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  "Title": "'LiNGAM' Algorithms for Causal Discovery",
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  "Description": "R implementation of 'LiNGAM' (Linear Non-Gaussian Acyclic\nModel) algorithms for causal discovery, following Shimizu et\nal. (2011) <https://www.jmlr.org/papers/v12/shimizu11a.html>.\nBased on the 'Python' implementation by Ikeuchi et al. (2023)\n<https://github.com/cdt15/lingam>. The 'VAR-LiNGAM' residual\ndiagnostics are inspired by the 'VARLiNGAM' R code of Moneta et\nal.\n<https://sites.google.com/site/dorisentner/publications/VARLiNGAM>.",
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  "_exports": [
    "as_bootstrap_result",
    "bootstrap_with_imputation",
    "check_var_stationarity",
    "estimate_all_total_effects",
    "estimate_total_effect",
    "estimate_total_effect_parce",
    "estimate_total_effect_rcd",
    "estimate_var_total_effect",
    "evaluate_model_fit",
    "generate_lim_sample",
    "generate_lingam_hard_sample",
    "generate_lingam_large_sample",
    "generate_lingam_paradox_data",
    "generate_lingam_sample_10",
    "generate_lingam_sample_6",
    "generate_multi_group_sample",
    "generate_parce_sample",
    "generate_rcd_sample",
    "generate_varlingam_sample",
    "get_adjacency_matrix_summary",
    "get_causal_direction_counts",
    "get_causal_order_stability",
    "get_directed_acyclic_graph_counts",
    "get_error_independence_p_values",
    "get_error_independence_p_values_parce",
    "get_error_independence_p_values_rcd",
    "get_group_result",
    "get_paths",
    "get_probabilities",
    "get_total_causal_effects",
    "get_var_paths",
    "get_var_probabilities",
    "glance",
    "lingam_direct",
    "lingam_direct_bootstrap",
    "lingam_high_dim",
    "lingam_lim",
    "lingam_multi_group",
    "lingam_multi_group_bootstrap",
    "lingam_parce",
    "lingam_parce_bootstrap",
    "lingam_rcd",
    "lingam_rcd_bootstrap",
    "lingam_var",
    "lingam_var_bootstrap",
    "make_prior_knowledge",
    "plot_adjacency",
    "plot_bootstrap_probabilities",
    "plot_residual_qq",
    "plot_varlingam_residual_qq",
    "summary_lingam",
    "test_residual_normality",
    "test_varlingam_residual_normality",
    "test_varlingam_residual_normality_all",
    "tidy"
  ],
  "_help": [
    {
      "page": "as_bootstrap_result",
      "title": "Collapse an ImputationBootstrapResult into a BootstrapResult",
      "topics": [
        "as_bootstrap_result"
      ]
    },
    {
      "page": "autoplot.LiMResult",
      "title": "Plot the causal graph of a LiMResult with ggplot2",
      "topics": [
        "autoplot.LiMResult"
      ]
    },
    {
      "page": "autoplot.LingamResult",
      "title": "Plot the causal graph of a LingamResult with ggplot2",
      "topics": [
        "autoplot.LingamResult"
      ]
    },
    {
      "page": "autoplot.MultiGroupLingamResult",
      "title": "Plot one group of a MultiGroupLingamResult with ggplot2",
      "topics": [
        "autoplot.MultiGroupLingamResult"
      ]
    },
    {
      "page": "autoplot.ParceLingamResult",
      "title": "Plot the causal graph of a ParceLingamResult with ggplot2",
      "topics": [
        "autoplot.ParceLingamResult"
      ]
    },
    {
      "page": "autoplot.RCDResult",
      "title": "Plot the causal graph of an RCDResult with ggplot2",
      "topics": [
        "autoplot.RCDResult"
      ]
    },
    {
      "page": "bootstrap_with_imputation",
      "title": "Bootstrap with Multiple Imputation for Direct LiNGAM",
      "topics": [
        "bootstrap_with_imputation"
      ]
    },
    {
      "page": "check_var_stationarity",
      "title": "Check the stationarity of a fitted VAR-LiNGAM model",
      "topics": [
        "check_var_stationarity"
      ]
    },
    {
      "page": "estimate_all_total_effects",
      "title": "Estimate the total causal effects between all variables at once",
      "topics": [
        "estimate_all_total_effects"
      ]
    },
    {
      "page": "estimate_total_effect",
      "title": "Estimate the total causal effect between two specified variables",
      "topics": [
        "estimate_total_effect"
      ]
    },
    {
      "page": "estimate_total_effect_parce",
      "title": "Estimate the total causal effect between two variables (ParceLiNGAM)",
      "topics": [
        "estimate_total_effect_parce"
      ]
    },
    {
      "page": "estimate_total_effect_rcd",
      "title": "Estimate the total causal effect between two variables (RCD)",
      "topics": [
        "estimate_total_effect_rcd"
      ]
    },
    {
      "page": "estimate_var_total_effect",
      "title": "Estimate a total causal effect in a VAR-LiNGAM model",
      "topics": [
        "estimate_var_total_effect"
      ]
    },
    {
      "page": "evaluate_model_fit",
      "title": "Evaluate model fit of an estimated causal graph",
      "topics": [
        "evaluate_model_fit"
      ]
    },
    {
      "page": "generate_lim_sample",
      "title": "Generate sample data for LiM (3 mixed variables)",
      "topics": [
        "generate_lim_sample"
      ]
    },
    {
      "page": "generate_lingam_hard_sample",
      "title": "Generate a challenging sample data for Direct LiNGAM",
      "topics": [
        "generate_lingam_hard_sample"
      ]
    },
    {
      "page": "generate_lingam_large_sample",
      "title": "Generate large-scale sample data to benchmark Direct LiNGAM scalability",
      "topics": [
        "generate_lingam_large_sample"
      ]
    },
    {
      "page": "generate_lingam_paradox_data",
      "title": "Generate Paradoxical Data Where DirectLiNGAM Struggles",
      "topics": [
        "generate_lingam_paradox_data"
      ]
    },
    {
      "page": "generate_lingam_sample_10",
      "title": "Generate 10-variable sample data for Direct LiNGAM",
      "topics": [
        "generate_lingam_sample_10"
      ]
    },
    {
      "page": "generate_lingam_sample_6",
      "title": "Generate sample data for Direct LiNGAM (6 variables)",
      "topics": [
        "generate_lingam_sample_6"
      ]
    },
    {
      "page": "generate_multi_group_sample",
      "title": "Generate sample data for Multi-Group Direct LiNGAM (2 groups, 6 variables)",
      "topics": [
        "generate_multi_group_sample"
      ]
    },
    {
      "page": "generate_parce_sample",
      "title": "Generate sample data with a latent confounder (for BottomUpParceLiNGAM)",
      "topics": [
        "generate_parce_sample"
      ]
    },
    {
      "page": "generate_rcd_sample",
      "title": "Generate sample data with a latent confounder (for RCD)",
      "topics": [
        "generate_rcd_sample"
      ]
    },
    {
      "page": "generate_varlingam_sample",
      "title": "Generate sample data from a VAR-LiNGAM model",
      "topics": [
        "generate_varlingam_sample"
      ]
    },
    {
      "page": "get_adjacency_matrix_summary",
      "title": "Create an adjacency matrix of representative causal-effect values from bootstrap results",
      "topics": [
        "get_adjacency_matrix_summary"
      ]
    },
    {
      "page": "get_causal_direction_counts",
      "title": "Get counts, proportions, and causal effects of causal directions",
      "topics": [
        "get_causal_direction_counts"
      ]
    },
    {
      "page": "get_causal_order_stability",
      "title": "Evaluate the stability of the causal order from bootstrap",
      "topics": [
        "get_causal_order_stability"
      ]
    },
    {
      "page": "get_directed_acyclic_graph_counts",
      "title": "Get DAG counts",
      "topics": [
        "get_directed_acyclic_graph_counts"
      ]
    },
    {
      "page": "get_error_independence_p_values",
      "title": "Compute p-values for the independence test of the errors",
      "topics": [
        "get_error_independence_p_values"
      ]
    },
    {
      "page": "get_error_independence_p_values_parce",
      "title": "Compute p-values for the independence of ParceLiNGAM residuals (HSIC-based)",
      "topics": [
        "get_error_independence_p_values_parce"
      ]
    },
    {
      "page": "get_error_independence_p_values_rcd",
      "title": "Compute p-values for the independence of RCD residuals (HSIC-based)",
      "topics": [
        "get_error_independence_p_values_rcd"
      ]
    },
    {
      "page": "get_group_result",
      "title": "Extract a single group's result from a MultiGroupLingamResult",
      "topics": [
        "get_group_result"
      ]
    },
    {
      "page": "get_paths",
      "title": "Get all paths between two specified variables and their bootstrap probabilities",
      "topics": [
        "get_paths"
      ]
    },
    {
      "page": "get_probabilities",
      "title": "Get bootstrap probabilities",
      "topics": [
        "get_probabilities"
      ]
    },
    {
      "page": "get_total_causal_effects",
      "title": "Get a list of total causal effects",
      "topics": [
        "get_total_causal_effects"
      ]
    },
    {
      "page": "get_var_paths",
      "title": "Enumerate bootstrap paths between two variables in a VAR-LiNGAM model",
      "topics": [
        "get_var_paths"
      ]
    },
    {
      "page": "get_var_probabilities",
      "title": "Bootstrap probabilities for a VAR-LiNGAM model",
      "topics": [
        "get_var_probabilities"
      ]
    },
    {
      "page": "glance.LiMResult",
      "title": "Get a one-row summary of a LiMResult",
      "topics": [
        "glance.LiMResult"
      ]
    },
    {
      "page": "glance.LingamResult",
      "title": "Get a one-row summary of a LingamResult",
      "topics": [
        "glance.LingamResult"
      ]
    },
    {
      "page": "glance.MultiGroupLingamResult",
      "title": "Get a one-row summary of a MultiGroupLingamResult",
      "topics": [
        "glance.MultiGroupLingamResult"
      ]
    },
    {
      "page": "glance.ParceLingamResult",
      "title": "Get a one-row summary of a ParceLingamResult",
      "topics": [
        "glance.ParceLingamResult"
      ]
    },
    {
      "page": "glance.RCDResult",
      "title": "Get a one-row summary of an RCDResult",
      "topics": [
        "glance.RCDResult"
      ]
    },
    {
      "page": "lingam_direct",
      "title": "Direct LiNGAM",
      "topics": [
        "lingam_direct"
      ]
    },
    {
      "page": "lingam_direct_bootstrap",
      "title": "Bootstrap for Direct LiNGAM",
      "topics": [
        "lingam_direct_bootstrap"
      ]
    },
    {
      "page": "lingam_high_dim",
      "title": "High-Dimensional Direct LiNGAM",
      "topics": [
        "lingam_high_dim"
      ]
    },
    {
      "page": "lingam_lim",
      "title": "LiM: LiNGAM for Mixed Data",
      "topics": [
        "lingam_lim"
      ]
    },
    {
      "page": "lingam_multi_group",
      "title": "Multi-Group Direct LiNGAM",
      "topics": [
        "lingam_multi_group"
      ]
    },
    {
      "page": "lingam_multi_group_bootstrap",
      "title": "Bootstrap for Multi-Group Direct LiNGAM",
      "topics": [
        "lingam_multi_group_bootstrap"
      ]
    },
    {
      "page": "lingam_parce",
      "title": "Bottom-Up ParceLiNGAM",
      "topics": [
        "lingam_parce"
      ]
    },
    {
      "page": "lingam_parce_bootstrap",
      "title": "Bootstrap for Bottom-Up ParceLiNGAM",
      "topics": [
        "lingam_parce_bootstrap"
      ]
    },
    {
      "page": "lingam_rcd",
      "title": "RCD (Repetitive Causal Discovery)",
      "topics": [
        "lingam_rcd"
      ]
    },
    {
      "page": "lingam_rcd_bootstrap",
      "title": "Bootstrap for RCD",
      "topics": [
        "lingam_rcd_bootstrap"
      ]
    },
    {
      "page": "lingam_var",
      "title": "VAR-LiNGAM for time series causal discovery",
      "topics": [
        "lingam_var"
      ]
    },
    {
      "page": "lingam_var_bootstrap",
      "title": "Bootstrap for VAR-LiNGAM",
      "topics": [
        "lingam_var_bootstrap"
      ]
    },
    {
      "page": "make_prior_knowledge",
      "title": "Create a prior knowledge matrix",
      "topics": [
        "make_prior_knowledge"
      ]
    },
    {
      "page": "plot_adjacency",
      "title": "Plot a causal graph from an adjacency matrix with DiagrammeR",
      "topics": [
        "plot_adjacency"
      ]
    },
    {
      "page": "plot_bootstrap_probabilities",
      "title": "Draw bootstrap probabilities with DiagrammeR",
      "topics": [
        "plot_bootstrap_probabilities"
      ]
    },
    {
      "page": "plot_residual_qq",
      "title": "plot QQ",
      "topics": [
        "plot_residual_qq"
      ]
    },
    {
      "page": "plot_varlingam_residual_qq",
      "title": "Q-Q plots of VAR-LiNGAM residuals",
      "topics": [
        "plot_varlingam_residual_qq"
      ]
    },
    {
      "page": "print.BootstrapResult",
      "title": "Display the contents of a BootstrapResult",
      "topics": [
        "print.BootstrapResult"
      ]
    },
    {
      "page": "print.causal_order_stability",
      "title": "print method for causal_order_stability",
      "topics": [
        "print.causal_order_stability"
      ]
    },
    {
      "page": "print.ImputationBootstrapResult",
      "title": "Print method for ImputationBootstrapResult",
      "topics": [
        "print.ImputationBootstrapResult"
      ]
    },
    {
      "page": "print.LiMResult",
      "title": "Print method for LiMResult",
      "topics": [
        "print.LiMResult"
      ]
    },
    {
      "page": "print.lingam_normality_test",
      "title": "Print method for lingam_normality_test",
      "topics": [
        "print.lingam_normality_test"
      ]
    },
    {
      "page": "print.lingam_summary",
      "title": "print method for lingam_summary",
      "topics": [
        "print.lingam_summary"
      ]
    },
    {
      "page": "print.LingamResult",
      "title": "Print method for LingamResult",
      "topics": [
        "print.LingamResult"
      ]
    },
    {
      "page": "print.MultiGroupBootstrapResult",
      "title": "Print method for MultiGroupBootstrapResult",
      "topics": [
        "print.MultiGroupBootstrapResult"
      ]
    },
    {
      "page": "print.MultiGroupLingamResult",
      "title": "Print method for MultiGroupLingamResult",
      "topics": [
        "print.MultiGroupLingamResult"
      ]
    },
    {
      "page": "print.ParceLingamResult",
      "title": "Print method for ParceLingamResult",
      "topics": [
        "print.ParceLingamResult"
      ]
    },
    {
      "page": "print.RCDResult",
      "title": "Print method for RCDResult",
      "topics": [
        "print.RCDResult"
      ]
    },
    {
      "page": "print.var_stationarity",
      "title": "Print method for var_stationarity",
      "topics": [
        "print.var_stationarity"
      ]
    },
    {
      "page": "print.VARBootstrapResult",
      "title": "Print a VARBootstrapResult",
      "topics": [
        "print.VARBootstrapResult"
      ]
    },
    {
      "page": "print.VARLiNGAMResult",
      "title": "Print method for VARLiNGAMResult",
      "topics": [
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      "page": "summary_lingam",
      "title": "Summarize the goodness-of-fit of a Direct LiNGAM model at once",
      "topics": [
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    },
    {
      "page": "test_residual_normality",
      "title": "Test normality of residuals from Direct LiNGAM",
      "topics": [
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    {
      "page": "test_varlingam_residual_normality",
      "title": "Test the non-Gaussianity of VAR-LiNGAM residuals",
      "topics": [
        "test_varlingam_residual_normality"
      ]
    },
    {
      "page": "test_varlingam_residual_normality_all",
      "title": "Run several normality tests on VAR-LiNGAM residuals at once",
      "topics": [
        "test_varlingam_residual_normality_all"
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    },
    {
      "page": "tidy.BootstrapResult",
      "title": "Convert a BootstrapResult to a tidy data.frame",
      "topics": [
        "tidy.BootstrapResult"
      ]
    },
    {
      "page": "tidy.ImputationBootstrapResult",
      "title": "Convert an ImputationBootstrapResult to a tidy data.frame",
      "topics": [
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    },
    {
      "page": "tidy.LiMResult",
      "title": "Convert a LiMResult to a tidy data.frame",
      "topics": [
        "tidy.LiMResult"
      ]
    },
    {
      "page": "tidy.LingamResult",
      "title": "Convert a LingamResult to a tidy data.frame",
      "topics": [
        "tidy.LingamResult"
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    },
    {
      "page": "tidy.MultiGroupBootstrapResult",
      "title": "Convert a MultiGroupBootstrapResult to a tidy data.frame",
      "topics": [
        "tidy.MultiGroupBootstrapResult"
      ]
    },
    {
      "page": "tidy.MultiGroupLingamResult",
      "title": "Convert a MultiGroupLingamResult to a tidy data.frame",
      "topics": [
        "tidy.MultiGroupLingamResult"
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    },
    {
      "page": "tidy.ParceLingamResult",
      "title": "Convert a ParceLingamResult to a tidy data.frame",
      "topics": [
        "tidy.ParceLingamResult"
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    },
    {
      "page": "tidy.RCDResult",
      "title": "Convert an RCDResult to a tidy data.frame",
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  ],
  "_pkglogo": "https://github.com/cran/lingamr/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/cran/lingamr/raw/HEAD/README.md",
  "_rundeps": [
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  "_vignettes": [
    {
      "source": "lingamr.Rmd",
      "filename": "lingamr.html",
      "title": "Causal Discovery with lingamr",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Sample Data",
        "generate_lingam_sample_6()",
        "Causal Discovery",
        "Causal Order",
        "Estimated Adjacency Matrix",
        "Drawing the Causal Graph",
        "Comparing the Estimated and True Structures",
        "Static Plotting with ggplot2",
        "Total Causal Effect",
        "Comparison with Multiple Regression Coefficients",
        "Inference with Prior Knowledge",
        "Format of the Prior Knowledge Matrix",
        "Usage Example",
        "Specifying by Index",
        "Specifying by Variable Name",
        "Running Direct LiNGAM with Prior Knowledge",
        "Choosing a Regression Method (reg_method)",
        "Comparison of the Four Methods",
        "Choosing lambda (common to LASSO / Adaptive LASSO)",
        "Independence between Error Variables",
        "The Non-Gaussianity Assumption",
        "Non-Gaussian Errors (Uniform Distribution) -- When It Works",
        "Gaussian Errors -- When It Fails",
        "Testing the Normality of Residuals",
        "Model Summary",
        "Bootstrap Direct LiNGAM",
        "Inspecting the Bootstrap Results",
        "Adjacency Matrix of Mean Causal Effects",
        "Matrix of Path Occurrence Frequencies",
        "Mean Total Effects",
        "Stability of the Causal Order",
        "Integration with broom (tidy / glance)",
        "A Larger Dataset (10 Variables)",
        "Comparing ICA-LiNGAM and Direct LiNGAM",
        "Running Both Algorithms",
        "Comparing the Estimated Coefficients",
        "Comparing the DAG Structures",
        "When There Are Many Variables: The Scalability Wall",
        "Generating the Data",
        "Comparing Execution Times",
        "Checking Estimation Accuracy (p = 10)",
        "High-Dimensional Direct LiNGAM",
        "A Case Where DirectLiNGAM Struggles: The Measurement Error Paradox",
        "VAR-LiNGAM: Causal Discovery in Time Series",
        "Fitting VAR-LiNGAM",
        "Lag Order Selection",
        "Stationarity Check",
        "Residual Diagnostics",
        "Total Causal Effects",
        "Bootstrap",
        "LiNGAM for Mixed Data (LiM)",
        "Multi-Group Direct LiNGAM",
        "Causal Discovery with Missing Data",
        "Latent Confounders: Bottom-Up ParceLiNGAM",
        "Latent Confounders: RCD",
        "Evaluating Model Fit",
        "When LiNGAM Cannot Be Used",
        "A Checklist to Verify in Advance"
      ],
      "created": "2026-07-17 13:20:07",
      "modified": "2026-07-17 13:20:07",
      "commits": 1
    }
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  "_indexed": true,
  "_nocasepkg": "lingamr",
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