org/84af3819b12231f96ff472e63293ad3cfa32d9d5c4c2154c4d2e9880613bce28",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/shaunpwilkinson/actions/runs/39117226126"
    }
  ]
}