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  "Package": "antedep",
  "Title": "Antedependence Models for Longitudinal Data",
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  "Author": "Chenyang Li [aut, cre], Dale Zimmerman [aut, ctb]",
  "Maintainer": "Chenyang Li <chenyang-li@uiowa.edu>",
  "Description": "Fitting, simulation, and inference for antedependence\nmodels for longitudinal data, as described in Zimmerman and\nNunez-Anton (2009, ISBN:9781420011074). Supports integer-valued\nantedependence (INAD) models for count data with thinning\noperators (binomial, Poisson, negative binomial) and flexible\ninnovation distributions (Poisson, Bell, negative binomial),\ncategorical antedependence models for discrete-state\nlongitudinal outcomes, and Gaussian antedependence (AD) models\nfor continuous data. Implements maximum likelihood estimation\nvia time-separable optimization and block coordinate descent,\nwith confidence intervals based on Louis' identity and profile\nlikelihood.",
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    "extra/citation.txt",
    "extra/contents.json",
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  "_exports": [
    "aic_cat",
    "aic_gau",
    "aic_inad",
    "bic_cat",
    "bic_gau",
    "bic_inad",
    "bic_order_cat",
    "bic_order_gau",
    "bic_order_inad",
    "ci_cat",
    "ci_gau",
    "ci_inad",
    "dbell",
    "em_cat",
    "em_gau",
    "em_inad",
    "fit_cat",
    "fit_gau",
    "fit_inad",
    "logL_cat",
    "logL_gau",
    "logL_inad",
    "logL_inad_i",
    "partial_corr",
    "pbell",
    "plot_prism",
    "plot_profile",
    "qbell",
    "rbell",
    "run_homogeneity_tests_inad",
    "run_order_tests_cat",
    "run_stationarity_tests_cat",
    "run_stationarity_tests_gau",
    "run_stationarity_tests_inad",
    "simulate_cat",
    "simulate_gau",
    "simulate_inad",
    "test_contrast_gau",
    "test_homogeneity_cat",
    "test_homogeneity_gau",
    "test_homogeneity_inad",
    "test_one_sample_gau",
    "test_order_cat",
    "test_order_gau",
    "test_order_inad",
    "test_stationarity_cat",
    "test_stationarity_gau",
    "test_stationarity_inad",
    "test_timeinvariance_cat",
    "test_two_sample_gau"
  ],
  "_datasets": [
    {
      "name": "bolus_inad",
      "title": "Morphine bolus analgesia counts",
      "object": "bolus_inad",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "cattle_growth",
      "title": "Cattle growth data (Treatments A and B)",
      "object": "cattle_growth",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "cochlear_implant",
      "title": "Cochlear implant speech recognition data",
      "object": "cochlear_implant",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "labor_force_cat",
      "title": "Labor force longitudinal categorical data (Table 1)",
      "object": "labor_force_cat",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "race_100km",
      "title": "100km race split-time data",
      "object": "race_100km",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "aic_cat",
      "title": "Akaike information criterion for fitted categorical AD models",
      "topics": [
        "aic_cat"
      ]
    },
    {
      "page": "aic_gau",
      "title": "Akaike information criterion for fitted Gaussian AD models",
      "topics": [
        "aic_gau"
      ]
    },
    {
      "page": "aic_inad",
      "title": "Akaike information criterion for fitted INAD models",
      "topics": [
        "aic_inad"
      ]
    },
    {
      "page": "Bell",
      "title": "The Bell distribution",
      "topics": [
        "Bell",
        "dbell",
        "pbell",
        "qbell",
        "rbell"
      ]
    },
    {
      "page": "bic_cat",
      "title": "Bayesian information criterion for fitted categorical AD models",
      "topics": [
        "bic_cat"
      ]
    },
    {
      "page": "bic_gau",
      "title": "Bayesian information criterion for fitted Gaussian AD models",
      "topics": [
        "bic_gau"
      ]
    },
    {
      "page": "bic_inad",
      "title": "Bayesian information criterion for fitted INAD models",
      "topics": [
        "bic_inad"
      ]
    },
    {
      "page": "bic_order_cat",
      "title": "BIC-based order selection for categorical AD models",
      "topics": [
        "bic_order_cat"
      ]
    },
    {
      "page": "bic_order_gau",
      "title": "BIC-based order selection for Gaussian AD models",
      "topics": [
        "bic_order_gau"
      ]
    },
    {
      "page": "bic_order_inad",
      "title": "BIC-based order selection for INAD models",
      "topics": [
        "bic_order_inad"
      ]
    },
    {
      "page": "bolus_inad",
      "title": "Morphine bolus analgesia counts",
      "topics": [
        "bolus_inad"
      ]
    },
    {
      "page": "cattle_growth",
      "title": "Cattle growth data (Treatments A and B)",
      "topics": [
        "cattle_growth"
      ]
    },
    {
      "page": "ci_cat",
      "title": "Confidence intervals for fitted categorical AD models",
      "topics": [
        "ci_cat"
      ]
    },
    {
      "page": "ci_gau",
      "title": "Confidence intervals for fitted Gaussian AD models",
      "topics": [
        "ci_gau"
      ]
    },
    {
      "page": "ci_inad",
      "title": "Confidence intervals for fitted INAD models",
      "topics": [
        "ci_inad"
      ]
    },
    {
      "page": "cochlear_implant",
      "title": "Cochlear implant speech recognition data",
      "topics": [
        "cochlear_implant"
      ]
    },
    {
      "page": "em_cat",
      "title": "EM algorithm for categorical AD model estimation",
      "topics": [
        "em_cat"
      ]
    },
    {
      "page": "em_gau",
      "title": "EM algorithm for Gaussian AD model estimation",
      "topics": [
        "em_gau"
      ]
    },
    {
      "page": "em_inad",
      "title": "EM algorithm for INAD model estimation",
      "topics": [
        "em_inad"
      ]
    },
    {
      "page": "fit_cat",
      "title": "Fit categorical antedependence model by maximum likelihood",
      "topics": [
        "fit_cat"
      ]
    },
    {
      "page": "fit_gau",
      "title": "Fit Gaussian antedependence model by maximum likelihood",
      "topics": [
        "fit_gau"
      ]
    },
    {
      "page": "fit_inad",
      "title": "Fit INAD antedependence model by maximum likelihood",
      "topics": [
        "fit_inad"
      ]
    },
    {
      "page": "labor_force_cat",
      "title": "Labor force longitudinal categorical data (Table 1)",
      "topics": [
        "labor_force_cat"
      ]
    },
    {
      "page": "logL_cat",
      "title": "Log-likelihood for categorical AD models (with missing data support)",
      "topics": [
        "logL_cat"
      ]
    },
    {
      "page": "logL_gau",
      "title": "Log-likelihood for Gaussian AD models (with missing data support)",
      "topics": [
        "logL_gau"
      ]
    },
    {
      "page": "logL_inad",
      "title": "Log-likelihood for INAD models (with missing data support)",
      "topics": [
        "logL_inad"
      ]
    },
    {
      "page": "logL_inad_i",
      "title": "INAD log likelihood contribution at time i (no fixed effect)",
      "topics": [
        "logL_inad_i"
      ]
    },
    {
      "page": "partial_corr",
      "title": "Compute intervenor-adjusted partial correlation matrix",
      "topics": [
        "partial_corr"
      ]
    },
    {
      "page": "plot_prism",
      "title": "PRISM plot (Partial Residual Intervenor Scatterplot Matrix)",
      "topics": [
        "plot_prism"
      ]
    },
    {
      "page": "plot_profile",
      "title": "Profile plot (spaghetti plot) for longitudinal data",
      "topics": [
        "plot_profile"
      ]
    },
    {
      "page": "print.cat_ci",
      "title": "Print method for cat_ci objects",
      "topics": [
        "print.cat_ci"
      ]
    },
    {
      "page": "print.cat_fit",
      "title": "Print method for cat_fit objects",
      "topics": [
        "print.cat_fit"
      ]
    },
    {
      "page": "print.cat_lrt",
      "title": "Print method for cat_lrt objects",
      "topics": [
        "print.cat_lrt"
      ]
    },
    {
      "page": "print.gau_bic_order",
      "title": "Print method for BIC order selection",
      "topics": [
        "print.gau_bic_order"
      ]
    },
    {
      "page": "print.gau_ci",
      "title": "Print method for AD confidence intervals",
      "topics": [
        "print.gau_ci"
      ]
    },
    {
      "page": "print.gau_contrast_test",
      "title": "Print method for AD contrast test",
      "topics": [
        "print.gau_contrast_test"
      ]
    },
    {
      "page": "print.gau_fit",
      "title": "Print method for gau_fit objects",
      "topics": [
        "print.gau_fit"
      ]
    },
    {
      "page": "print.gau_homogeneity_test",
      "title": "Print method for AD homogeneity test",
      "topics": [
        "print.gau_homogeneity_test"
      ]
    },
    {
      "page": "print.gau_mean_test",
      "title": "Print method for AD mean test",
      "topics": [
        "print.gau_mean_test"
      ]
    },
    {
      "page": "print.gau_order_test",
      "title": "Print method for AD order test",
      "topics": [
        "print.gau_order_test"
      ]
    },
    {
      "page": "print.homogeneity_tests_inad",
      "title": "Print method for homogeneity_tests_inad",
      "topics": [
        "print.homogeneity_tests_inad"
      ]
    },
    {
      "page": "print.inad_ci",
      "title": "Print method for INAD confidence intervals",
      "topics": [
        "print.inad_ci"
      ]
    },
    {
      "page": "print.inad_fit",
      "title": "Print method for INAD model fits",
      "topics": [
        "print.inad_fit"
      ]
    },
    {
      "page": "print.test_homogeneity_inad",
      "title": "Print method for test_homogeneity_inad",
      "topics": [
        "print.test_homogeneity_inad"
      ]
    },
    {
      "page": "race_100km",
      "title": "100km race split-time data",
      "topics": [
        "race_100km"
      ]
    },
    {
      "page": "run_homogeneity_tests_inad",
      "title": "Run all homogeneity tests for INAD",
      "topics": [
        "run_homogeneity_tests_inad"
      ]
    },
    {
      "page": "run_order_tests_cat",
      "title": "Run all pairwise order tests",
      "topics": [
        "run_order_tests_cat"
      ]
    },
    {
      "page": "run_stationarity_tests_cat",
      "title": "Run all stationarity-related tests for categorical AD",
      "topics": [
        "run_stationarity_tests_cat"
      ]
    },
    {
      "page": "run_stationarity_tests_gau",
      "title": "Run all stationarity-related tests for Gaussian AD",
      "topics": [
        "run_stationarity_tests_gau"
      ]
    },
    {
      "page": "run_stationarity_tests_inad",
      "title": "Run all stationarity-related tests for INAD",
      "topics": [
        "run_stationarity_tests_inad"
      ]
    },
    {
      "page": "simulate_cat",
      "title": "Simulate categorical antedependence series",
      "topics": [
        "simulate_cat"
      ]
    },
    {
      "page": "simulate_gau",
      "title": "Simulate Gaussian antedependence series",
      "topics": [
        "simulate_gau"
      ]
    },
    {
      "page": "simulate_inad",
      "title": "Simulate INAD antedependence series",
      "topics": [
        "simulate_inad"
      ]
    },
    {
      "page": "summary.cat_ci",
      "title": "Summary method for cat_ci objects",
      "topics": [
        "summary.cat_ci"
      ]
    },
    {
      "page": "summary.gau_ci",
      "title": "Summary method for gau_ci objects",
      "topics": [
        "summary.gau_ci"
      ]
    },
    {
      "page": "summary.inad_ci",
      "title": "Summary method for inad_ci objects",
      "topics": [
        "summary.inad_ci"
      ]
    },
    {
      "page": "test_contrast_gau",
      "title": "Test linear hypotheses on the mean under antedependence",
      "topics": [
        "test_contrast_gau"
      ]
    },
    {
      "page": "test_homogeneity_cat",
      "title": "Likelihood ratio test for homogeneity across groups (categorical AD data)",
      "topics": [
        "test_homogeneity_cat"
      ]
    },
    {
      "page": "test_homogeneity_gau",
      "title": "Likelihood ratio test for homogeneity across groups (Gaussian AD data)",
      "topics": [
        "test_homogeneity_gau"
      ]
    },
    {
      "page": "test_homogeneity_inad",
      "title": "Likelihood ratio test for homogeneity across groups (INAD data)",
      "topics": [
        "test_homogeneity_inad"
      ]
    },
    {
      "page": "test_one_sample_gau",
      "title": "One-sample test for mean structure under antedependence",
      "topics": [
        "test_one_sample_gau"
      ]
    },
    {
      "page": "test_order_cat",
      "title": "Likelihood ratio test for antedependence order (categorical AD data)",
      "topics": [
        "test_order_cat"
      ]
    },
    {
      "page": "test_order_gau",
      "title": "Likelihood ratio test for antedependence order (Gaussian AD data)",
      "topics": [
        "test_order_gau"
      ]
    },
    {
      "page": "test_order_inad",
      "title": "Likelihood ratio test for antedependence order (INAD data)",
      "topics": [
        "test_order_inad"
      ]
    },
    {
      "page": "test_stationarity_cat",
      "title": "Likelihood ratio test for stationarity (categorical AD data)",
      "topics": [
        "test_stationarity_cat"
      ]
    },
    {
      "page": "test_stationarity_gau",
      "title": "Likelihood ratio test for stationarity (Gaussian AD data)",
      "topics": [
        "test_stationarity_gau"
      ]
    },
    {
      "page": "test_stationarity_inad",
      "title": "Likelihood ratio test for stationarity (INAD data)",
      "topics": [
        "test_stationarity_inad"
      ]
    },
    {
      "page": "test_timeinvariance_cat",
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