searchAnalyzeR0.1.0 package

Advanced Analytics and Testing Framework for Systematic Review Search Strategies

export_results

Export Utilities for Search Analysis Results

export_to_bibtex

Export to BibTeX Format

export_to_csv

Export to CSV Format

export_to_endnote

Export to EndNote Format

export_to_ris

Export to RIS Format

export_to_xlsx

Export to Excel Format with Multiple Sheets

export_validation_csv

Export Validation Results to CSV

export_validation_json

Export Validation Results to JSON

export_validation_xlsx

Export Validation Results to Excel

export_validation

Export Validation Results

extract_screening

Extract Screening Data Structure

find_top_terms

Find Top Performing Terms

format_numbers

Format Numbers for Display

gen_repro_seed

Generate Reproducible Random Seed

get_pkg_versions

Extract Package Version Information

is_empty

Check if Object is Empty

mem_cleanup

Clean up Search Analysis Objects to Free Memory

mem_monitor

Monitor Memory Usage During Function Execution

mem_usage

Get Current Memory Usage

merge_results

Merge Search Results from Multiple Sources

meta_analyze

Meta-Analysis of Benchmark Results

opt_df

Memory-Efficient Data Frame

plot_db_performance

Create Database Performance Comparison

plot_keyword_eff

Create Keyword Effectiveness Analysis Plot

plot_overview

Visualization Functions for Search Strategy Analysis

plot_pr_curve

Create Precision-Recall Curve

plot_sensitivity

Create Sensitivity Analysis Heatmap

plot_temporal

Create Temporal Coverage Plot

plot_term_effectiveness

Plot Term Effectiveness Results

print.term_comparison

Print Method for Term Comparison

print.term_effectiveness

Print Method for term_effectiveness Objects

PRISMAReporter

PRISMA-Compliant Report Generator

PubMedConnector

PubMed Database Connector

rename_columns

Rename Columns Based on Mapping

ReproducibilityManager

Search Reproducibility Manager

run_benchmarks

Benchmark Suite Execution

safe_divide

Safe Division Function

safe_list_to_df

Convert List to Data Frame Safely

search_multiple_databases

Search Multiple Databases

search_pubmed

Search PubMed and Retrieve Articles

SearchAnalyzer

Search Strategy Analytics Engine

simulate_pubmed_results

Generate Simulated PubMed Results

simulate_search_execution

Simulate Search Strategy Execution

standardize_date

Standardize Date Formats

std_cochrane_results

Standardize Cochrane Results

std_embase_results

Standardize Embase Results

std_generic_results

Standardize Generic Results

std_pubmed_results

Standardize PubMed Results

std_scopus_results

Standardize Scopus Results

std_search_results

Standardize Search Results Format

std_wos_results

Standardize Web of Science Results

stream_file

Stream Process Large Files

term_effectiveness

Analyze Term Effectiveness in Search Results

validate_date_range

Validate Date Range

validate_strategy

Validate Search Strategy Object

analysis_env

Create a Temporary Analysis Environment

auto_detect_columns

Auto-detect Column Mappings

BenchmarkValidator

Benchmark Validation System

bootstrap_compare

Bootstrap Comparison of Search Strategies

cache_manage

Manage Search Results Cache

calc_ci

Calculate Confidence Intervals

calc_cosine

Calculate Cosine Similarity

calc_coverage

Calculate Coverage Metrics Across Databases

calc_efficiency

Calculate Search Efficiency Metrics

calc_jaccard

Calculate Jaccard Similarity

calc_precision_recall

Calculate Precision and Recall Metrics

calc_sample_size

Power Analysis for Search Strategy Evaluation

calc_search_stats

Calculate Search Result Statistics

calc_strategy_comparison

Calculate Strategy Comparison Metrics

calc_temporal_coverage

Calculate Temporal Coverage Metrics

calc_tes

Calculate Term Effectiveness Score

calc_text_sim

Calculate Text Similarity

check_deps

Utility Functions for searchAnalyzeR Package

chunk_process

Process Large Dataset in Chunks

clean_col_names

Clean Column Names

clean_text

Clean Text Fields

compare_strategies

Benchmark Testing Framework for Search Strategies

compare_terms

Compare Terms Across Strategies

complete_search_workflow

Complete Search and Analysis Workflow

create_analysis_template

Create Analysis Template Script

create_data_dictionary

Create Data Dictionary

create_data_package

Create Data Package for Sharing

create_package_manifest

Create Package Manifest

create_package_readme

Create Package README

create_prisma

Create PRISMA Flow Diagram with Proper Spacing and Text Enclosure

create_progress_bar

Create Progress Bar for Long Operations

create_strategy

Create Default Search Strategy Template

create_summary

Create Summary Statistics Table

cv_strategy

Cross-Validation Framework for Search Strategies

detect_doi_dupes

Detect DOI-based Duplicates

detect_dupes

Detect and Remove Duplicate Records

detect_exact_dupes

Detect Exact Duplicates

detect_fuzzy_dupes

Detect Fuzzy Duplicates

export_metrics_csv

Export Metrics to CSV

export_metrics_json

Export Metrics to JSON

export_metrics_xlsx

Export Metrics to Excel

export_metrics

Export Analysis Metrics

Provides comprehensive analytics, reporting, and testing capabilities for systematic review search strategies. The package focuses on validating search performance, generating standardized 'PRISMA'-compliant reports, and ensuring reproducibility in evidence synthesis. Features include precision-recall analysis, cross-database performance comparison, benchmark validation against gold standards, sensitivity analysis, temporal coverage assessment, automated report generation, and statistical comparison of search strategies. Supports multiple export formats including 'CSV', 'Excel', 'RIS', 'BibTeX', and 'EndNote'. Includes tools for duplicate detection, search strategy optimization, cross-validation frameworks, meta-analysis of benchmark results, power analysis for study design, and reproducibility package creation. Optionally connects to 'PubMed' for direct database searching and real-time strategy comparison using the 'E-utilities' 'API'. Enhanced with bootstrap comparison methods, 'McNemar' test for strategy evaluation, and comprehensive visualization tools for performance assessment. Methods based on Manning et al. (2008) for information retrieval metrics, Moher et al. (2009) for 'PRISMA' guidelines, and Sampson et al. (2006) for systematic review search methodology.

  • Maintainer: Chao Liu
  • License: GPL-3
  • Last published: 2025-08-28