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  "Package": "glinvci",
  "Type": "Package",
  "Title": "Phylogenetic Comparative Methods with Uncertainty Estimates",
  "Version": "1.2.4",
  "Date": "2024-04-16",
  "Authors@R": "c(person(family=\"Kiang\", given=\"Woodrow\", role=c(\"cre\",\"aut\"), email=\"hello@hckiang.com\"))",
  "Maintainer": "Woodrow Kiang <hello@hckiang.com>",
  "Description": "A framework for analytically computing the asymptotic\nconfidence intervals and maximum-likelihood estimates of a\nclass of continuous-time Gaussian branching processes defined\nby Mitov V, Bartoszek K, Asimomitis G, Stadler T (2019)\n<doi:10.1016/j.tpb.2019.11.005>. The class of model includes\nthe widely used Ornstein-Uhlenbeck and Brownian motion\nbranching processes. The framework is designed to be flexible\nenough so that the users can easily specify their own\nsub-models, or re-parameterizations, and obtain the\nmaximum-likelihood estimates and confidence intervals of their\nown custom models.",
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  "RoxygenNote": "7.2.2",
  "VignetteBuilder": "utils",
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  "Config/pak/sysreqs": "cmake",
  "Repository": "https://hckiang.r-universe.dev",
  "Date/Publication": "2024-04-16 22:15:52 UTC",
  "RemoteUrl": "https://github.com/hckiang/glinvci",
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    "author": "Hao Chi Kiang <hello@hckiang.com>",
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    "message": "Patch get_restriction_ou.Rd example\n",
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    "manual.pdf"
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    "brn_diagSig",
    "brn_fixedSig",
    "clone_model",
    "dbrn",
    "dbrn_diagSig",
    "dbrn_fixedSig",
    "dou_diagH",
    "dou_diagH_diagSig",
    "dou_diagH_fixedSig",
    "dou_diagH_fixedtheta",
    "dou_diagH_fixedtheta_diagSig",
    "dou_diagH_fixedtheta_fixedSig",
    "dou_diagSig",
    "dou_fixedH",
    "dou_fixedH_diagSig",
    "dou_fixedH_fixedSig",
    "dou_fixedH_fixedtheta",
    "dou_fixedH_fixedtheta_diagSig",
    "dou_fixedSig",
    "dou_fixedtheta",
    "dou_fixedtheta_diagSig",
    "dou_fixedtheta_fixedSig",
    "dou_haltlost",
    "dou_logdiagH",
    "dou_logdiagH_diagSig",
    "dou_logdiagH_fixedSig",
    "dou_logdiagH_fixedtheta",
    "dou_logdiagH_fixedtheta_diagSig",
    "dou_logdiagH_fixedtheta_fixedSig",
    "dou_logspdH",
    "dou_logspdH_diagSig",
    "dou_logspdH_fixedSig",
    "dou_logspdH_fixedtheta",
    "dou_logspdH_fixedtheta_diagSig",
    "dou_logspdH_fixedtheta_fixedSig",
    "dou_spdH",
    "dou_spdH_diagSig",
    "dou_spdH_fixedSig",
    "dou_spdH_fixedtheta",
    "dou_spdH_fixedtheta_diagSig",
    "dou_spdH_fixedtheta_fixedSig",
    "dou_symH",
    "dou_symH_diagSig",
    "dou_symH_fixedSig",
    "dou_symH_fixedtheta",
    "dou_symH_fixedtheta_diagSig",
    "dou_symH_fixedtheta_fixedSig",
    "dou_zaplost",
    "fit",
    "get_restricted_ou",
    "glinv",
    "glinv_gauss",
    "grad",
    "has_tipvals",
    "hbrn",
    "hbrn_diagSig",
    "hbrn_fixedSig",
    "hess",
    "hou_diagH",
    "hou_diagH_diagSig",
    "hou_diagH_fixedSig",
    "hou_diagH_fixedtheta",
    "hou_diagH_fixedtheta_diagSig",
    "hou_diagH_fixedtheta_fixedSig",
    "hou_diagSig",
    "hou_fixedH",
    "hou_fixedH_diagSig",
    "hou_fixedH_fixedSig",
    "hou_fixedH_fixedtheta",
    "hou_fixedH_fixedtheta_diagSig",
    "hou_fixedSig",
    "hou_fixedtheta",
    "hou_fixedtheta_diagSig",
    "hou_fixedtheta_fixedSig",
    "hou_haltlost",
    "hou_logdiagH",
    "hou_logdiagH_diagSig",
    "hou_logdiagH_fixedSig",
    "hou_logdiagH_fixedtheta",
    "hou_logdiagH_fixedtheta_diagSig",
    "hou_logdiagH_fixedtheta_fixedSig",
    "hou_logspdH",
    "hou_logspdH_diagSig",
    "hou_logspdH_fixedSig",
    "hou_logspdH_fixedtheta",
    "hou_logspdH_fixedtheta_diagSig",
    "hou_logspdH_fixedtheta_fixedSig",
    "hou_spdH",
    "hou_spdH_diagSig",
    "hou_spdH_fixedSig",
    "hou_spdH_fixedtheta",
    "hou_spdH_fixedtheta_diagSig",
    "hou_spdH_fixedtheta_fixedSig",
    "hou_symH",
    "hou_symH_diagSig",
    "hou_symH_fixedSig",
    "hou_symH_fixedtheta",
    "hou_symH_fixedtheta_diagSig",
    "hou_symH_fixedtheta_fixedSig",
    "hou_zaplost",
    "lik",
    "marginal_ci",
    "nparams_brn",
    "nparams_brn_diagSig",
    "nparams_brn_fixedSig",
    "nparams_ou",
    "nparams_ou_diagH",
    "nparams_ou_diagH_diagSig",
    "nparams_ou_diagH_fixedSig",
    "nparams_ou_diagH_fixedtheta",
    "nparams_ou_diagH_fixedtheta_diagSig",
    "nparams_ou_diagH_fixedtheta_fixedSig",
    "nparams_ou_diagSig",
    "nparams_ou_fixedH",
    "nparams_ou_fixedH_diagSig",
    "nparams_ou_fixedH_fixedSig",
    "nparams_ou_fixedH_fixedtheta",
    "nparams_ou_fixedH_fixedtheta_diagSig",
    "nparams_ou_fixedSig",
    "nparams_ou_fixedtheta",
    "nparams_ou_fixedtheta_diagSig",
    "nparams_ou_fixedtheta_fixedSig",
    "nparams_ou_logdiagH",
    "nparams_ou_logdiagH_diagSig",
    "nparams_ou_logdiagH_fixedSig",
    "nparams_ou_logdiagH_fixedtheta",
    "nparams_ou_logdiagH_fixedtheta_diagSig",
    "nparams_ou_logdiagH_fixedtheta_fixedSig",
    "nparams_ou_logspdH",
    "nparams_ou_logspdH_diagSig",
    "nparams_ou_logspdH_fixedSig",
    "nparams_ou_logspdH_fixedtheta",
    "nparams_ou_logspdH_fixedtheta_diagSig",
    "nparams_ou_logspdH_fixedtheta_fixedSig",
    "nparams_ou_spdH",
    "nparams_ou_spdH_diagSig",
    "nparams_ou_spdH_fixedSig",
    "nparams_ou_spdH_fixedtheta",
    "nparams_ou_spdH_fixedtheta_diagSig",
    "nparams_ou_spdH_fixedtheta_fixedSig",
    "nparams_ou_symH",
    "nparams_ou_symH_diagSig",
    "nparams_ou_symH_fixedSig",
    "nparams_ou_symH_fixedtheta",
    "nparams_ou_symH_fixedtheta_diagSig",
    "nparams_ou_symH_fixedtheta_fixedSig",
    "ou_diagH",
    "ou_diagH_diagSig",
    "ou_diagH_fixedSig",
    "ou_diagH_fixedtheta",
    "ou_diagH_fixedtheta_diagSig",
    "ou_diagH_fixedtheta_fixedSig",
    "ou_diagSig",
    "ou_fixedH",
    "ou_fixedH_diagSig",
    "ou_fixedH_fixedSig",
    "ou_fixedH_fixedtheta",
    "ou_fixedH_fixedtheta_diagSig",
    "ou_fixedSig",
    "ou_fixedtheta",
    "ou_fixedtheta_diagSig",
    "ou_fixedtheta_fixedSig",
    "ou_haltlost",
    "ou_logdiagH",
    "ou_logdiagH_diagSig",
    "ou_logdiagH_fixedSig",
    "ou_logdiagH_fixedtheta",
    "ou_logdiagH_fixedtheta_diagSig",
    "ou_logdiagH_fixedtheta_fixedSig",
    "ou_logspdH",
    "ou_logspdH_diagSig",
    "ou_logspdH_fixedSig",
    "ou_logspdH_fixedtheta",
    "ou_logspdH_fixedtheta_diagSig",
    "ou_logspdH_fixedtheta_fixedSig",
    "ou_spdH",
    "ou_spdH_diagSig",
    "ou_spdH_fixedSig",
    "ou_spdH_fixedtheta",
    "ou_spdH_fixedtheta_diagSig",
    "ou_spdH_fixedtheta_fixedSig",
    "ou_symH",
    "ou_symH_diagSig",
    "ou_symH_fixedSig",
    "ou_symH_fixedtheta",
    "ou_symH_fixedtheta_diagSig",
    "ou_symH_fixedtheta_fixedSig",
    "ou_zaplost",
    "ouhess",
    "oujac",
    "oupar",
    "rglinv",
    "set_tips",
    "varest"
  ],
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    {
      "page": "clone_model",
      "title": "Clone a GLInv model",
      "topics": [
        "clone_model",
        "clone_model.glinv",
        "clone_model.glinv_gauss"
      ]
    },
    {
      "page": "fit.glinv",
      "title": "Fitting a GLInv model via numerical optimisation",
      "topics": [
        "fit.glinv"
      ]
    },
    {
      "page": "get_restricted_ou",
      "title": "Convenience function for constructing restricted/reparameterised OU parameterisation function.",
      "topics": [
        "get_restricted_ou"
      ]
    },
    {
      "page": "glinv",
      "title": "Construct an GLInv model with respect to user-specified parametrisation",
      "topics": [
        "glinv",
        "grad.glinv",
        "hess.glinv",
        "lik.glinv",
        "plot.glinv",
        "print.glinv"
      ]
    },
    {
      "page": "glinv_gauss",
      "title": "Construct an object representing a GLInv model with respect to the underlying Gaussian process parameters.",
      "topics": [
        "glinv_gauss",
        "grad.glinv_gauss",
        "hess.glinv_gauss",
        "lik.glinv_gauss",
        "print.glinv_gauss"
      ]
    },
    {
      "page": "glinvci",
      "title": "glinvci: Confidence intervals and hypothesis testing for GLInv model",
      "topics": [
        "glinvci-package",
        "glinvci"
      ]
    },
    {
      "page": "grad",
      "title": "Compute the log-likelihood gradients of GLInv models",
      "topics": [
        "grad"
      ]
    },
    {
      "page": "has_tipvals",
      "title": "Check if a 'glinv_gauss' model contains trait values at their tips.",
      "topics": [
        "has_tipvals",
        "has_tipvals.glinv",
        "has_tipvals.glinv_gauss"
      ]
    },
    {
      "page": "hess",
      "title": "Compute the log-likelihood Hessian of GLInv models",
      "topics": [
        "hess"
      ]
    },
    {
      "page": "lik",
      "title": "Compute the likelihood of a GLInv model",
      "topics": [
        "lik"
      ]
    },
    {
      "page": "marginal_ci",
      "title": "Getting marginal confidence interval for GLInv model",
      "topics": [
        "marginal_ci"
      ]
    },
    {
      "page": "nparams_ou",
      "title": "Get the number of parameters of the unrestricted OU model",
      "topics": [
        "nparams_ou"
      ]
    },
    {
      "page": "ou_haltlost",
      "title": "Handling missing data and lost traits in Ornstein-Uhlenbeck processes",
      "topics": [
        "dou_haltlost",
        "dou_zaplost",
        "hou_haltlost",
        "hou_zaplost",
        "ou_haltlost",
        "ou_zaplost"
      ]
    },
    {
      "page": "oupar",
      "title": "Parameterisation functions of Ornstein-Uhlenbeck model",
      "topics": [
        "ouhess",
        "oujac",
        "oupar"
      ]
    },
    {
      "page": "parameter_restriction",
      "title": "Restrict the parameters space of OU and Brownian motion models.",
      "topics": [
        "avail_restrictions",
        "brn",
        "brn_diagSig",
        "brn_fixedSig",
        "dbrn",
        "dbrn_diagSig",
        "dbrn_fixedSig",
        "dou_diagH",
        "dou_diagH_diagSig",
        "dou_diagH_fixedSig",
        "dou_diagH_fixedtheta",
        "dou_diagH_fixedtheta_diagSig",
        "dou_diagH_fixedtheta_fixedSig",
        "dou_diagSig",
        "dou_fixedH",
        "dou_fixedH_diagSig",
        "dou_fixedH_fixedSig",
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        "dou_logdiagH_diagSig",
        "dou_logdiagH_fixedSig",
        "dou_logdiagH_fixedtheta",
        "dou_logdiagH_fixedtheta_diagSig",
        "dou_logdiagH_fixedtheta_fixedSig",
        "dou_logspdH",
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        "dou_logspdH_fixedtheta",
        "dou_logspdH_fixedtheta_diagSig",
        "dou_logspdH_fixedtheta_fixedSig",
        "dou_spdH",
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        "dou_spdH_fixedSig",
        "dou_spdH_fixedtheta",
        "dou_spdH_fixedtheta_diagSig",
        "dou_spdH_fixedtheta_fixedSig",
        "dou_symH",
        "dou_symH_diagSig",
        "dou_symH_fixedSig",
        "dou_symH_fixedtheta",
        "dou_symH_fixedtheta_diagSig",
        "dou_symH_fixedtheta_fixedSig",
        "hbrn",
        "hbrn_diagSig",
        "hbrn_fixedSig",
        "hou_diagH",
        "hou_diagH_diagSig",
        "hou_diagH_fixedSig",
        "hou_diagH_fixedtheta",
        "hou_diagH_fixedtheta_diagSig",
        "hou_diagH_fixedtheta_fixedSig",
        "hou_diagSig",
        "hou_fixedH",
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        "hou_fixedH_fixedtheta_diagSig",
        "hou_fixedSig",
        "hou_fixedtheta",
        "hou_fixedtheta_diagSig",
        "hou_fixedtheta_fixedSig",
        "hou_logdiagH",
        "hou_logdiagH_diagSig",
        "hou_logdiagH_fixedSig",
        "hou_logdiagH_fixedtheta",
        "hou_logdiagH_fixedtheta_diagSig",
        "hou_logdiagH_fixedtheta_fixedSig",
        "hou_logspdH",
        "hou_logspdH_diagSig",
        "hou_logspdH_fixedSig",
        "hou_logspdH_fixedtheta",
        "hou_logspdH_fixedtheta_diagSig",
        "hou_logspdH_fixedtheta_fixedSig",
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        "hou_spdH_fixedSig",
        "hou_spdH_fixedtheta",
        "hou_spdH_fixedtheta_diagSig",
        "hou_spdH_fixedtheta_fixedSig",
        "hou_symH",
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        "hou_symH_fixedtheta",
        "hou_symH_fixedtheta_diagSig",
        "hou_symH_fixedtheta_fixedSig",
        "nparams_brn",
        "nparams_brn_diagSig",
        "nparams_brn_fixedSig",
        "nparams_ou_diagH",
        "nparams_ou_diagH_diagSig",
        "nparams_ou_diagH_fixedSig",
        "nparams_ou_diagH_fixedtheta",
        "nparams_ou_diagH_fixedtheta_diagSig",
        "nparams_ou_diagH_fixedtheta_fixedSig",
        "nparams_ou_diagSig",
        "nparams_ou_fixedH",
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        "nparams_ou_fixedH_fixedSig",
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