{
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  "Package": "BioPred",
  "Type": "Package",
  "Title": "An R Package for Biomarkers Analysis in Precision Medicine",
  "Version": "1.0.2",
  "Date": "2024-11-03",
  "Authors@R": "c(\nperson(\"Zihuan\", \"Liu\", , \"zihuan.liu@abbvie.com\", role = c(\"aut\", \"cre\")),\nperson(\"Yan\", \"Sun\", , \"yan.sun@abbvie.com\", role = \"aut\"),\nperson(\"Xin\",\"Huang\", , \"xin.huang@abbvie.com\", role = \"aut\"))",
  "Maintainer": "Zihuan Liu <zihuan.liu@abbvie.com>",
  "Description": "Provides functions for training extreme gradient boosting\nmodel using propensity score A-learning and weight-learning\nmethods. For further details, see Liu et al. (2024)\n<doi:10.1093/bioinformatics/btae592>.",
  "Encoding": "UTF-8",
  "Language": "en",
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    "User": "root"
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  "Author": "Zihuan Liu [aut, cre], Yan Sun [aut], Xin Huang [aut]",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2024-11-04 08:30:13 UTC",
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    "XGBoostSub_bin",
    "XGBoostSub_con",
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        "x2",
        "x3",
        "x4",
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        "x9",
        "x10",
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        "y.bin",
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        "y.event",
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      "rows": 1000,
      "table": true,
      "tojson": true
    }
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    {
      "page": "cat_summary",
      "title": "Summarize Categorical Variables in Subgroup",
      "topics": [
        "cat_summary"
      ]
    },
    {
      "page": "cdf_plot",
      "title": "CDF Plot for a biomarker",
      "topics": [
        "cdf_plot"
      ]
    },
    {
      "page": "cut_perf",
      "title": "Cutoff Performance Evaluation",
      "topics": [
        "cut_perf"
      ]
    },
    {
      "page": "eval_metric_bin",
      "title": "Evaluation Metrics for XGBoostSub_bin Model",
      "topics": [
        "eval_metric_bin"
      ]
    },
    {
      "page": "eval_metric_con",
      "title": "Evaluation Metrics for XGBoostSub_con Model",
      "topics": [
        "eval_metric_con"
      ]
    },
    {
      "page": "eval_metric_sur",
      "title": "Evaluation Metrics for XGBoostSub_sur Model",
      "topics": [
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      ]
    },
    {
      "page": "fixcut_bin",
      "title": "Fixed Cutoff Analysis for Individual Biomarker Associated with Binary Outcome Variables",
      "topics": [
        "fixcut_bin"
      ]
    },
    {
      "page": "fixcut_con",
      "title": "Fixed Cutoff Analysis for Individual Biomarker Associated with Continuous Outcome",
      "topics": [
        "fixcut_con"
      ]
    },
    {
      "page": "fixcut_sur",
      "title": "Fixed Cutoff Analysis for Individual Biomarker Associated with Survival Outcome",
      "topics": [
        "fixcut_sur"
      ]
    },
    {
      "page": "gam_ctr_plot",
      "title": "GAM Contrast Plot",
      "topics": [
        "gam_ctr_plot"
      ]
    },
    {
      "page": "gam_plot",
      "title": "GAM Plot",
      "topics": [
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      ]
    },
    {
      "page": "get_subgroup_results",
      "title": "Get Subgroup Results",
      "topics": [
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      ]
    },
    {
      "page": "predictive_biomarker_imp",
      "title": "Plot Predictive Biomarker Importance based on XGBoost-based Subgroup Model",
      "topics": [
        "predictive_biomarker_imp"
      ]
    },
    {
      "page": "roc_bin",
      "title": "AUC ROC Table for Biomarkers Associated with Binary Outcomes",
      "topics": [
        "roc_bin"
      ]
    },
    {
      "page": "roc_bin_plot",
      "title": "ROC Plot Biomarkers Associated with Binary Outcomes",
      "topics": [
        "roc_bin_plot"
      ]
    },
    {
      "page": "scat_cont_plot",
      "title": "Scatter Plot for a Biomarker Associated with Continuous Outcome",
      "topics": [
        "scat_cont_plot"
      ]
    },
    {
      "page": "subgrp_perf",
      "title": "Subgroup Performance Evaluation for Prognostic Cases",
      "topics": [
        "subgrp_perf"
      ]
    },
    {
      "page": "subgrp_perf_pred",
      "title": "Subgroup Performance Evaluation for Predictive Cases",
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        "subgrp_perf_pred"
      ]
    },
    {
      "page": "tutorial_data",
      "title": "Tutorial Data",
      "topics": [
        "tutorial_data"
      ]
    },
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      "page": "XGBoostSub_bin",
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      "topics": [
        "XGBoostSub_bin"
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      "topics": [
        "XGBoostSub_con"
      ]
    },
    {
      "page": "XGBoostSub_sur",
      "title": "XGBoost Model with Modified Loss Function for Subgroup Identification with Survival Outcomes",
      "topics": [
        "XGBoostSub_sur"
      ]
    }
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      "filename": "Tutorial.html",
      "title": "BioPred Package Tutorial",
      "author": "Zihuan Liu, 11/2024",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Install from GitHub",
        "Install from CRAN",
        "Loading the Data",
        "Data Description",
        "1 Example Analysis for Continuous Outcomes",
        "1.1 Training the XGBoostSub_con Model",
        "1.2 Evaluating Predictive Biomarker Importance with XGBoostSub_con",
        "1.3 Obtaining subgroup results with XGBoostSub_con",
        "1.4 Commonly used subgroup/biomarker analysis tools",
        "2 Example Analysis for Binary Outcomes",
        "2.1 Train the XGBoostSub_bin Model",
        "2.2 Predictive biomarker importance",
        "2.3 Get subgroup results",
        "2.4 Post-Hoc analysis based on subgroup and biomarker results",
        "3 Example Analysis for time-to-event outcome",
        "3.1 Train the XGBoostSub_sur model",
        "3.1 Predictive biomarker importance using XGBoostSub_sur",
        "3.2 Get subgroup results based on XGBoostSub_sur",
        "4. Other functions for biomarker analysis in clinical practice"
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      "modified": "2024-11-04 08:30:13",
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