{
  "_id": "6ad0c3859a0ea1f99f78c1fc",
  "Package": "phylopred",
  "Type": "Package",
  "Title": "Predicting Species Interactions from Phylogenetic Distance",
  "Version": "0.1.0",
  "Authors@R": "c(\nperson(\"Angel\", \"Robles\", , \"a.l.robles.fernandez@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-4674-4270\")))",
  "Description": "Tools to model and predict host-parasite (and other\npairwise species) interactions from phylogenetic distance under\npresence-only data. Provides pairwise host-sharing logistic\nmodels with cluster-aware bootstrap and slope comparison\nbetween clades, presence-only performance metrics (a threshold\nefficiency metric and a phylogenetic partial receiver operating\ncharacteristic (ROC) adapted from Peterson, Papes and Soberon\n(2008) <doi:10.1016/j.ecolmodel.2007.11.008>),\npositive-unlabeled host prediction, and leave-hosts-out\nvalidation. Methods build on Robles-Fernandez and Lira-Noriega\n(2017) <doi:10.3389/fams.2017.00017>.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/alrobles/phylopred,\nhttps://alrobles.github.io/phylopred/",
  "BugReports": "https://github.com/alrobles/phylopred/issues",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Config/testthat/edition": "3",
  "Config/roxygen2/version": "8.0.0",
  "Repository": "https://alrobles.r-universe.dev",
  "Date/Publication": "2026-09-27 13:56:28 UTC",
  "RemoteUrl": "https://github.com/alrobles/phylopred",
  "RemoteRef": "HEAD",
  "RemoteSha": "ee81eb0b56a0ab8b7236b03b53132362ac943480",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-15 12:06:24 UTC",
    "User": "root"
  },
  "Author": "Angel Robles [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-4674-4270>)",
  "Maintainer": "Angel Robles <a.l.robles.fernandez@gmail.com>",
  "_user": "alrobles",
  "_type": "src",
  "_file": "phylopred_0.1.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/213e52dd3529768d1639af7a1180ac282e265d8a0b55dba665ef13bd6378d436",
  "_filesize": 283100,
  "_sha256": "213e52dd3529768d1639af7a1180ac282e265d8a0b55dba665ef13bd6378d436",
  "_expires": "2027-01-23T12:13:55.000Z",
  "_created": "2026-10-15T12:06:24.000Z",
  "_published": "2026-10-15T12:13:57.482Z",
  "_buildurl": "https://github.com/r-universe/alrobles/actions/runs/38731803176",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 116412411185,
      "time": 163,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11970772460"
    },
    {
      "job": 116412411177,
      "time": 111,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11970667478"
    },
    {
      "job": 116412411156,
      "time": 92,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11971137922"
    },
    {
      "job": 116412411244,
      "time": 117,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11970293280"
    },
    {
      "job": 116411266114,
      "time": 165,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11971416583"
    },
    {
      "job": 116412411052,
      "time": 92,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11971386726"
    },
    {
      "job": 116412411237,
      "time": 83,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11971371962"
    },
    {
      "job": 116412411413,
      "time": 81,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11970496970"
    },
    {
      "job": 116412411375,
      "time": 83,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11970277125"
    }
  ],
  "_upstream": "https://github.com/alrobles/phylopred",
  "_commit": {
    "id": "ee81eb0b56a0ab8b7236b03b53132362ac943480",
    "author": "Angel Robles <a.l.robles.fernandez@gmail.com>",
    "committer": "Angel Robles <a.l.robles.fernandez@gmail.com>",
    "message": "docs: move vignette to articles so it stays off the CRAN tarball\n\nVignette published by pkgdown under articles/ but excluded from the\npackage via .Rbuildignore (same pattern as xplus). Drops\nVignetteBuilder; knitr/rmarkdown remain in Suggests for CI.\n\nCo-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>\n",
    "time": 1790517388
  },
  "_maintainer": {
    "name": "Angel Robles",
    "email": "a.l.robles.fernandez@gmail.com",
    "login": "alrobles",
    "orcid": "0000-0002-4674-4270",
    "description": "Postdoctoral Research at University of Kansas",
    "uuid": 22551963
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "xplus",
      "role": "Imports"
    },
    {
      "package": "ape",
      "role": "Suggests"
    },
    {
      "package": "cofid",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "alrobles",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-39",
      "n": 15
    }
  ],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "alrobles",
      "count": 15,
      "uuid": 22551963
    }
  ],
  "_userbio": {
    "uuid": 22551963,
    "type": "user",
    "name": "Angel Luis Robles Fernández",
    "followers": 15,
    "description": "Postdoctoral Research at University of Kansas"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/phylopred"
  },
  "_devurl": "https://github.com/alrobles/phylopred",
  "_pkgdown": "https://alrobles.github.io/phylopred/",
  "_searchresults": 2,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/phylopred.html",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/alrobles/phylopred",
  "_realowner": "alrobles",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2026-10-14"
    }
  ],
  "_exports": [
    "align_phylopred_inputs",
    "bootstrap_phylopred_model",
    "cluster_bootstrap_phylopred",
    "compare_phylopred_slopes",
    "evaluate_phylopred_model",
    "extract_phylopred_coefficients",
    "fit_phylopred_model",
    "fit_phylopred_pu",
    "host_specificity_index",
    "host_threshold_metric",
    "phylo_partial_roc",
    "phylopred_confidence_ellipse",
    "poulin_std",
    "predict_phylopred_probability",
    "prepare_incidence_matrix",
    "prepare_pair_data",
    "taxonomic_step_matrix",
    "validate_host_prediction"
  ],
  "_datasets": [
    {
      "name": "beetleTreeInteractions",
      "title": "Beetle tree interaction table.",
      "object": "beetleTreeInteractions",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "beetle",
        "genus"
      ],
      "rows": 565,
      "table": true,
      "tojson": true
    },
    {
      "name": "fish_tree",
      "title": "Phylogenetic tree of marine fish hosts of Caligus and Lepeophtheirus",
      "object": "fish_tree",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "phy_dist",
      "title": "Phylogenetic distance matrix among host data on phylopred",
      "object": "phy_dist",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [],
      "rows": 235,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "align_phylopred_inputs",
      "title": "Align incidence matrix and phylogenetic distance matrix",
      "topics": [
        "align_phylopred_inputs"
      ]
    },
    {
      "page": "beetleTreeInteractions",
      "title": "Beetle tree interaction table.",
      "topics": [
        "beetleTreeInteractions"
      ]
    },
    {
      "page": "bootstrap_phylopred_model",
      "title": "Bootstrap a phylopred logistic regression model",
      "topics": [
        "bootstrap_phylopred_model"
      ]
    },
    {
      "page": "cluster_bootstrap_phylopred",
      "title": "Cluster bootstrap for pairwise host-sharing models",
      "topics": [
        "cluster_bootstrap_phylopred"
      ]
    },
    {
      "page": "compare_phylopred_slopes",
      "title": "Compare host-sharing slopes between two clades",
      "topics": [
        "compare_phylopred_slopes"
      ]
    },
    {
      "page": "evaluate_phylopred_model",
      "title": "Evaluate the predictive capacity of a pairwise host-sharing model",
      "topics": [
        "evaluate_phylopred_model"
      ]
    },
    {
      "page": "extract_phylopred_coefficients",
      "title": "Extract coefficients from a phylopred model or bootstrap object",
      "topics": [
        "extract_phylopred_coefficients"
      ]
    },
    {
      "page": "fish_tree",
      "title": "Phylogenetic tree of marine fish hosts of Caligus and Lepeophtheirus",
      "topics": [
        "fish_tree"
      ]
    },
    {
      "page": "fit_phylopred_model",
      "title": "Fit a phylopred logistic regression model",
      "topics": [
        "fit_phylopred_model"
      ]
    },
    {
      "page": "fit_phylopred_pu",
      "title": "Positive-unlabeled host prediction via xplus (PLUS algorithm)",
      "topics": [
        "fit_phylopred_pu"
      ]
    },
    {
      "page": "host_specificity_index",
      "title": "Host specificity index (S_TD) for every parasite in an interaction table",
      "topics": [
        "host_specificity_index"
      ]
    },
    {
      "page": "host_threshold_metric",
      "title": "Threshold metric f_gamma for predicted host suitability",
      "topics": [
        "host_threshold_metric"
      ]
    },
    {
      "page": "phy_dist",
      "title": "Phylogenetic distance matrix among host data on phylopred",
      "topics": [
        "phy_dist"
      ]
    },
    {
      "page": "phylo_partial_roc",
      "title": "Phylogenetic partial ROC (Peterson, Papes & Soberon 2008 analogue)",
      "topics": [
        "phylo_partial_roc"
      ]
    },
    {
      "page": "phylopred_confidence_ellipse",
      "title": "Joint confidence ellipse for intercept and slope",
      "topics": [
        "phylopred_confidence_ellipse"
      ]
    },
    {
      "page": "poulin_std",
      "title": "Poulin and Mouillot taxonomic/phylogenetic distinctness index (S_TD)",
      "topics": [
        "poulin_std"
      ]
    },
    {
      "page": "predict_phylopred_probability",
      "title": "Predict host susceptibility probabilities from logistic regression coefficients",
      "topics": [
        "predict_phylopred_probability"
      ]
    },
    {
      "page": "prepare_incidence_matrix",
      "title": "Prepare an incidence matrix from an interaction table",
      "topics": [
        "prepare_incidence_matrix"
      ]
    },
    {
      "page": "prepare_pair_data",
      "title": "Build a pairwise host-sharing data set from an interaction table",
      "topics": [
        "prepare_pair_data"
      ]
    },
    {
      "page": "taxonomic_step_matrix",
      "title": "Build a taxonomic step-distance matrix (Poulin & Mouillot scale)",
      "topics": [
        "taxonomic_step_matrix"
      ]
    },
    {
      "page": "validate_host_prediction",
      "title": "Leave-hosts-out validation of host predictions",
      "topics": [
        "validate_host_prediction"
      ]
    }
  ],
  "_readme": "https://github.com/alrobles/phylopred/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "codetools",
    "foreach",
    "glmnet",
    "glue",
    "iterators",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "pillar",
    "pkgconfig",
    "Rcpp",
    "RcppEigen",
    "rlang",
    "shape",
    "survival",
    "tibble",
    "utf8",
    "vctrs",
    "xplus"
  ],
  "_score": 2.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "phylopred",
  "_universes": [
    "alrobles"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-10-15T12:08:59.000Z",
      "distro": "resolute",
      "commit": "ee81eb0b56a0ab8b7236b03b53132362ac943480",
      "fileid": "https://r2.ropensci.org/0bddcded11f21bb8e96ef48800c9e54805622833e70feff4be9d8fdef29836f9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alrobles/actions/runs/38731803176"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-10-15T12:08:11.000Z",
      "distro": "resolute",
      "commit": "ee81eb0b56a0ab8b7236b03b53132362ac943480",
      "fileid": "https://r2.ropensci.org/3a9f69478bd526ec43ba4503cae0dcf55578af9950780b17662acb4b129cf9d2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alrobles/actions/runs/38731803176"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-10-15T12:13:19.000Z",
      "commit": "ee81eb0b56a0ab8b7236b03b53132362ac943480",
      "fileid": "https://r2.ropensci.org/da429a9f2f3053af6aee489f06f6510ad4f802854a5caccfa00225e78cba18ec",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alrobles/actions/runs/38731803176"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-10-15T12:11:34.000Z",
      "commit": "ee81eb0b56a0ab8b7236b03b53132362ac943480",
      "fileid": "https://r2.ropensci.org/afe8a17875658fcb2bf25cf4e324cb9bd016342c3f6ac39f9163190e53480ce4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alrobles/actions/runs/38731803176"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.0",
      "date": "2026-10-15T12:08:14.000Z",
      "commit": "ee81eb0b56a0ab8b7236b03b53132362ac943480",
      "fileid": "https://r2.ropensci.org/2708ecebb507fe7b25c597386a11ff184da56d5a9387e3fe8074d2f910d680f2",
      "status": "success",
      "buildurl": "https://github.com/r-universe/alrobles/actions/runs/38731803176"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-10-15T12:07:31.000Z",
      "commit": "ee81eb0b56a0ab8b7236b03b53132362ac943480",
      "fileid": "https://r2.ropensci.org/7abf16a5bfeb47b254203ca7c22da823db83fde90e1698885ea84d30b2e7630f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alrobles/actions/runs/38731803176"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-10-15T12:07:31.000Z",
      "commit": "ee81eb0b56a0ab8b7236b03b53132362ac943480",
      "fileid": "https://r2.ropensci.org/49bb564ef5cf67b7d7d01708b7d17106f21f5c2693ecd54ed6095bbd0f36bcc6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alrobles/actions/runs/38731803176"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-10-15T12:07:33.000Z",
      "commit": "ee81eb0b56a0ab8b7236b03b53132362ac943480",
      "fileid": "https://r2.ropensci.org/41b99e5fb6cf565daa41890719b4f4013dbbd3aa447b363a4f21a706a26fb13b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alrobles/actions/runs/38731803176"
    }
  ]
}