{
  "_id": "6ace3753a14063b82c3b169d",
  "Package": "tramME",
  "Title": "Transformation Models with Mixed Effects",
  "Version": "1.0.4",
  "Date": "2023-04-04",
  "Authors@R": "c(person(\"Balint\", \"Tamasi\", role = c(\"aut\", \"cre\"),\nemail = \"balint.tamasi@uzh.ch\",\ncomment = c(ORCID = \"0000-0002-2629-7362\")),\nperson(\"Torsten\", \"Hothorn\",  role = \"ctb\",\nemail = \"Torsten.Hothorn@R-project.org\",\ncomment = c(ORCID = \"0000-0001-8301-0471\")))",
  "Description": "Likelihood-based estimation of mixed-effects\ntransformation models using the Template Model Builder ('TMB',\nKristensen et al., 2016) <doi:10.18637/jss.v070.i05>. The\ntechnical details of transformation models are given in Hothorn\net al. (2018) <doi:10.1111/sjos.12291>. Likelihood\ncontributions of exact, randomly censored (left, right,\ninterval) and truncated observations are supported. The random\neffects are assumed to be normally distributed on the scale of\nthe transformation function, the marginal likelihood is\nevaluated using the Laplace approximation, and the gradients\nare calculated with automatic differentiation (Tamasi &\nHothorn, 2021) <doi:10.32614/RJ-2021-075>. Penalized smooth\nshift terms can be defined using 'mgcv'.",
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  "Packaged": {
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  "Author": "Balint Tamasi [aut, cre]\n(<https://orcid.org/0000-0002-2629-7362>), Torsten Hothorn\n[ctb] (<https://orcid.org/0000-0001-8301-0471>)",
  "Maintainer": "Balint Tamasi <balint.tamasi@uzh.ch>",
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    "BoxCoxME",
    "ColrME",
    "CoxphME",
    "duplicate",
    "edf_smooth",
    "LehmannME",
    "LmME",
    "optim_control",
    "PolrME",
    "ranef",
    "Resp",
    "smooth_terms",
    "SurvregME",
    "tramME",
    "tramME_model",
    "tramTMB",
    "VarCorr",
    "varcov",
    "varcov<-"
  ],
  "_help": [
    {
      "page": "anova.tramME",
      "title": "Comparison of nested tramME models.",
      "topics": [
        "anova.tramME"
      ]
    },
    {
      "page": "BoxCoxME",
      "title": "Mixed-effects version of 'BoxCox'",
      "topics": [
        "BoxCoxME"
      ]
    },
    {
      "page": "coef.LmME",
      "title": "Extract the coefficients of the fixed effects terms of an LmME model.",
      "topics": [
        "coef.LmME"
      ]
    },
    {
      "page": "coef.SurvregME",
      "title": "Extract the coefficients of the fixed effects terms of an SurvregME model.",
      "topics": [
        "coef.SurvregME"
      ]
    },
    {
      "page": "coef.tramME",
      "title": "Extract the coefficients of the fixed effects terms.",
      "topics": [
        "coef.tramME"
      ]
    },
    {
      "page": "coef-set-.tramME",
      "title": "Set coefficients of a tramME model.",
      "topics": [
        "coef<-.tramME"
      ]
    },
    {
      "page": "ColrME",
      "title": "Mixed-effects version of 'Colr'",
      "topics": [
        "ColrME"
      ]
    },
    {
      "page": "confint.LmME",
      "title": "Confidence intervals for LmME model parameters",
      "topics": [
        "confint.LmME"
      ]
    },
    {
      "page": "confint.tramME",
      "title": "Confidence intervals for tramME model parameters",
      "topics": [
        "confint.tramME"
      ]
    },
    {
      "page": "CoxphME",
      "title": "Mixed-effects version of 'Coxph'",
      "topics": [
        "CoxphME"
      ]
    },
    {
      "page": "duplicate",
      "title": "Generic for copying objects that are (partly) modified in place",
      "topics": [
        "duplicate"
      ]
    },
    {
      "page": "duplicate.tramTMB",
      "title": "Create a duplicate of the tramTMB object",
      "topics": [
        "duplicate.tramTMB"
      ]
    },
    {
      "page": "edf_smooth.tramME",
      "title": "EDFs of smooth shift terms",
      "topics": [
        "edf_smooth",
        "edf_smooth.tramME"
      ]
    },
    {
      "page": "LehmannME",
      "title": "Mixed-effects version of 'Lehmann'",
      "topics": [
        "LehmannME"
      ]
    },
    {
      "page": "LmME",
      "title": "Mixed-effects version of 'Lm'",
      "topics": [
        "LmME"
      ]
    },
    {
      "page": "logLik.tramME",
      "title": "Get the log-likelihood of the tramME model",
      "topics": [
        "logLik.tramME"
      ]
    },
    {
      "page": "model.frame.tramME",
      "title": "Extract model frame from a tramME model",
      "topics": [
        "model.frame.tramME"
      ]
    },
    {
      "page": "model.matrix.tramME",
      "title": "Model matrices for 'tramME' models",
      "topics": [
        "model.matrix.tramME"
      ]
    },
    {
      "page": "optim_control",
      "title": "Set up and control optimization parameters",
      "topics": [
        "optim_control"
      ]
    },
    {
      "page": "plot.smooth.tramME",
      "title": "Plot smooth terms of a tramME model.",
      "topics": [
        "plot.smooth.tramME"
      ]
    },
    {
      "page": "plot.tramME",
      "title": "Plotting method for tramME objects",
      "topics": [
        "plot.tramME"
      ]
    },
    {
      "page": "PolrME",
      "title": "Mixed-effects version of 'Polr'",
      "topics": [
        "PolrME"
      ]
    },
    {
      "page": "predict.tramME",
      "title": "Predict method for tramME objects",
      "topics": [
        "predict.tramME"
      ]
    },
    {
      "page": "predict.tramTMB",
      "title": "Post-estimation calculations in a tramTMB model",
      "topics": [
        "predict.tramTMB"
      ]
    },
    {
      "page": "print.anova.tramME",
      "title": "Printing 'anova.tramME' table",
      "topics": [
        "print.anova.tramME"
      ]
    },
    {
      "page": "print.summary.tramME",
      "title": "Print method for tramME model summary",
      "topics": [
        "print.summary.tramME"
      ]
    },
    {
      "page": "print.tramME",
      "title": "Print tramME model",
      "topics": [
        "print.tramME"
      ]
    },
    {
      "page": "print.VarCorr.tramME",
      "title": "Print method for the variance-correlation parameters of a tramME object",
      "topics": [
        "print.VarCorr.tramME"
      ]
    },
    {
      "page": "ranef.LmME",
      "title": "Extract the conditional modes of random effects of an LmME model",
      "topics": [
        "ranef.LmME"
      ]
    },
    {
      "page": "ranef.tramME",
      "title": "Point estimates and conditional variances of random effects.",
      "topics": [
        "ranef",
        "ranef.tramME"
      ]
    },
    {
      "page": "residuals.LmME",
      "title": "Residuals of a LmME model",
      "topics": [
        "residuals.LmME"
      ]
    },
    {
      "page": "residuals.tramME",
      "title": "Residuals of a tramME model",
      "topics": [
        "residuals.tramME"
      ]
    },
    {
      "page": "Resp",
      "title": "Response objects",
      "topics": [
        "format.Resp",
        "is.na.Resp",
        "length.Resp",
        "print.Resp",
        "R.Resp",
        "Resp",
        "[.Resp"
      ]
    },
    {
      "page": "sigma.LmME",
      "title": "Extract the SD of the error term of an LmME model.",
      "topics": [
        "sigma.LmME"
      ]
    },
    {
      "page": "simulate.tramME",
      "title": "Simulate from a 'tramME' model",
      "topics": [
        "simulate.tramME"
      ]
    },
    {
      "page": "smooth_terms.LmME",
      "title": "Evaluate smooth terms of a 'LmME' model.",
      "topics": [
        "smooth_terms.LmME"
      ]
    },
    {
      "page": "smooth_terms.tramME",
      "title": "Extract and evaluate the smooth terms of a tramME model",
      "topics": [
        "smooth_terms",
        "smooth_terms.tramME"
      ]
    },
    {
      "page": "summary.tramME",
      "title": "Summary method for tramME model",
      "topics": [
        "summary.tramME"
      ]
    },
    {
      "page": "SurvregME",
      "title": "Mixed-effects version of 'Survreg'",
      "topics": [
        "SurvregME"
      ]
    },
    {
      "page": "tramME",
      "title": "General function to define and fit tramME models",
      "topics": [
        "tramME"
      ]
    },
    {
      "page": "tramME_model",
      "title": "Create an object that defines a tramME_model",
      "topics": [
        "tramME_model"
      ]
    },
    {
      "page": "tramTMB",
      "title": "Create a tramTMB object",
      "topics": [
        "tramTMB"
      ]
    },
    {
      "page": "VarCorr.LmME",
      "title": "Variances and correlation matrices of random effects of an LmME object",
      "topics": [
        "VarCorr.LmME"
      ]
    },
    {
      "page": "VarCorr.tramME",
      "title": "Variances and correlation matrices of random effects",
      "topics": [
        "VarCorr",
        "VarCorr.tramME"
      ]
    },
    {
      "page": "varcov",
      "title": "Generic method for 'varcov'",
      "topics": [
        "varcov"
      ]
    },
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