{
  "_id": "6a1efa21b401979e7341851e",
  "Package": "phyr",
  "Type": "Package",
  "Title": "Model Based Phylogenetic Analysis",
  "Version": "1.2.1",
  "Authors@R": "c(\nperson(\"Anthony\", \"Ives\", , \"arives@wisc.edu\", role = c(\"aut\")),\nperson(\"Russell\", \"Dinnage\", , \"r.dinnage@gmail.com\", role = c(\"aut\"), comment = c(ORCID = \"0000-0003-0846-2819\")),\nperson(c(\"Lucas\", \"A.\"), \"Nell\", , \"lucas@lucasnell.com\", role = c(\"aut\"), comment = c(ORCID = \"0000-0003-3209-0517\")),\nperson(\"Matthew\", \"Helmus\", , \"mrhelmus@temple.edu\", role = c(\"aut\")),\nperson(\"Daijiang\", \"Li\", , \"daijianglee@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-0925-3421\")))",
  "Description": "A collection of functions to do model-based phylogenetic\nanalysis. It includes functions to calculate community\nphylogenetic diversity, to estimate correlations among\nfunctional traits while accounting for phylogenetic\nrelationships, and to fit phylogenetic generalized linear mixed\nmodels. The Bayesian phylogenetic generalized linear mixed\nmodels are fitted with the 'INLA' package\n(<https://www.r-inla.org>).",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
  "VignetteBuilder": "knitr",
  "URL": "https://daijiang.github.io/phyr/,\nhttps://github.com/daijiang/phyr/",
  "BugReports": "https://github.com/daijiang/phyr/issues",
  "Additional_repositories": "https://inla.r-inla-download.org/R/stable/",
  "Config/testthat/edition": "3",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "cmake make libicu-dev libjpeg-dev libpng-dev",
  "Repository": "https://daijiang.r-universe.dev",
  "Date/Publication": "2026-05-18 20:05:08 UTC",
  "RemoteUrl": "https://github.com/daijiang/phyr",
  "RemoteRef": "HEAD",
  "RemoteSha": "b34dc3a3674c852f535a33b384dedcc0cff4447e",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-18 21:13:43 UTC",
    "User": "root"
  },
  "Author": "Anthony Ives [aut],\nRussell Dinnage [aut] (ORCID: <https://orcid.org/0000-0003-0846-2819>),\nLucas A. Nell [aut] (ORCID: <https://orcid.org/0000-0003-3209-0517>),\nMatthew Helmus [aut],\nDaijiang Li [aut, cre] (ORCID: <https://orcid.org/0000-0002-0925-3421>)",
  "Maintainer": "Daijiang Li <daijianglee@gmail.com>",
  "MD5sum": "080d825fa79529d32cb3afcc5a3e9daa",
  "_user": "daijiang",
  "_type": "src",
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  "_created": "2026-05-18T21:13:43.000Z",
  "_published": "2026-06-02T15:43:29.293Z",
  "_distro": "noble",
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    "author": "Daijiang <daijianglee@gmail.com>",
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    "message": "try to pass ubuntu-latest test\n",
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  "_tags": [],
  "_topics": [
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    "glmm",
    "inla",
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    "species-distribution-modeling",
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  "_devurl": "https://github.com/daijiang/phyr",
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.json",
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  "_realowner": "daijiang",
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  "_exports": [
    "%nin%",
    "align_comm_V",
    "boot_ci",
    "communityPGLMM",
    "communityPGLMM.matrix.structure",
    "communityPGLMM.plot.re",
    "communityPGLMM.predicted.values",
    "communityPGLMM.profile.LRT",
    "communityPGLMM.show.re",
    "cor_phylo",
    "fixef",
    "get_design_matrix",
    "match_comm_tree",
    "pcd",
    "pcd_pred",
    "pglmm",
    "pglmm_compare",
    "pglmm_matrix_structure",
    "pglmm_plot_ranef",
    "pglmm_plot_re",
    "pglmm_predicted_values",
    "pglmm_profile_LRT",
    "plot_bayes",
    "plot_data",
    "prep_dat_pglmm",
    "psc",
    "psd",
    "pse",
    "psr",
    "psv",
    "psv.spp",
    "ranef",
    "refit_boots",
    "rm_site_noobs",
    "rm_sp_noobs",
    "vcv2"
  ],
  "_datasets": [
    {
      "name": "comm_a",
      "title": "Example community data",
      "object": "comm_a",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Acer_rubrum",
        "Achillea_millefolium",
        "Amelanchier_spp",
        "Andropogon_gerardii",
        "Anemone_quinquefolia",
        "Apocynum_androsaemifolium",
        "Aquilegia_canadensis",
        "Aralia_nudicaulis",
        "Betula_papyrifera",
        "Chimaphila_umbellata",
        "Clintonia_borealis",
        "Comandra_umbellata",
        "Comptonia_peregrina",
        "Cornus_canadensis",
        "Corylus_americana"
      ],
      "rows": 15,
      "table": true,
      "tojson": true
    },
    {
      "name": "comm_b",
      "title": "Example community data",
      "object": "comm_b",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Acer_rubrum",
        "Amelanchier_spp",
        "Anemone_quinquefolia",
        "Apocynum_androsaemifolium",
        "Aralia_nudicaulis",
        "Aronia_melanocarpa",
        "Betula_papyrifera",
        "Brachyelytrum_erectum",
        "Carex_spp"
      ],
      "rows": 15,
      "table": true,
      "tojson": true
    },
    {
      "name": "envi",
      "title": "Example environmental data",
      "object": "envi",
      "class": [
        "data.frame"
      ],
      "fields": [
        "site",
        "sand",
        "shade",
        "precip",
        "tmin"
      ],
      "rows": 15,
      "table": true,
      "tojson": true
    },
    {
      "name": "oldfield",
      "title": "Phylogeny and community data from an Oldfield ecosystem in Southern Ontario, Canada",
      "object": "oldfield",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "phylotree",
      "title": "Example phylogeny",
      "object": "phylotree",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "traits",
      "title": "Example species traits data",
      "object": "traits",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sp",
        "sla",
        "veg.height",
        "disp.mode"
      ],
      "rows": 18,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "nin",
      "title": "Not in",
      "topics": [
        "%nin%"
      ]
    },
    {
      "page": "align_comm_V",
      "title": "Create phylogenetic var-cov matrix based on phylogeny and community data",
      "topics": [
        "align_comm_V"
      ]
    },
    {
      "page": "boot_ci",
      "title": "Generic method to output bootstrap confidence intervals from an object.",
      "topics": [
        "boot_ci"
      ]
    },
    {
      "page": "comm_a",
      "title": "Example community data",
      "topics": [
        "comm_a"
      ]
    },
    {
      "page": "comm_b",
      "title": "Example community data",
      "topics": [
        "comm_b"
      ]
    },
    {
      "page": "cor_phylo",
      "title": "Correlations among multiple variates with phylogenetic signal",
      "topics": [
        "boot_ci.cor_phylo",
        "cor_phylo",
        "print.cor_phylo"
      ]
    },
    {
      "page": "envi",
      "title": "Example environmental data",
      "topics": [
        "envi"
      ]
    },
    {
      "page": "family.communityPGLMM",
      "title": "Family Objects for communityPGLMM objects",
      "topics": [
        "family.communityPGLMM"
      ]
    },
    {
      "page": "fitted.communityPGLMM",
      "title": "Fitted values for communityPGLMM",
      "topics": [
        "fitted.communityPGLMM"
      ]
    },
    {
      "page": "fixef",
      "title": "Extract fixed-effects estimates",
      "topics": [
        "fixed.effects",
        "fixef",
        "fixef.communityPGLMM"
      ]
    },
    {
      "page": "get_design_matrix_pglmm",
      "title": "'get_design_matrix' gets design matrix for gaussian, binomial, and poisson models",
      "topics": [
        "get_design_matrix"
      ]
    },
    {
      "page": "match_comm_tree",
      "title": "Match phylogeny with community data",
      "topics": [
        "match_comm_tree"
      ]
    },
    {
      "page": "model.frame.communityPGLMM",
      "title": "Extracting the Model Frame from a communityPGLMM Model object",
      "topics": [
        "model.frame.communityPGLMM"
      ]
    },
    {
      "page": "nobs.communityPGLMM",
      "title": "Number of Observation in a communityPGLMM Model",
      "topics": [
        "nobs.communityPGLMM"
      ]
    },
    {
      "page": "oldfield",
      "title": "Phylogeny and community data from an Oldfield ecosystem in Southern Ontario, Canada",
      "topics": [
        "oldfield"
      ]
    },
    {
      "page": "pcd",
      "title": "pairwise site phylogenetic community dissimilarity (PCD) within a community",
      "topics": [
        "pcd"
      ]
    },
    {
      "page": "pcd_pred",
      "title": "Predicted PCD with species pool",
      "topics": [
        "pcd_pred"
      ]
    },
    {
      "page": "pglmm",
      "title": "Phylogenetic Generalized Linear Mixed Model for Community Data",
      "topics": [
        "communityPGLMM",
        "pglmm"
      ]
    },
    {
      "page": "pglmm_compare",
      "title": "Phylogenetic Generalized Linear Mixed Model for Comparative Data",
      "topics": [
        "pglmm_compare"
      ]
    },
    {
      "page": "pglmm-matrix-structure",
      "title": "'pglmm_matrix_structure' produces the entire covariance matrix structure (V) when you specify random effects.",
      "topics": [
        "communityPGLMM.matrix.structure",
        "pglmm_matrix_structure"
      ]
    },
    {
      "page": "pglmm-plot-re",
      "title": "Visualize random terms of communityPGLMMs",
      "topics": [
        "communityPGLMM.plot.re",
        "communityPGLMM.show.re",
        "pglmm_plot_ranef",
        "pglmm_plot_re"
      ]
    },
    {
      "page": "pglmm-predicted-values",
      "title": "Predicted values of PGLMM",
      "topics": [
        "communityPGLMM.predicted.values",
        "pglmm_predicted_values"
      ]
    },
    {
      "page": "pglmm-profile-LRT",
      "title": "Testing statistical significance of random effect",
      "topics": [
        "communityPGLMM.profile.LRT",
        "pglmm_profile_LRT"
      ]
    },
    {
      "page": "phylotree",
      "title": "Example phylogeny",
      "topics": [
        "phylotree"
      ]
    },
    {
      "page": "plot_bayes",
      "title": "plot_bayes generic",
      "topics": [
        "plot_bayes"
      ]
    },
    {
      "page": "pglmm-plot-data",
      "title": "Plot the original dataset and predicted values (optional)",
      "topics": [
        "plot_bayes.communityPGLMM",
        "plot_data"
      ]
    },
    {
      "page": "predict.communityPGLMM",
      "title": "Predict Function for communityPGLMM Model Objects",
      "topics": [
        "predict.communityPGLMM"
      ]
    },
    {
      "page": "prep_dat_pglmm",
      "title": "Prepare data for 'pglmm'",
      "topics": [
        "prep_dat_pglmm"
      ]
    },
    {
      "page": "print.communityPGLMM",
      "title": "Print summary information of fitted model",
      "topics": [
        "print.communityPGLMM"
      ]
    },
    {
      "page": "print.pglmm_compare",
      "title": "Print summary information of fitted model",
      "topics": [
        "print.pglmm_compare"
      ]
    },
    {
      "page": "psd",
      "title": "Phylogenetic Species Diversity Metrics",
      "topics": [
        "psc",
        "psd",
        "pse",
        "psr",
        "psv",
        "psv.spp"
      ]
    },
    {
      "page": "ranef",
      "title": "Extract random-effects estimates",
      "topics": [
        "random.effects",
        "ranef",
        "ranef.communityPGLMM"
      ]
    },
    {
      "page": "refit_boots",
      "title": "Refit bootstrap replicates that failed to converge in a call to 'cor_phylo'",
      "topics": [
        "print.cp_refits",
        "refit_boots"
      ]
    },
    {
      "page": "residuals.communityPGLMM",
      "title": "Residuals of communityPGLMM objects",
      "topics": [
        "residuals.communityPGLMM"
      ]
    },
    {
      "page": "rm_site_noobs",
      "title": "Remove site that has no observations of any species",
      "topics": [
        "rm_site_noobs"
      ]
    },
    {
      "page": "rm_sp_noobs",
      "title": "Remove species that not observed in any site",
      "topics": [
        "rm_sp_noobs"
      ]
    },
    {
      "page": "simulate.communityPGLMM",
      "title": "Simulate from a communityPGLMM object",
      "topics": [
        "simulate.communityPGLMM"
      ]
    },
    {
      "page": "summary.communityPGLMM",
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