Comprehensive method comparison analysis including Bland-Altman plots, Passing-Bablok regression, and Deming regression. Essential for validating new laboratory methods, diagnostic tests, and measurement techniques.
Usage
methodcomparison(
data,
method1,
method2,
grouping,
comparison_method = "bland_altman",
confidence_level = 0.95,
bland_altman_options = TRUE,
limits_method = "standard",
proportional_bias = TRUE,
outlier_detection = TRUE,
passing_bablok_options = FALSE,
pb_alpha = 0.05,
deming_options = FALSE,
error_ratio = 1,
correlation_analysis = TRUE,
concordance_correlation = TRUE,
regression_comparison = TRUE,
clinical_limits = FALSE,
clinical_lower = -10,
clinical_upper = 10,
transformation = "none",
plots_options = TRUE,
bland_altman_plot = TRUE,
scatter_plot = TRUE,
residual_plots = FALSE,
mountain_plot = FALSE,
missing_treatment = "complete",
bootstrap_samples = 1000
)Arguments
- data
The data as a data frame.
- method1
.
- method2
.
- grouping
.
- comparison_method
Primary method comparison approach
- confidence_level
Confidence level for limits of agreement and regression
- bland_altman_options
Enable Bland-Altman specific analysis options
- limits_method
Method for calculating limits of agreement
- proportional_bias
Test if bias changes with measurement magnitude
- outlier_detection
Identify potential outliers in method comparison
- passing_bablok_options
Enable Passing-Bablok specific analysis options
- pb_alpha
Significance level for Passing-Bablok regression
- deming_options
Enable Deming regression specific options
- error_ratio
Ratio of error variances (σ²y/σ²x) for Deming regression
- correlation_analysis
Include Pearson and Spearman correlation analysis
- concordance_correlation
Calculate Lin concordance correlation coefficient for agreement assessment
- regression_comparison
Compare ordinary least squares vs method comparison regressions
- clinical_limits
Specify clinical acceptability criteria
- clinical_lower
Lower bound for clinically acceptable difference
- clinical_upper
Upper bound for clinically acceptable difference
- transformation
Apply transformation to improve normality
- plots_options
Control plot generation and formatting
- bland_altman_plot
Generate Bland-Altman plot with limits of agreement
- scatter_plot
Scatter plot with regression lines
- residual_plots
Generate residual plots for regression diagnostics
- mountain_plot
Generate mountain plot (percentile-based differences)
- missing_treatment
How to handle missing data
- bootstrap_samples
Number of bootstrap samples for confidence intervals
Value
A results object containing:
results$todo | a html | ||||
results$summary | a html | ||||
results$descriptiveStats | a table | ||||
results$correlationTable | a table | ||||
results$concordanceTable | a table | ||||
results$blandAltmanStats | a table | ||||
results$passingBablokResults | a table | ||||
results$demingResults | a table | ||||
results$regressionComparison | a table | ||||
results$biasAnalysis | a table | ||||
results$outlierAnalysis | a table | ||||
results$clinicalAssessment | a table | ||||
results$blandAltmanPlot | an image | ||||
results$scatterPlot | an image | ||||
results$residualPlots | an image | ||||
results$mountainPlot | an image | ||||
results$methodGuidance | a html | ||||
results$technicalNotes | a html |
Tables can be converted to data frames with asDF or as.data.frame. For example:
results$descriptiveStats$asDF
as.data.frame(results$descriptiveStats)