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  "Package": "graphicalMCP",
  "Title": "Graphical Multiple Comparison Procedures",
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  "Authors@R": "c(\nperson(\"Dong\", \"Xi\", , \"dong.xi1@gilead.com\", role = c(\"aut\", \"cre\")),\nperson(\"Ethan\", \"Brockmann\", , \"ethan.brockmann@atorusresearch.com\", role = \"aut\"),\nperson(\"Gilead Sciences, Inc.\", role = c(\"cph\", \"fnd\"))\n)",
  "Description": "Multiple comparison procedures (MCPs) control the\nfamilywise error rate in clinical trials. Graphical MCPs\ninclude many commonly used procedures as special cases; see\nBretz et al. (2011) <doi:10.1002/bimj.201000239>, Lu (2016)\n<doi:10.1002/sim.6985>, and Xi et al. (2017)\n<doi:10.1002/bimj.201600233>. This package is a low-dependency\nimplementation of graphical MCPs which allow mixed types of\ntests. It also includes power simulations and visualization of\ngraphical MCPs.",
  "License": "Apache License (>= 2)",
  "URL": "https://openpharma.github.io/graphicalMCP/,\nhttps://github.com/openpharma/graphicalMCP",
  "BugReports": "https://github.com/openpharma/graphicalMCP/issues",
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  "Date/Publication": "2026-10-12 01:42:12 UTC",
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    "message": "Merge pull request #112 from openpharma/fix-47-boundary-marginal-power\n\nFix graph_calculate_power() edge cases for marginal power and alpha (#47)",
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    "adjust_p_bonferroni",
    "adjust_p_hochberg",
    "adjust_p_parametric",
    "adjust_p_simes",
    "adjust_weights_hochberg",
    "adjust_weights_parametric",
    "adjust_weights_simes",
    "as_graphMCP",
    "as_igraph",
    "as_initial_graph",
    "bonferroni",
    "bonferroni_holm",
    "bonferroni_holm_weighted",
    "bonferroni_weighted",
    "dunnett_closure_weighted",
    "dunnett_single_step",
    "dunnett_single_step_weighted",
    "fallback",
    "fallback_improved_1",
    "fallback_improved_2",
    "fixed_sequence",
    "graph_calculate_power",
    "graph_create",
    "graph_generate_weights",
    "graph_rejection_orderings",
    "graph_test_closure",
    "graph_test_shortcut",
    "graph_test_shortcut_gsd",
    "graph_update",
    "gs_boundaries",
    "gs_corr",
    "hochberg",
    "hommel",
    "huque_etal",
    "random_graph",
    "repeated_p",
    "sequential_p",
    "sidak",
    "simple_successive_1",
    "simple_successive_2",
    "spending_hsd",
    "spending_linear",
    "spending_of",
    "spending_pocock",
    "spending_with_time",
    "spending_wt",
    "three_doses_two_primary_two_secondary",
    "two_doses_two_primary_two_secondary"
  ],
  "_help": [
    {
      "page": "adjust_p",
      "title": "Calculate adjusted p-values",
      "topics": [
        "adjust_p_bonferroni",
        "adjust_p_hochberg",
        "adjust_p_parametric",
        "adjust_p_simes"
      ]
    },
    {
      "page": "adjust_weights",
      "title": "Calculate adjusted hypothesis weights",
      "topics": [
        "adjust_weights_hochberg",
        "adjust_weights_parametric",
        "adjust_weights_simes"
      ]
    },
    {
      "page": "as_graph",
      "title": "Convert between graphicalMCP, gMCP, and igraph graph classes",
      "topics": [
        "as_graphMCP",
        "as_graphMCP.initial_graph",
        "as_igraph",
        "as_igraph.initial_graph",
        "as_initial_graph",
        "as_initial_graph.graphMCP",
        "as_initial_graph.igraph"
      ]
    },
    {
      "page": "example_graphs",
      "title": "Example graphs of commonly used multiple comparison procedures",
      "topics": [
        "bonferroni",
        "bonferroni_holm",
        "bonferroni_holm_weighted",
        "bonferroni_weighted",
        "dunnett_closure_weighted",
        "dunnett_single_step",
        "dunnett_single_step_weighted",
        "fallback",
        "fallback_improved_1",
        "fallback_improved_2",
        "fixed_sequence",
        "hochberg",
        "hommel",
        "huque_etal",
        "random_graph",
        "sidak",
        "simple_successive_1",
        "simple_successive_2",
        "three_doses_two_primary_two_secondary",
        "two_doses_two_primary_two_secondary"
      ]
    },
    {
      "page": "graph_calculate_power",
      "title": "Calculate power values for a graphical multiple comparison procedure",
      "topics": [
        "graph_calculate_power"
      ]
    },
    {
      "page": "graph_create",
      "title": "Create the initial graph for a multiple comparison procedure",
      "topics": [
        "graph_create"
      ]
    },
    {
      "page": "graph_generate_weights",
      "title": "Generate the weighting strategy based on a graphical multiple comparison procedure",
      "topics": [
        "graph_generate_weights"
      ]
    },
    {
      "page": "graph_rejection_orderings",
      "title": "Find alternate rejection orderings (sequences) for shortcut tests",
      "topics": [
        "graph_rejection_orderings"
      ]
    },
    {
      "page": "graph_test_closure",
      "title": "Perform closed graphical multiple comparison procedures",
      "topics": [
        "graph_test_closure"
      ]
    },
    {
      "page": "graph_test_shortcut",
      "title": "Perform shortcut (sequentially rejective) graphical multiple comparison procedures",
      "topics": [
        "graph_test_shortcut"
      ]
    },
    {
      "page": "graph_test_shortcut_gsd",
      "title": "Perform shortcut graphical multiple comparison procedures with group sequential designs",
      "topics": [
        "graph_test_shortcut_gsd"
      ]
    },
    {
      "page": "graph_update",
      "title": "Obtain an updated graph by updating an initial graphical after deleting hypotheses",
      "topics": [
        "graph_update"
      ]
    },
    {
      "page": "gs_boundaries",
      "title": "Compute group sequential boundaries from an alpha spending function",
      "topics": [
        "gs_boundaries"
      ]
    },
    {
      "page": "gs_corr",
      "title": "Compute the correlation matrix for group sequential test statistics",
      "topics": [
        "gs_corr"
      ]
    },
    {
      "page": "plot.initial_graph",
      "title": "S3 plot method for class 'initial_graph'",
      "topics": [
        "plot.initial_graph"
      ]
    },
    {
      "page": "plot.updated_graph",
      "title": "S3 plot method for the class 'updated_graph'",
      "topics": [
        "plot.updated_graph"
      ]
    },
    {
      "page": "print.graph_report",
      "title": "S3 print method for the class 'graph_report'",
      "topics": [
        "print.graph_report"
      ]
    },
    {
      "page": "print.gsd_graph_report",
      "title": "S3 print method for the class 'gsd_graph_report'",
      "topics": [
        "print.gsd_graph_report"
      ]
    },
    {
      "page": "print.initial_graph",
      "title": "S3 print method for the class 'initial_graph'",
      "topics": [
        "print.initial_graph"
      ]
    },
    {
      "page": "print.power_report",
      "title": "S3 print method for the class 'power_report'",
      "topics": [
        "print.power_report"
      ]
    },
    {
      "page": "print.updated_graph",
      "title": "S3 print method for the class 'updated_graph'",
      "topics": [
        "print.updated_graph"
      ]
    },
    {
      "page": "repeated_p",
      "title": "Calculate the repeated p-value for a single hypothesis at a given analysis",
      "topics": [
        "repeated_p"
      ]
    },
    {
      "page": "sequential_p",
      "title": "Calculate the sequential p-value for a single hypothesis",
      "topics": [
        "sequential_p"
      ]
    },
    {
      "page": "spending_functions",
      "title": "Alpha spending functions for group sequential designs",
      "topics": [
        "spending_hsd",
        "spending_linear",
        "spending_of",
        "spending_pocock"
      ]
    },
    {
      "page": "spending_with_time",
      "title": "Create a spending function with a custom spending time",
      "topics": [
        "spending_with_time"
      ]
    },
    {
      "page": "spending_wt",
      "title": "Wang-Tsiatis spending function",
      "topics": [
        "spending_wt"
      ]
    }
  ],
  "_pkglogo": "https://github.com/openpharma/graphicalmcp/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/openpharma/graphicalmcp/raw/HEAD/README.md",
  "_rundeps": [
    "matrixStats",
    "mvtnorm"
  ],
  "_vignettes": [
    {
      "source": "graph-examples.Rmd",
      "filename": "graph-examples.html",
      "title": "Common multiple comparison procedures illustrated using graphicalMCP",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Bonferroni-based procedures",
        "Bonferroni test",
        "Weighted Bonferroni test",
        "Holm Procedure",
        "Weighted Holm Procedure",
        "Fixed sequence procedure",
        "Fallback procedure",
        "Serial gatekeeping procedure",
        "Parallel gatekeeping procedure",
        "Successive procedure",
        "Hochberg-based procedures",
        "Hochberg procedure",
        "Simes-based procedures",
        "Hommel procedure",
        "Parametric procedures",
        "Šidák test",
        "Dunnett test",
        "Weighted Dunnett test",
        "Dunnett procedure",
        "Reference"
      ],
      "created": "2024-01-23 20:28:26",
      "modified": "2026-08-21 16:38:48",
      "commits": 6
    },
    {
      "source": "graphicalMCP.Rmd",
      "filename": "graphicalMCP.html",
      "title": "Get started",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Basic usage",
        "Initial graph",
        "Update graph",
        "Perform graphical MCPs",
        "Power simulations",
        "References"
      ],
      "created": "2024-01-23 20:28:26",
      "modified": "2026-08-21 16:38:48",
      "commits": 4
    },
    {
      "source": "glossary.Rmd",
      "filename": "glossary.html",
      "title": "Glossary",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2024-01-23 20:28:26",
      "modified": "2024-02-12 21:28:07",
      "commits": 13
    },
    {
      "source": "closed-testing.Rmd",
      "filename": "closed-testing.html",
      "title": "Graphical multiple comparison procedures based on the closure principle",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Motivating example",
        "Create a graph",
        "Perform the graphical multiple comparison procedure based on the closure principle",
        "Bonferroni tests",
        "Obtain the closure",
        "Obtain adjusted significance levels",
        "Mixed procedures for graphical approaches",
        "Parametric tests for primary hypotheses",
        "Parametric tests for primary hypotheses and Simes tests for secondary hypotheses",
        "Power calculation",
        "Input: Marginal power for primary hypotheses",
        "Input: Marginal power for secondary hypotheses",
        "Input: Correlation structure to simulate test statistics",
        "User-defined success criteria",
        "Output: Calculate power",
        "Reference"
      ],
      "created": "2024-01-23 20:28:26",
      "modified": "2024-06-04 16:12:16",
      "commits": 4
    },
    {
      "source": "group-sequential-testing.Rmd",
      "filename": "group-sequential-testing.html",
      "title": "Group Sequential Design with Graphical Approaches",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Alpha Spending Functions",
        "From Spending to Boundaries",
        "Repeated and Sequential P-values",
        "Case Study using repeated p-values and look_back = FALSE",
        "Hypotheses and Graph",
        "Observed P-values",
        "Running the Procedure (look_back = FALSE)",
        "Repeated p-values",
        "Nominal boundaries",
        "Comparison with Paper Values",
        "Boundary table",
        "Case Study using sequential p-values and look_back = TRUE",
        "Trial Setup",
        "Graph and Alpha Allocation",
        "P-values and Information Fractions",
        "Sequential P-values (look_back = TRUE)",
        "Per-hypothesis look_back",
        "When look_back makes a difference",
        "Customizing Spending Functions: Spending Time",
        "Monitoring: Adjusting for Changed Final Information",
        "Additional Examples",
        "Different Spending Functions per Hypothesis",
        "Using Spending Functions from Other Packages",
        "User-Defined Spending Functions",
        "Summary",
        "References"
      ],
      "created": "2026-08-21 16:38:48",
      "modified": "2026-08-26 19:55:34",
      "commits": 2
    },
    {
      "source": "internal-validation.Rmd",
      "filename": "internal-validation.html",
      "title": "Power simulations using multiple approaches for internal validation",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Power simulations",
        "Bonferroni tests",
        "Hochberg tests",
        "Simes tests",
        "Parametric tests",
        "Mixed tests of Bonferroni, Hochberg and Simes",
        "Mixed tests of parametric and one of Bonferroni, Hochberg and Simes",
        "Conclusions"
      ],
      "created": "2025-05-06 21:52:56",
      "modified": "2025-05-06 21:52:56",
      "commits": 1
    },
    {
      "source": "shortcut-testing.Rmd",
      "filename": "shortcut-testing.html",
      "title": "Sequentially rejective graphical multiple comparison procedures based on Bonferroni tests",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Motivating example",
        "Create the graph",
        "Perform the graphical multiple comparison procedure",
        "Adjusted p-values and rejections",
        "Obtain final and intermediate graphs after rejections",
        "Obtain possible orders of rejections",
        "Obtain adjusted significance levels",
        "Power simulation",
        "Input: Marginal power for primary hypotheses",
        "Input: Marginal power for secondary hypotheses",
        "Input: Correlation structure to simulate test statistics",
        "User-defined success criteria",
        "Output: Simulate power",
        "Reference"
      ],
      "created": "2024-01-23 20:28:26",
      "modified": "2026-08-21 16:38:48",
      "commits": 3
    },
    {
      "source": "gsd-validation.Rmd",
      "filename": "gsd-validation.html",
      "title": "Validation of Group Sequential Functions Against gsDesign and rpact",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "1. Alpha Spending Functions",
        "Comparison with gsDesign",
        "Comparison with rpact",
        "Detailed Example",
        "2. Group Sequential Boundaries",
        "3. Correlation Matrix",
        "4. Repeated P-values",
        "5. Sequential P-values",
        "Relationship Between Sequential and Repeated P-values",
        "6. Wang-Tsiatis Boundaries",
        "Verification of boundary shape",
        "Summary",
        "References"
      ],
      "created": "2026-08-21 16:38:48",
      "modified": "2026-08-21 16:38:48",
      "commits": 1
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