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  "Title": "Advanced Analytics and Testing Framework for Systematic Review\nSearch Strategies",
  "Version": "0.1.0",
  "Date": "2025-08-12",
  "Authors@R": "person(\"Chao Liu\",\nemail = \"chaoliu@cedarville.edu\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-9979-8272\"))",
  "Description": "Provides comprehensive analytics, reporting, and testing\ncapabilities for systematic review search strategies. The\npackage focuses on validating search performance, generating\nstandardized 'PRISMA'-compliant reports, and ensuring\nreproducibility in evidence synthesis. Features include\nprecision-recall analysis, cross-database performance\ncomparison, benchmark validation against gold standards,\nsensitivity analysis, temporal coverage assessment, automated\nreport generation, and statistical comparison of search\nstrategies. Supports multiple export formats including 'CSV',\n'Excel', 'RIS', 'BibTeX', and 'EndNote'. Includes tools for\nduplicate detection, search strategy optimization,\ncross-validation frameworks, meta-analysis of benchmark\nresults, power analysis for study design, and reproducibility\npackage creation. Optionally connects to 'PubMed' for direct\ndatabase searching and real-time strategy comparison using the\n'E-utilities' 'API'. Enhanced with bootstrap comparison\nmethods, 'McNemar' test for strategy evaluation, and\ncomprehensive visualization tools for performance assessment.\nMethods based on Manning et al. (2008) for information\nretrieval metrics, Moher et al. (2009) for 'PRISMA' guidelines,\nand Sampson et al. (2006) for systematic review search\nmethodology.",
  "License": "GPL-3",
  "URL": "https://github.com/chaoliu-cl/searchAnalyzeR,\nhttp://liu-chao.site/searchAnalyzeR/",
  "BugReports": "https://github.com/chaoliu-cl/searchAnalyzeR/issues",
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  "Repository": "https://chaoliu-cl.r-universe.dev",
  "Date/Publication": "2025-11-03 15:35:20 UTC",
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    "calc_efficiency",
    "calc_precision_recall",
    "calc_sample_size",
    "calc_search_stats",
    "calc_strategy_comparison",
    "calc_temporal_coverage",
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    "compare_terms",
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    "create_data_package",
    "create_prisma",
    "create_progress_bar",
    "create_strategy",
    "create_summary",
    "cv_strategy",
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    "export_metrics",
    "export_results",
    "export_validation",
    "extract_screening",
    "find_top_terms",
    "format_numbers",
    "gen_repro_seed",
    "get_pkg_versions",
    "mem_cleanup",
    "mem_monitor",
    "mem_usage",
    "merge_results",
    "meta_analyze",
    "opt_df",
    "plot_db_performance",
    "plot_keyword_eff",
    "plot_overview",
    "plot_pr_curve",
    "plot_sensitivity",
    "plot_temporal",
    "plot_term_effectiveness",
    "PRISMAReporter",
    "PubMedConnector",
    "ReproducibilityManager",
    "run_benchmarks",
    "search_multiple_databases",
    "search_pubmed",
    "SearchAnalyzer",
    "std_search_results",
    "stream_file",
    "term_effectiveness",
    "validate_strategy"
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      "title": "Create a Temporary Analysis Environment",
      "topics": [
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      ]
    },
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      "title": "Auto-detect Column Mappings",
      "topics": [
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      ]
    },
    {
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      "title": "Benchmark Validation System",
      "topics": [
        "BenchmarkValidator"
      ]
    },
    {
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      "title": "Bootstrap Comparison of Search Strategies",
      "topics": [
        "bootstrap_compare"
      ]
    },
    {
      "page": "cache_manage",
      "title": "Manage Search Results Cache",
      "topics": [
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      ]
    },
    {
      "page": "calc_ci",
      "title": "Calculate Confidence Intervals",
      "topics": [
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      ]
    },
    {
      "page": "calc_cosine",
      "title": "Calculate Cosine Similarity",
      "topics": [
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      ]
    },
    {
      "page": "calc_coverage",
      "title": "Calculate Coverage Metrics Across Databases",
      "topics": [
        "calc_coverage"
      ]
    },
    {
      "page": "calc_efficiency",
      "title": "Calculate Search Efficiency Metrics",
      "topics": [
        "calc_efficiency"
      ]
    },
    {
      "page": "calc_jaccard",
      "title": "Calculate Jaccard Similarity",
      "topics": [
        "calc_jaccard"
      ]
    },
    {
      "page": "calc_precision_recall",
      "title": "Calculate Precision and Recall Metrics",
      "topics": [
        "calc_precision_recall"
      ]
    },
    {
      "page": "calc_sample_size",
      "title": "Power Analysis for Search Strategy Evaluation",
      "topics": [
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      ]
    },
    {
      "page": "calc_search_stats",
      "title": "Calculate Search Result Statistics",
      "topics": [
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      ]
    },
    {
      "page": "calc_strategy_comparison",
      "title": "Calculate Strategy Comparison Metrics",
      "topics": [
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      ]
    },
    {
      "page": "calc_temporal_coverage",
      "title": "Calculate Temporal Coverage Metrics",
      "topics": [
        "calc_temporal_coverage"
      ]
    },
    {
      "page": "calc_tes",
      "title": "Calculate Term Effectiveness Score",
      "topics": [
        "calc_tes"
      ]
    },
    {
      "page": "calc_text_sim",
      "title": "Calculate Text Similarity",
      "topics": [
        "calc_text_sim"
      ]
    },
    {
      "page": "check_deps",
      "title": "Utility Functions for searchAnalyzeR Package",
      "topics": [
        "check_deps"
      ]
    },
    {
      "page": "chunk_process",
      "title": "Process Large Dataset in Chunks",
      "topics": [
        "chunk_process"
      ]
    },
    {
      "page": "clean_col_names",
      "title": "Clean Column Names",
      "topics": [
        "clean_col_names"
      ]
    },
    {
      "page": "clean_text",
      "title": "Clean Text Fields",
      "topics": [
        "clean_text"
      ]
    },
    {
      "page": "compare_strategies",
      "title": "Benchmark Testing Framework for Search Strategies",
      "topics": [
        "compare_strategies"
      ]
    },
    {
      "page": "compare_terms",
      "title": "Compare Terms Across Strategies",
      "topics": [
        "compare_terms"
      ]
    },
    {
      "page": "complete_search_workflow",
      "title": "Complete Search and Analysis Workflow",
      "topics": [
        "complete_search_workflow"
      ]
    },
    {
      "page": "create_analysis_template",
      "title": "Create Analysis Template Script",
      "topics": [
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      ]
    },
    {
      "page": "create_data_dictionary",
      "title": "Create Data Dictionary",
      "topics": [
        "create_data_dictionary"
      ]
    },
    {
      "page": "create_data_package",
      "title": "Create Data Package for Sharing",
      "topics": [
        "create_data_package"
      ]
    },
    {
      "page": "create_package_manifest",
      "title": "Create Package Manifest",
      "topics": [
        "create_package_manifest"
      ]
    },
    {
      "page": "create_package_readme",
      "title": "Create Package README",
      "topics": [
        "create_package_readme"
      ]
    },
    {
      "page": "create_prisma",
      "title": "Create PRISMA Flow Diagram with Proper Spacing and Text Enclosure",
      "topics": [
        "create_prisma"
      ]
    },
    {
      "page": "create_progress_bar",
      "title": "Create Progress Bar for Long Operations",
      "topics": [
        "create_progress_bar"
      ]
    },
    {
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      "title": "Create Default Search Strategy Template",
      "topics": [
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    },
    {
      "page": "create_summary",
      "title": "Create Summary Statistics Table",
      "topics": [
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      ]
    },
    {
      "page": "cv_strategy",
      "title": "Cross-Validation Framework for Search Strategies",
      "topics": [
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    },
    {
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      "title": "Detect DOI-based Duplicates",
      "topics": [
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    },
    {
      "page": "detect_dupes",
      "title": "Detect and Remove Duplicate Records",
      "topics": [
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      ]
    },
    {
      "page": "detect_exact_dupes",
      "title": "Detect Exact Duplicates",
      "topics": [
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      ]
    },
    {
      "page": "detect_fuzzy_dupes",
      "title": "Detect Fuzzy Duplicates",
      "topics": [
        "detect_fuzzy_dupes"
      ]
    },
    {
      "page": "export_metrics",
      "title": "Export Analysis Metrics",
      "topics": [
        "export_metrics"
      ]
    },
    {
      "page": "export_metrics_csv",
      "title": "Export Metrics to CSV",
      "topics": [
        "export_metrics_csv"
      ]
    },
    {
      "page": "export_metrics_json",
      "title": "Export Metrics to JSON",
      "topics": [
        "export_metrics_json"
      ]
    },
    {
      "page": "export_metrics_xlsx",
      "title": "Export Metrics to Excel",
      "topics": [
        "export_metrics_xlsx"
      ]
    },
    {
      "page": "export_results",
      "title": "Export Utilities for Search Analysis Results",
      "topics": [
        "export_results"
      ]
    },
    {
      "page": "export_to_bibtex",
      "title": "Export to BibTeX Format",
      "topics": [
        "export_to_bibtex"
      ]
    },
    {
      "page": "export_to_csv",
      "title": "Export to CSV Format",
      "topics": [
        "export_to_csv"
      ]
    },
    {
      "page": "export_to_endnote",
      "title": "Export to EndNote Format",
      "topics": [
        "export_to_endnote"
      ]
    },
    {
      "page": "export_to_ris",
      "title": "Export to RIS Format",
      "topics": [
        "export_to_ris"
      ]
    },
    {
      "page": "export_to_xlsx",
      "title": "Export to Excel Format with Multiple Sheets",
      "topics": [
        "export_to_xlsx"
      ]
    },
    {
      "page": "export_validation",
      "title": "Export Validation Results",
      "topics": [
        "export_validation"
      ]
    },
    {
      "page": "export_validation_csv",
      "title": "Export Validation Results to CSV",
      "topics": [
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    },
    {
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      "title": "Export Validation Results to JSON",
      "topics": [
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    },
    {
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      "title": "Export Validation Results to Excel",
      "topics": [
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      "title": "Extract Screening Data Structure",
      "topics": [
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      ]
    },
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      "title": "Find Top Performing Terms",
      "topics": [
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      ]
    },
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      "page": "format_numbers",
      "title": "Format Numbers for Display",
      "topics": [
        "format_numbers"
      ]
    },
    {
      "page": "gen_repro_seed",
      "title": "Generate Reproducible Random Seed",
      "topics": [
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      ]
    },
    {
      "page": "get_pkg_versions",
      "title": "Extract Package Version Information",
      "topics": [
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      ]
    },
    {
      "page": "is_empty",
      "title": "Check if Object is Empty",
      "topics": [
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      "title": "Clean up Search Analysis Objects to Free Memory",
      "topics": [
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    },
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      "page": "mem_monitor",
      "title": "Monitor Memory Usage During Function Execution",
      "topics": [
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      ]
    },
    {
      "page": "mem_usage",
      "title": "Get Current Memory Usage",
      "topics": [
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    },
    {
      "page": "merge_results",
      "title": "Merge Search Results from Multiple Sources",
      "topics": [
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      ]
    },
    {
      "page": "meta_analyze",
      "title": "Meta-Analysis of Benchmark Results",
      "topics": [
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      ]
    },
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      "title": "Memory-Efficient Data Frame",
      "topics": [
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    },
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      "title": "Create Database Performance Comparison",
      "topics": [
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      ]
    },
    {
      "page": "plot_keyword_eff",
      "title": "Create Keyword Effectiveness Analysis Plot",
      "topics": [
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    {
      "page": "plot_pr_curve",
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      "page": "plot_sensitivity",
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      "page": "plot_temporal",
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      "page": "print.term_comparison",
      "title": "Print Method for Term Comparison",
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    {
      "page": "print.term_effectiveness",
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    {
      "page": "PubMedConnector",
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      "page": "rename_columns",
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      "page": "ReproducibilityManager",
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      "title": "Benchmark Suite Execution",
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