nogoldstandard Low Agreement Data
Source:R/data_nogoldstandard_docs.R
nogoldstandard_lowagreement.RdDataset with 140 patients where two tests show low agreement. Tests have moderate and different diagnostic characteristics (Sens: 0.70, 0.65; Spec: 0.80, 0.75).
Format
A data frame with 140 rows and 3 variables:
- patient_id
Character: Patient identifier (PT001-PT140)
- Test1
Factor: First test ("Negative", "Positive"), Sens=0.70, Spec=0.80
- Test2
Factor: Second test ("Negative", "Positive"), Sens=0.65, Spec=0.75
- age
Numeric: Patient age in years (mean 58, SD 14)
Details
Simulated with 30% prevalence. Tests have low correlation, representing tests measuring different aspects of disease.
Examples
data(nogoldstandard_lowagreement)
nogoldstandard(data = nogoldstandard_lowagreement,
test1 = "Test1", test1Positive = "Positive",
test2 = "Test2", test2Positive = "Positive",
test3Positive = "", test4Positive = "",
test5Positive = "")
#>
#> ANALYSIS WITHOUT GOLD STANDARD
#>
#> Agreement Statistics (Cohen's Kappa)
#> ─────────────────────────────────────────────────────────
#> Test Pair Kappa p-value Agreement
#> ─────────────────────────────────────────────────────────
#> Test1 vs Test2 0.2295840 0.0085860 64.28571
#> ─────────────────────────────────────────────────────────
#>
#>
#> <div class='clinical-summary' style='background: #f0f8ff; padding:
#> 15px; border-radius: 8px; margin: 10px 0;'><h4 style='color: #1565c0;
#> margin-top: 0;'> Clinical Summary
#>
#> Analysis: No gold standard analysis using all_positive method
#>
#> Tests analyzed: Test1, Test2 (N=2)
#>
#> Disease prevalence: 18.6%
#>
#> Test sensitivities: Range from 100.0% to 100.0%
#>
#> Clinical interpretation: Moderate prevalence setting - balanced
#> diagnostic performance
#>
#> <div style='background: #f8f9fa; padding: 20px; border-radius: 8px;
#> margin: 15px 0; border-left: 4px solid #007bff;'><h3 style='color:
#> #007bff; margin-top: 0;'> Method Selection Guide
#>
#> <div style='margin: 15px 0; padding: 15px; background: #e8f5e8;
#> border-radius: 5px;'><h4 style='color: #2e7d32; margin-top: 0;'>
#> Latent Class Analysis (Recommended)
#>
#> Description: Most robust method using mixture models. Estimates
#> disease prevalence and test parameters simultaneously.
#>
#> Best for: Diagnostic validation studies with 3+ tests and N>=100
#>
#> Strengths: Handles conditional dependence, provides model fit
#> statistics, most statistically rigorous
#>
#> <div style='margin: 15px 0; padding: 15px; background: #e3f2fd;
#> border-radius: 5px;'><h4 style='color: #1565c0; margin-top: 0;'>
#> Bayesian Analysis
#>
#> Description: Incorporates prior knowledge about test performance using
#> Bayesian methods.
#>
#> Best for: Studies where you have prior information about expected
#> sensitivity/specificity
#>
#> Strengths: Uses prior knowledge, handles uncertainty well, good for
#> smaller samples
#>
#> <div style='margin: 15px 0; padding: 15px; background: #fff3e0;
#> border-radius: 5px;'><h4 style='color: #ef6c00; margin-top: 0;'>
#> Composite Reference
#>
#> Description: Uses majority vote of available tests as pseudo-gold
#> standard.
#>
#> Best for: Inter-rater agreement studies with 3+ tests, exploratory
#> analysis
#>
#> Strengths: Simple and intuitive, requires minimal assumptions, good
#> starting point
#>
#> <div style='margin: 15px 0; padding: 15px; background: #fce4ec;
#> border-radius: 5px;'><h4 style='color: #c2185b; margin-top: 0;'> All
#> Tests Positive
#>
#> Description: Conservative approach - disease present only if ALL tests
#> are positive.
#>
#> Best for: Highly specific diagnoses where false positives are very
#> costly
#>
#> Strengths: High specificity reference, minimizes false positives
#>
#> <div style='margin: 15px 0; padding: 15px; background: #e8f5e8;
#> border-radius: 5px;'><h4 style='color: #388e3c; margin-top: 0;'> Any
#> Test Positive
#>
#> Description: Liberal approach - disease present if ANY test is
#> positive.
#>
#> Best for: Population screening scenarios where missing cases is costly
#>
#> Strengths: High sensitivity reference, minimizes false negatives
#>
#> <div style='margin: 15px 0; padding: 10px; background: #fff8e1;
#> border-radius: 5px; border-left: 3px solid #ffb300;'><h4 style='color:
#> #e65100; margin-top: 0;'> Selection Tips
#>
#> Start with Latent Class Analysis for most diagnostic studiesUse
#> Composite Reference for quick exploratory analysisChoose All/Any Tests
#> Positive based on clinical consequences of errorsConsider Bayesian if
#> you have strong prior information
#>
#> Disease Prevalence
#> ───────────────────────────────────────
#> Estimate Lower CI Upper CI
#> ───────────────────────────────────────
#> 18.57143 12.12981 25.01305
#> ───────────────────────────────────────
#>
#>
#> Test Performance Metrics
#> ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#> Test Sensitivity Lower CI Upper CI Specificity Lower CI Upper CI PPV NPV
#> ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#> Test1 100.00000 100.00000 100.00000 79.82456 73.17698 86.47215 53.06122 100.00000
#> Test2 100.00000 100.00000 100.00000 76.31579 69.27339 83.35819 49.05660 100.00000
#> ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#>
#>
#> Test Cross-Tabulation
#> ───────────────────────────────────────────
#> Test Combination Count Percentage
#> ───────────────────────────────────────────
#> Test1-, Test2- 64 45.71429
#> Test1-, Test2+ 27 19.28571
#> Test1+, Test2+ 26 18.57143
#> Test1+, Test2- 23 16.42857
#> ───────────────────────────────────────────
#>
