{
  "_id": "6a47953a2f27a93436c0e0ec",
  "Package": "extBatchMarking",
  "Type": "Package",
  "Title": "Extended Batch Marking Models",
  "Version": "1.1.0",
  "Date": "2024-10-04",
  "Maintainer": "Kehinde Olobatuyi <olobatuyikenny@uvic.ca>",
  "Authors@R": "c(person(given = \"Kehinde\",\nfamily = \"Olobatuyi\",\nrole = c(\"aut\", \"cre\"),\nemail = \"olobatuyikenny@uvic.ca\",\ncomment = c(ORCID = \"0000-0002-4635-7895\")),\nperson(given = \"Simon\",\nfamily = \"Johns\",\nrole = c(\"aut\"),\nemail = \"simon737@outlook.com\"),\nperson(given = \"Matthew RP\",\nfamily = \"Parker\",\nrole = c(\"aut\"),\nemail = \"mrparker909@gmail.com\",\ncomment = c(ORCID = \"0000-0003-3021-7959\")),\nperson(given = \"Steve\",\nfamily = \"Hof\",\nrole = c(\"aut\"),\nemail = \"steven.Hof@icloud.com\"),\nperson(given = \"Laura LE\",\nfamily = \"Cowen\",\nrole = c(\"aut\"),\nemail = \"lcowen@uvic.ca\",\ncomment = c(ORCID = \"0000-0002-0853-1450\")) )",
  "Description": "A system for batch-marking data analysis to estimate\nsurvival probabilities, capture probabilities, and enumerate\nthe population abundance for both marked and unmarked\nindividuals. The estimation of only marked individuals can be\nachieved through the batchMarkOptim() function. Similarly, the\ncombined marked and unmarked can be achieved through the\nbatchMarkUnmarkOptim() function. The algorithm was also\nimplemented for the hidden Markov model encapsulated in\nbatchMarkUnmarkOptim() to estimate the abundance of both marked\nand unmarked individuals in the population. The package is\nbased on the paper: \"Hidden Markov Models for Extended Batch\nData\" of Cowen et al. (2017) <doi:10.1111/biom.12701>.",
  "License": "AGPL (>= 3)",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "LazyData": "true",
  "Config/testthat/edition": "3",
  "URL": "https://github.com/Olobatuyi/extBatchMarking",
  "BugReports": "https://github.com/Olobatuyi/extBatchMarking/issues",
  "Repository": "https://olobatuyi.r-universe.dev",
  "Date/Publication": "2025-06-07 01:56:18 UTC",
  "RemoteUrl": "https://github.com/olobatuyi/extbatchmarking_cov",
  "RemoteRef": "HEAD",
  "RemoteSha": "aad4d3bef205480a434eb77ccddac3eacb48978f",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-07-03 05:18:26 UTC",
    "User": "root"
  },
  "Author": "Kehinde Olobatuyi [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-4635-7895>),\nSimon Johns [aut],\nMatthew RP Parker [aut] (ORCID:\n<https://orcid.org/0000-0003-3021-7959>),\nSteve Hof [aut],\nLaura LE Cowen [aut] (ORCID: <https://orcid.org/0000-0002-0853-1450>)",
  "_user": "olobatuyi",
  "_type": "src",
  "_file": "extBatchMarking_1.1.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/8ffa3949b96555ea2b8107722cdef1e1211fbca7bf914510adfbfaba2c7518fa",
  "_filesize": 156159,
  "_sha256": "8ffa3949b96555ea2b8107722cdef1e1211fbca7bf914510adfbfaba2c7518fa",
  "_expires": "2026-10-11T10:55:54.000Z",
  "_created": "2026-07-03T05:18:26.000Z",
  "_published": "2026-07-03T10:55:54.758Z",
  "_jobs": [
    {
      "job": 84985074707,
      "time": 152,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8058390751"
    },
    {
      "job": 84985074627,
      "time": 138,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8058386916"
    },
    {
      "job": 84985074756,
      "time": 159,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8058392253"
    },
    {
      "job": 84985074915,
      "time": 134,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8058385695"
    },
    {
      "job": 84985074548,
      "time": 145,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8058383128"
    },
    {
      "job": 84985074738,
      "time": 290,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8058414618"
    },
    {
      "job": 84985074557,
      "time": 134,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8058380785"
    },
    {
      "job": 84985074540,
      "time": 233,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8058404490"
    },
    {
      "job": 84985074496,
      "time": 185,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8058355394"
    },
    {
      "job": 84985074565,
      "time": 152,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8058389867"
    },
    {
      "job": 84985074580,
      "time": 125,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8058384022"
    },
    {
      "job": 84985074617,
      "time": 106,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8058379492"
    },
    {
      "job": 84985074800,
      "time": 112,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8058380924"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/olobatuyi/actions/runs/28640034261",
  "_status": "success",
  "_upstream": "https://github.com/olobatuyi/extbatchmarking_cov",
  "_commit": {
    "id": "aad4d3bef205480a434eb77ccddac3eacb48978f",
    "author": "Kehinde Olobatuyi <olobatuyikenny@uvic.ca>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #1 from Olobatuyi/Olobatuyi-patch-1\n\nUpdate README.md",
    "time": 1749261378
  },
  "_maintainer": {
    "name": "Kehinde Olobatuyi",
    "email": "olobatuyikenny@uvic.ca",
    "login": "olobatuyi",
    "description": "Post-doc",
    "uuid": 39940583,
    "orcid": "0000-0002-4635-7895"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "optimbase",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    }
  ],
  "_owner": "olobatuyi",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "olobatuyi",
      "count": 7,
      "uuid": 39940583
    }
  ],
  "_userbio": {
    "uuid": 39940583,
    "type": "user",
    "name": "Kehinde Olobatuyi",
    "followers": 1,
    "description": "Post-doc"
  },
  "_downloads": {
    "count": 248,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/extBatchMarking"
  },
  "_devurl": "https://github.com/olobatuyi/extbatchmarking",
  "_searchresults": 11,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/extBatchMarking.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/olobatuyi/extbatchmarking_cov",
  "_realowner": "olobatuyi",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0",
      "date": "2023-12-17"
    },
    {
      "version": "1.0.1",
      "date": "2024-01-10"
    },
    {
      "version": "1.1.0",
      "date": "2024-10-04"
    }
  ],
  "_exports": [
    "batchMarkHmmLL",
    "batchMarkOptim",
    "batchMarkUnmarkHmmLL",
    "batchMarkUnmarkOptim"
  ],
  "_datasets": [
    {
      "name": "WeatherLoach",
      "title": "Weather Loach data",
      "object": "WeatherLoach",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [],
      "rows": 11,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "batchLL",
      "title": "batchLL function provides the batch marking log-likelihood",
      "topics": [
        "batchLL"
      ]
    },
    {
      "page": "batchLogit",
      "title": "batchLogit function",
      "topics": [
        "batchLogit"
      ]
    },
    {
      "page": "batchMarkHmmLL",
      "title": "Log-likelihood function for marked model.",
      "topics": [
        "batchMarkHmmLL"
      ]
    },
    {
      "page": "batchMarkOptim",
      "title": "Marked model only.",
      "topics": [
        "batchMarkOptim"
      ]
    },
    {
      "page": "batchMarkUnmarkHmmLL",
      "title": "Log-likelihood function for combined model.",
      "topics": [
        "batchMarkUnmarkHmmLL"
      ]
    },
    {
      "page": "batchMarkUnmarkOptim",
      "title": "Combined Marked and Unmarked models.",
      "topics": [
        "batchMarkUnmarkOptim"
      ]
    },
    {
      "page": "batchUnmark2Viterbi",
      "title": "batchUnmark2Viterbi function provides a wrapper for the batchUnmarkViterbi to compute the popuation abundance",
      "topics": [
        "batchUnmark2Viterbi"
      ]
    },
    {
      "page": "batchUnmarkHmmLL",
      "title": "batchUnmarkHmmLL function provides the unmarked function to be optimized",
      "topics": [
        "batchUnmarkHmmLL"
      ]
    },
    {
      "page": "batchUnmarkViterbi",
      "title": "batchUnmarkViterbi function provides the implementation of the Viterbi alogrithm for the unmarked model",
      "topics": [
        "batchUnmarkViterbi"
      ]
    },
    {
      "page": "dbinpois",
      "title": "Convolution of Poisson and Binomial for Batch",
      "topics": [
        "dbinpois"
      ]
    },
    {
      "page": "delta_g",
      "title": "initial probability function",
      "topics": [
        "delta_g"
      ]
    },
    {
      "page": "gamma_gt",
      "title": "Transition State Probability 'gamma_gt' computes the transition probability matrix",
      "topics": [
        "gamma_gt"
      ]
    },
    {
      "page": "plot.batchMarkOptim",
      "title": "Plot Method for batchMarkUnmarkOptim Objects",
      "topics": [
        "plot.batchMarkOptim"
      ]
    },
    {
      "page": "plot.batchMarkUnmarkOptim",
      "title": "Plot Method for batchMarkUnmarkOptim Objects",
      "topics": [
        "plot.batchMarkUnmarkOptim"
      ]
    },
    {
      "page": "print.batchMarkOptim",
      "title": "Print Method for batchMarkOptim Objects",
      "topics": [
        "print.batchMarkOptim"
      ]
    },
    {
      "page": "print.batchMarkUnmarkOptim",
      "title": "Print Method for batchMarkUnmarkOptim Objects",
      "topics": [
        "print.batchMarkUnmarkOptim"
      ]
    },
    {
      "page": "probs",
      "title": "State-dependent probability function",
      "topics": [
        "probs"
      ]
    },
    {
      "page": "WeatherLoach",
      "title": "Weather Loach data",
      "topics": [
        "WeatherLoach"
      ]
    }
  ],
  "_readme": "https://github.com/olobatuyi/extbatchmarking_cov/raw/HEAD/README.md",
  "_rundeps": [
    "codetools",
    "doParallel",
    "foreach",
    "iterators",
    "lattice",
    "Matrix",
    "optimbase",
    "Rcpp",
    "RcppArmadillo"
  ],
  "_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"
    }
  ],
  "_score": 2.740362689494244,
  "_indexed": true,
  "_nocasepkg": "extbatchmarking",
  "_universes": [
    "olobatuyi"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-07-03T05:21:01.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "aad4d3bef205480a434eb77ccddac3eacb48978f",
      "fileid": "https://r2.ropensci.org/4252567a694d852396f3387aea7d7bc1a7fec196de218d8422b2bd9d15216d59",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/olobatuyi/actions/runs/28640034261"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-07-03T05:20:37.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "aad4d3bef205480a434eb77ccddac3eacb48978f",
      "fileid": "https://r2.ropensci.org/2816c6acfc29b4c821cc9fa42378c7a7dda43be184d47465014194ad38181353",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/olobatuyi/actions/runs/28640034261"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-07-03T05:21:07.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "aad4d3bef205480a434eb77ccddac3eacb48978f",
      "fileid": "https://r2.ropensci.org/46d99ade816e029f354be35c26c2d053b98e57f06bdac64ea5be81e10af21017",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/olobatuyi/actions/runs/28640034261"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-07-03T05:20:33.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "aad4d3bef205480a434eb77ccddac3eacb48978f",
      "fileid": "https://r2.ropensci.org/6bf990e4bea5a0a39bed88906b16063f3e57c2f7b15342c12263842e34bf8600",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/olobatuyi/actions/runs/28640034261"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-07-03T05:20:32.000Z",
      "arch": "aarch64",
      "commit": "aad4d3bef205480a434eb77ccddac3eacb48978f",
      "fileid": "https://r2.ropensci.org/cedb850bd07a460d865dbd83adc2fe7f93cd38a8cad77b5f2b4e0b6e8e7f848d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/olobatuyi/actions/runs/28640034261"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-07-03T05:22:08.000Z",
      "arch": "x86_64",
      "commit": "aad4d3bef205480a434eb77ccddac3eacb48978f",
      "fileid": "https://r2.ropensci.org/17857b96c9d7b423764380d36733ac24cd4f6649659b8086b8901acf74073133",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/olobatuyi/actions/runs/28640034261"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-07-03T05:20:19.000Z",
      "arch": "aarch64",
      "commit": "aad4d3bef205480a434eb77ccddac3eacb48978f",
      "fileid": "https://r2.ropensci.org/449c236b5c82f596ef109ffd8cc7f9a96a312217d7d533ce16c7c2d778fdeb0d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/olobatuyi/actions/runs/28640034261"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-07-03T05:21:31.000Z",
      "arch": "x86_64",
      "commit": "aad4d3bef205480a434eb77ccddac3eacb48978f",
      "fileid": "https://r2.ropensci.org/a44aef464e0b9a5dfdbc4950d5ddd10a0921d6ff6d8809c8f5a5e1c45a34a1c5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/olobatuyi/actions/runs/28640034261"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.0",
      "date": "2026-07-03T05:21:16.000Z",
      "arch": "emscripten",
      "commit": "aad4d3bef205480a434eb77ccddac3eacb48978f",
      "fileid": "https://r2.ropensci.org/3a03fc62f36cd648c95bd8cbdc2aaf361e14e91eac2b7e7dda1e783c7c6bd2f4",
      "status": "success",
      "buildurl": "https://github.com/r-universe/olobatuyi/actions/runs/28640034261"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-07-03T05:19:57.000Z",
      "arch": "x86_64",
      "commit": "aad4d3bef205480a434eb77ccddac3eacb48978f",
      "fileid": "https://r2.ropensci.org/c93286e5ee75aed14a9bd0d047cbd5c7b758d01ae00cfcc9a4b582b60b94365f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/olobatuyi/actions/runs/28640034261"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-07-03T05:19:41.000Z",
      "arch": "x86_64",
      "commit": "aad4d3bef205480a434eb77ccddac3eacb48978f",
      "fileid": "https://r2.ropensci.org/57b09784fbc5cc7fa1869a6f1cd27395df5c5eb02bca500990dd381892a0fbc3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/olobatuyi/actions/runs/28640034261"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-07-03T05:19:48.000Z",
      "arch": "x86_64",
      "commit": "aad4d3bef205480a434eb77ccddac3eacb48978f",
      "fileid": "https://r2.ropensci.org/bd71feb25d054ebc810c018b42b5039f316a5ba0671acbecbd2950f367eca9ea",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/olobatuyi/actions/runs/28640034261"
    }
  ]
}