{
  "_id": "6af51ac3b90b31e79afd4de5",
  "Package": "prsladder",
  "Title": "Polygenic Risk Scores and Time to Disease Progression",
  "Version": "2026.9.23",
  "Authors@R": "c(\nperson(\"Brett\", \"Klamer\", email = \"code@brettklamer.com\", role = c(\"cre\", \"aut\", \"cph\")),\nperson(\"Ying\", \"Wang\", email = \"ying.wang@osumc.edu\", role = c(\"aut\", \"cph\"))\n)",
  "Description": "Measures the association of one or more polygenic risk\nscores with time to a disease event among persons who have a\nfirst diagnosis. Fits a ladder of Cox proportional-hazards\nmodels over all subsets of the scores, compares nested models,\npredicts absolute risk at a horizon with delayed entry, and\nevaluates discrimination, calibration, and reclassification.\nWith competing events, fits cause-specific hazard models and\nestimates the cumulative incidence. Draws risk curves with risk\ntables, hazard ratios across the ladder, and calibration and\ndiscrimination, and makes tables of risk by score group.\nEstimates standardized risk at score percentiles, risk ratios,\ncase shares, and time lost by score group, and net benefit.\nIncludes a simulator with known hazard ratios.",
  "URL": "https://brettklamer.com/work/prsladder/,\nhttps://bitbucket.org/bklamer/prsladder/",
  "License": "MIT + file LICENSE",
  "RdMacros": "Rdpack",
  "Language": "en-US",
  "VignetteBuilder": "knitr",
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  "Repository": "https://bklamer.r-universe.dev",
  "Date/Publication": "2026-11-12 01:33:12 UTC",
  "RemoteUrl": "https://bitbucket.org/bklamer/prsladder",
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  "NeedsCompilation": "no",
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    "User": "root"
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  "Author": "Brett Klamer [cre, aut, cph],\nYing Wang [aut, cph]",
  "Maintainer": "Brett Klamer <code@brettklamer.com>",
  "_user": "bklamer",
  "_type": "src",
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  "_created": "2026-11-12T01:38:44.000Z",
  "_published": "2026-11-12T01:47:47.491Z",
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    "simulate_prs_data",
    "standardized_risk"
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    {
      "page": "assess_calibration",
      "title": "Assess the Calibration of a Ladder",
      "topics": [
        "assess_calibration"
      ]
    },
    {
      "page": "assess_discrimination",
      "title": "Assess the Discrimination of a Ladder",
      "topics": [
        "assess_discrimination"
      ]
    },
    {
      "page": "assess_net_benefit",
      "title": "Assess Net Benefit for Decision Curves",
      "topics": [
        "assess_net_benefit"
      ]
    },
    {
      "page": "assess_stability",
      "title": "Assess the Stability of the Predicted Risks",
      "topics": [
        "assess_stability"
      ]
    },
    {
      "page": "assess_thresholds",
      "title": "Assess Risk Thresholds and Reclassification",
      "topics": [
        "assess_thresholds"
      ]
    },
    {
      "page": "bootstrap_plan",
      "title": "Plan the Bootstrap of an Internal Validation",
      "topics": [
        "bootstrap_plan"
      ]
    },
    {
      "page": "check_design",
      "title": "Test the Entry Terms and Pick a Design for Absolute Risks",
      "topics": [
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      ]
    },
    {
      "page": "check_entry",
      "title": "Test the Quasi-Independence of Entry and Exit",
      "topics": [
        "check_entry"
      ]
    },
    {
      "page": "compare_ladder",
      "title": "Compare Nested Models of a Ladder",
      "topics": [
        "compare_ladder"
      ]
    },
    {
      "page": "cumulative_risk",
      "title": "Cumulative Risk by Score Group",
      "topics": [
        "cumulative_risk",
        "print.prs_cumulative_risk"
      ]
    },
    {
      "page": "describe_case_mix",
      "title": "Compare the Case Mix of Two Cohorts",
      "topics": [
        "describe_case_mix"
      ]
    },
    {
      "page": "describe_cohort",
      "title": "Describe the Participants of a Cohort",
      "topics": [
        "describe_cohort"
      ]
    },
    {
      "page": "describe_risk",
      "title": "Table of Cumulative Risk by Score Group",
      "topics": [
        "describe_risk"
      ]
    },
    {
      "page": "export_ladder",
      "title": "Export a Ladder for External Validation",
      "topics": [
        "export_ladder"
      ]
    },
    {
      "page": "fit_ladder",
      "title": "Fit the Ladder of Cox Models",
      "topics": [
        "fit_ladder"
      ]
    },
    {
      "page": "horizon_support",
      "title": "Check the Support of Prediction Horizons",
      "topics": [
        "horizon_support"
      ]
    },
    {
      "page": "plot_calibration",
      "title": "Plot Observed Against Predicted Risk",
      "topics": [
        "plot_calibration"
      ]
    },
    {
      "page": "plot_discrimination",
      "title": "Plot the AUC or Brier Score of the Ladder",
      "topics": [
        "plot_discrimination"
      ]
    },
    {
      "page": "plot_gradient",
      "title": "Plot the Risk at One Time by Score Group",
      "topics": [
        "plot_gradient"
      ]
    },
    {
      "page": "plot_ladder",
      "title": "Plot the Hazard Ratios of the Scores Across the Ladder",
      "topics": [
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      ]
    },
    {
      "page": "plot_net_benefit",
      "title": "Plot Decision Curves",
      "topics": [
        "plot_net_benefit"
      ]
    },
    {
      "page": "plot_risk",
      "title": "Plot Cumulative Risk Curves by Score Group",
      "topics": [
        "plot_risk"
      ]
    },
    {
      "page": "plot_stacked",
      "title": "Plot the Cumulative Incidence of Both Events as a Stack",
      "topics": [
        "plot_stacked"
      ]
    },
    {
      "page": "predict_risk",
      "title": "Predict Absolute Risk at a Horizon",
      "topics": [
        "predict_risk"
      ]
    },
    {
      "page": "prediction_data",
      "title": "Build Prediction Data for Persons Without Outcome Data",
      "topics": [
        "prediction_data"
      ]
    },
    {
      "page": "print.prs_cohort",
      "title": "Print a Cohort",
      "topics": [
        "print.prs_cohort"
      ]
    },
    {
      "page": "print.prs_export",
      "title": "Print an Export",
      "topics": [
        "print.prs_export"
      ]
    },
    {
      "page": "print.prs_ladder",
      "title": "Print or Summarize a Ladder",
      "topics": [
        "print.prs_ladder",
        "summary.prs_ladder"
      ]
    },
    {
      "page": "prs_cohort",
      "title": "Build a Cohort for a Ladder of Polygenic Risk Score Models",
      "topics": [
        "prs_cohort"
      ]
    },
    {
      "page": "simulate_prs_data",
      "title": "Simulate a Polygenic Risk Score Cohort",
      "topics": [
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      ]
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      "title": "Standardized Risk at Score Percentiles",
      "topics": [
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        "standardized_risk"
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      "title": "From type 2 diabetes to coronary artery disease: a prsladder tutorial",
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        "Step 3: fit the ladder of models",
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