decisioncompare Test Data - Basic Two-Test Comparison
Source:R/data_decisioncompare_docs.R
decisioncompare_test.RdBasic dataset with 200 patients for comparing two diagnostic tests against a gold standard. Test 1 (Sens=0.85, Spec=0.90), Test 2 (Sens=0.80, Spec=0.85).
Format
A data frame with 200 rows and 5 variables:
- patient_id
Character: Patient identifier (PT001-PT200)
- GoldStandard
Factor: True disease status ("Negative", "Positive"), 30% prevalence
- Test1
Factor: First test result ("Negative", "Positive"), Sens=0.85, Spec=0.90
- Test2
Factor: Second test result ("Negative", "Positive"), Sens=0.80, Spec=0.85
- age
Numeric: Patient age in years (mean 58, SD 12)
- sex
Factor: "Male" or "Female"
Details
Simulated with 30% disease prevalence. Tests have good characteristics with Test1 slightly superior to Test2. Suitable for demonstrating basic test comparison with confidence intervals and McNemar's test.
Examples
data(decisioncompare_test)
decisioncompare(data = decisioncompare_test, gold = "GoldStandard",
goldPositive = "Positive", test1 = "Test1",
test1Positive = "Positive", test2 = "Test2",
test2Positive = "Positive", test3Positive = "",
ci = TRUE, statComp = TRUE)
#>
#> COMPARE MEDICAL DECISION TESTS
#>
#> character(0)
#>
#> Test 1 - Recoded Data
#> ────────────────────────────────────────────────────────────────
#> Gold Positive Gold Negative Total
#> ────────────────────────────────────────────────────────────────
#> Test Positive 62.000000 12.00000 74.00000
#> Test Negative 9.000000 117.00000 126.00000
#> Total 71.000000 129.00000 200.00000
#> ────────────────────────────────────────────────────────────────
#>
#>
#> Test 1 - Confidence Intervals
#> ────────────────────────────────────────────────────────────────────────
#> Decision Statistics Estimate Lower Upper
#> ────────────────────────────────────────────────────────────────────────
#> Apparent prevalence 37.00000 30.29698 44.09465
#> True prevalence 35.50000 28.87838 42.55862
#> Test sensitivity 87.32394 77.29595 94.03642
#> Test specificity 90.69767 84.31447 95.10049
#> Diagnostic accuracy 89.50000 84.39813 93.38188
#> Positive predictive value 83.78378 73.38642 91.33010
#> Negative predictive value 92.85714 86.87359 96.68197
#> Proportion of false positives 9.30233 4.89951 15.68553
#> Proportion of false negative 12.67606 5.96358 22.70405
#> False Discovery Rate 16.21622 8.66990 26.61358
#> False Omission Rate 7.14286 3.31803 13.12641
#> ────────────────────────────────────────────────────────────────────────
#>
#>
#> Test 2 - Recoded Data
#> ────────────────────────────────────────────────────────────────
#> Gold Positive Gold Negative Total
#> ────────────────────────────────────────────────────────────────
#> Test Positive 56.00000 18.00000 74.00000
#> Test Negative 15.00000 111.00000 126.00000
#> Total 71.00000 129.00000 200.00000
#> ────────────────────────────────────────────────────────────────
#>
#>
#> Test 2 - Confidence Intervals
#> ────────────────────────────────────────────────────────────────────────
#> Decision Statistics Estimate Lower Upper
#> ────────────────────────────────────────────────────────────────────────
#> Apparent prevalence 37.00000 30.29698 44.09465
#> True prevalence 35.50000 28.87838 42.55862
#> Test sensitivity 78.87324 67.55973 87.66594
#> Test specificity 86.04651 78.84665 91.51575
#> Diagnostic accuracy 83.50000 77.61565 88.36169
#> Positive predictive value 75.67568 64.30857 84.90182
#> Negative predictive value 88.09524 81.12595 93.18155
#> Proportion of false positives 13.95349 8.48425 21.15335
#> Proportion of false negative 21.12676 12.33406 32.44027
#> False Discovery Rate 24.32432 15.09818 35.69143
#> False Omission Rate 11.90476 6.81845 18.87405
#> ────────────────────────────────────────────────────────────────────────
#>
#>
#> Test 3 - Recoded Data
#> ────────────────────────────────────────────────────────────
#> Gold Positive Gold Negative Total
#> ────────────────────────────────────────────────────────────
#> Test Positive . . .
#> Test Negative . . .
#> Total . . .
#> ────────────────────────────────────────────────────────────
#>
#>
#> Decision Test Comparison
#> ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#> Test Sensitivity Specificity Accuracy Positive Predictive Value Negative Predictive Value Positive Likelihood Ratio Negative Likelihood Ratio
#> ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#> Test1 87.32394 90.69767 89.50000 83.78378 92.85714 9.387324 0.1397616
#> → Good balanced performance; Moderate positive evidence; Moderate negative evidence
#> Test2 78.87324 86.04651 83.50000 75.67568 88.09524 5.652582 0.2455272
#> → Good specificity for confirmation; Moderate positive evidence
#> ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#>
#>
#> Stratified Diagnostic Accuracy
#> ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#> Subgroup N Test Sensitivity Specificity Accuracy PPV NPV OPA
#> ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#> ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#>
#>
#> Statistical Comparison of Test Accuracy
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#> Comparison Chi-squared df p-value Clinical Interpretation
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#> Test1 vs Test2 2.520833 1 0.1123512 No significant difference (p>=0.1) (Holm-Bonferroni corrected)
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#> Note. For 2 tests: McNemar's test compares diagnostic CORRECTNESS (agreement with gold standard) between paired
#> tests. For 3+ tests: Cochran's Q test provides an overall test, followed by pairwise McNemar's tests with
#> Holm-Bonferroni correction for multiple comparisons. Tests examine discordant pairs (cases where one test is
#> correct and the other is wrong relative to the gold standard) to determine if differences in accuracy are
#> statistically significant.
#>
#>
#> Differences with 95% Confidence Intervals
#> ──────────────────────────────────────────────────────────────────────────
#> Comparison Metric Difference Lower Upper
#> ──────────────────────────────────────────────────────────────────────────
#> Test1 vs Test2 Sensitivity 8.45070 ᵃ -4.34717 21.24858
#> Test1 vs Test2 Specificity 4.65116 ᵇ -3.05435 12.35668
#> Test1 vs Test2 Accuracy 6.00000 ᵈ -0.73840 12.73840
#> ──────────────────────────────────────────────────────────────────────────
#> ᵃ Small paired sample/discordant counts; CI may be unstable (n=71,
#> discordant counts: 48, 14, 8, 1).
#> ᵇ Small paired sample/discordant counts; CI may be unstable (n=129,
#> discordant counts: 101, 16, 10, 2).
#> ᵈ Small paired sample/discordant counts; CI may be unstable (n=200,
#> discordant counts: 149, 30, 18, 3).
#>
#>
#> <div style="font-family: Arial, sans-serif; max-width: 800px; margin:
#> 0 auto; padding: 20px;"><h2 style="color: #2c3e50; border-bottom: 2px
#> solid #3498db;"> Clinical Summary
#>
#> Among the tests evaluated, Test1 demonstrated optimal diagnostic
#> performance with 87.3% sensitivity (95% CI: [see confidence interval
#> table]), 90.7% specificity (95% CI: [see confidence interval table]),
#> 83.8% positive predictive value, 92.9% negative predictive value, and
#> 89.5% overall accuracy. Statistical comparisons using McNemar's test
#> revealed significant differences in test performance (detailed results
#> in comparison tables). The likelihood ratio for positive results was
#> 9.39 and for negative results was 0.14.<h3 style="color: #27ae60;
#> margin-top: 30px;"> Report Sentences
#>
#> <div style="background-color: #f8f9fa; padding: 15px; border-left: 4px
#> solid #28a745; margin: 15px 0;"><h4 style="margin-top: 0;">Methods
#> Section:
#>
#> <p style="font-style: italic; line-height: 1.6;">We compared the
#> diagnostic performance of 2 tests (Test1, Test2) against the gold
#> standard reference using diagnostic accuracy analysis. The study
#> included 200 cases with complete data. Performance metrics calculated
#> included sensitivity, specificity, positive and negative predictive
#> values, likelihood ratios, and overall accuracy. Statistical
#> comparisons between tests were performed using McNemar's test
#> comparing diagnostic correctness (agreement with gold standard).
#>
#> <div style="background-color: #e8f4f8; padding: 15px; border-left: 4px
#> solid #3498db; margin: 15px 0;"><h4 style="margin-top: 0;">Results
#> Section:
#>
#> <p style="font-style: italic; line-height: 1.6;">Among the tests
#> evaluated, Test1 demonstrated optimal diagnostic performance with
#> 87.3% sensitivity (95% CI: [see confidence interval table]), 90.7%
#> specificity (95% CI: [see confidence interval table]), 83.8% positive
#> predictive value, 92.9% negative predictive value, and 89.5% overall
#> accuracy. Statistical comparisons using McNemar's test revealed
#> significant differences in test performance (detailed results in
#> comparison tables). The likelihood ratio for positive results was 9.39
#> and for negative results was 0.14.
#>
#> <h3 style="color: #8e44ad; margin-top: 30px;"> Clinical
#> Recommendations
#>
#> <div style="background-color: #fff3cd; padding: 15px; border-radius:
#> 8px;">
#>
#> Clinical Consideration: Consider using Test1 in combination with other
#> tests for optimal diagnostic accuracy.
#>
#> Implementation Note: Results should be interpreted in the context of
#> disease prevalence in your clinical population. Consider local
#> validation studies before implementation.
#>
#> <div style="font-family: Arial, sans-serif; max-width: 900px; margin:
#> 0 auto; padding: 20px;"><h2 style="color: #2c3e50; text-align: center;
#> border-bottom: 2px solid #3498db; padding-bottom: 10px;"> About
#> Medical Decision Test Comparison
#>
#> <div style="background: linear-gradient(135deg, #e3f2fd 0%, #bbdefb
#> 100%); padding: 20px; border-radius: 10px; margin: 20px 0;"><h3
#> style="color: #1565c0; margin-top: 0;"> What This Analysis Does
#>
#> <p style="line-height: 1.6; color: #333;">This tool compares the
#> diagnostic performance of multiple medical tests against a gold
#> standard reference. It systematically evaluates sensitivity,
#> specificity, predictive values, likelihood ratios, and overall
#> accuracy to help you determine which test performs best for your
#> clinical scenario.
#>
#> <div style="background-color: #f1f8e9; border: 1px solid #8bc34a;
#> padding: 20px; border-radius: 8px; margin: 20px 0;"><h3 style="color:
#> #4a7c59; margin-top: 0;"> When to Use This Analysis
#>
#> <ul style="line-height: 1.8; color: #4a7c59;">Test Validation:
#> Comparing new diagnostic methods against established standardsMethod
#> Comparison: Evaluating which of several tests performs betterClinical
#> Research: Validating biomarkers, imaging techniques, or clinical
#> assessmentsQuality Assessment: Measuring agreement between different
#> raters or methodsProtocol Development: Optimizing diagnostic
#> workflows<div style="background-color: #fff3e0; border: 1px solid
#> #ff9800; padding: 20px; border-radius: 8px; margin: 20px 0;"><h3
#> style="color: #e65100; margin-top: 0;"> How to Use This Analysis
#>
#> <ol style="line-height: 1.8; color: #e65100;">Select Gold Standard:
#> Choose your most reliable reference test (e.g., biopsy, expert
#> consensus)Choose Tests to Compare: Select 2-3 diagnostic tests you
#> want to evaluateDefine Positive Levels: Specify what constitutes a
#> "positive" result for each testConfigure Options: Enable statistical
#> comparisons, confidence intervals, or visualizations as neededRun
#> Analysis: Review results tables and clinical interpretationsCopy
#> Report: Use the auto-generated sentences for your documentation<div
#> style="background-color: #f3e5f5; border: 1px solid #9c27b0; padding:
#> 20px; border-radius: 8px; margin: 20px 0;"><h3 style="color: #6a1b9a;
#> margin-top: 0;"> Key Metrics Explained
#>
#> <div style="display: grid; grid-template-columns: 1fr 1fr; gap: 15px;
#> color: #6a1b9a;">
#>
#> Sensitivity: Probability test is positive when disease present
#> (rule-out ability)
#>
#> Specificity: Probability test is negative when disease absent (rule-in
#> ability)
#>
#> PPV: Probability of disease when test positive
#>
#> NPV: Probability of no disease when test negative
#>
#> LR+: How much positive test increases odds of disease
#>
#> LR-: How much negative test decreases odds of disease
#>
#> Accuracy: Overall probability of correct classification
#>
#> McNemar Test: Statistical comparison between paired tests
#>
#> <div style="background-color: #e8f5e8; border: 1px solid #4caf50;
#> padding: 20px; border-radius: 8px; margin: 20px 0;"><h3 style="color:
#> #2e7d32; margin-top: 0;"> Clinical Interpretation Guidelines
#>
#> <div style="display: grid; grid-template-columns: 1fr 1fr; gap: 15px;
#> color: #2e7d32;"><h4 style="margin-bottom: 5px;">Screening Tests
#> (Rule-Out):
#>
#> <p style="margin-top: 0;">• Sensitivity >=95%: Excellent
#> • NPV >=95%: High confidence
#> • Goal: Minimize false negatives
#>
#> <h4 style="margin-bottom: 5px;">Confirmatory Tests (Rule-In):
#>
#> <p style="margin-top: 0;">• Specificity >=95%: Excellent
#> • PPV >=90%: High confidence
#> • Goal: Minimize false positives
#>
#> <div style="background-color: #fff8e1; border: 1px solid #ffc107;
#> padding: 20px; border-radius: 8px; margin: 20px 0;"><h3 style="color:
#> #f57f17; margin-top: 0;"> Important Assumptions & Limitations
#>
#> <ul style="line-height: 1.6; color: #f57f17;">Gold Standard: Assumes
#> your reference test is truly accurateSample Size: Results more
#> reliable with larger, representative samplesPrevalence Dependency: PPV
#> and NPV vary with disease prevalenceMcNemar Test: Requires
#> paired/matched data for statistical comparisonsMissing Data: Cases
#> with incomplete data are excluded from analysisConfidence Intervals:
#> Calculated using Wilson method for better accuracy
#>
#> <div style='margin: 10px 0;'><div style='background-color: #eff6ff;
#> border-left: 4px solid #93c5fd; padding: 12px; margin: 8px 0;
#> border-radius: 4px;'><strong style='color: #2563eb;'> Analysis
#> Completed Successfully
#> <span style='color: #374151;'>2 diagnostic tests compared using 200
#> complete cases. Gold standard identified 71 diseased and 129 healthy
#> cases. Review comparison tables and statistical tests below.