Enhanced categorical analysis with chi-square tests, Fisher's exact tests, effect sizes, and association measures. Addresses the critical issue where 25 percent of pathology studies use categorical analysis incorrectly.
Usage
categoricaladvanced(
data,
rows,
cols,
stratify,
test_type = "enhanced",
fisher_exact = TRUE,
effect_sizes = TRUE,
association_measures = TRUE,
residual_analysis = TRUE,
posthoc_comparisons = FALSE,
correction_method = "bonferroni",
confidence_level = 0.95,
exact_threshold = 50,
simulation_runs = 5000,
show_expected = TRUE,
plot_mosaic = TRUE,
plot_residuals = TRUE
)Arguments
- data
the data as a data frame
- rows
Row variable for the contingency table
- cols
Column variable for the contingency table
- stratify
Optional stratification variable for Mantel-Haenszel tests
- test_type
Type of categorical analysis to perform
- fisher_exact
Perform Fisher's exact test when appropriate
- effect_sizes
Calculate effect sizes (Cramér's V, phi coefficient, Cohen's w)
- association_measures
Calculate association measures (Lambda, Tau, Gamma)
- residual_analysis
Perform standardized residual analysis
- posthoc_comparisons
Perform pairwise comparisons for tables larger than 2×2
- correction_method
Multiple testing correction method
- confidence_level
Confidence level for effect size intervals
- exact_threshold
Maximum total sample size for automatic exact tests
- simulation_runs
Number of Monte Carlo simulations for exact p-values
- show_expected
Display expected frequencies in contingency table
- plot_mosaic
Generate mosaic plot showing association patterns
- plot_residuals
Generate standardized residuals plot
Value
A results object containing:
results$instructions | a html | ||||
results$contingencytable | a table | ||||
results$chisquaretest | a table | ||||
results$fishertest | a table | ||||
results$effectsizes | a table | ||||
results$associations | a table | ||||
results$residuals | a table | ||||
results$posthoc | a table | ||||
results$stratifiedanalysis | a table | ||||
results$mosaicplot | an image | ||||
results$residualsplot | an image | ||||
results$interpretation | a html |
Tables can be converted to data frames with asDF or as.data.frame. For example:
results$contingencytable$asDF
as.data.frame(results$contingencytable)
Examples
# \donttest{
data('histopathology')
categoricaladvanced(data = histopathology,
rows = tumor_type,
cols = grade)
#> Error in categoricaladvanced(data = histopathology, rows = tumor_type, cols = grade): argument "stratify" is missing, with no default
# }