Package 'wmwAUC'

Synthetic data

Description

A data frame with numeric y and factor group

Usage

data(Ex2)

Format

A data frame with 200 observations on 2 variables.

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Plot Method for wmw_test Objects

Description

Creates empirical ROC curve plot with test results (p-value, eAUC with confidence interval) displayed in subtitle. If ci_method = 'boot' was used in wmw_test(), the plot includes confidence bands for the ROC curve constructed using the same bootstrap resamples used for the AUC confidence interval.

Usage

## S3 method for class 'wmw_test'
plot(x, combine_plots = TRUE, ...)

Arguments

x	Object of class 'wmw_test' returned by wmw_test()
combine_plots	Logical, whether to return combined plot using patchwork (TRUE) or list of individual plots (FALSE). Only relevant when special_case = TRUE
...	Additional arguments (not currently used)

Details

When special_case = TRUE was used in wmw_test(), an additional boxplot with swarmplot overlay is created, showing the eAUC as effect size estimate with confidence interval in the subtitle (demonstrating the dual interpretation of eAUC in the location-shift case).

Value

No return value, called for side effects. Creates a plot visualizing the Wilcoxon-Mann-Whitney test results including distributions, test statistic, and confidence information.

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Print Method for wmw_test Objects

Description

Prints summary of Wilcoxon-Mann-Whitney discrimination test results.

Usage

## S3 method for class 'wmw_test'
print(x, digits = 3, ...)

Arguments

x	Object of class 'wmw_test' returned by wmw_test()
digits	Integer, number of digits to display for numeric results (default: 4)
...	Additional arguments (not currently used)

Value

Invisibly returns the input object x (of class "wmw_test"). Called primarily for side effects to print a formatted summary of the Wilcoxon-Mann-Whitney test results to the console.

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Confidence Interval for Hodges-Lehmann Pseudomedian via Test Inversion

Description

Computes confidence interval for the pseudomedian under $\mathrm{H_0\colon AUC} = 0.5$ by test inversion.

Usage

pseudomedian_ci(x, y, conf.level = 0.95, pvalue_method = "EU", n_grid = 1000)

Arguments

x	numeric vector, first sample
y	numeric vector, second sample
conf.level	confidence level (default 0.95)
pvalue_method	character, either 'EU' or 'BC'
n_grid	number of grid points for search (default 1000)

Value

list with conf.int, estimate and conf.level

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Four EDA Plots for Visual Assessment of Location-Shift Assumption

Description

Creates four diagnostic plots to visually assess whether the location-shift assumption $F_1(x) = F_2(x - \delta)$ holds: (1) boxplot with swarmplot overlay, (2) density plot comparison, (3) wormplot of median-centered residuals, and (4) empirical CDF comparison with confidence band for median-centered data.

Usage

quadruplot(
  formula,
  data,
  ref_level = NULL,
  test = "ks",
  seed = 123L,
  ylab = NULL,
  color_palette = "lancet",
  combine_plots = TRUE,
  distribution = "norm",
  show_colors = TRUE,
  show_legend = TRUE
)

Arguments

formula	Formula of the form response ~ group
data	Data frame containg response, group
ref_level	Character, reference level of the grouping factor. If NULL (default), uses first factor level
test	Character, statistical test for shift-equivalence assumption. Tests for distributional equality applied to median-centered data: "ks" (Kolmogorov-Smirnov) (default), "kuiper" (Kuiper), "cvm" (Cramér-von Mises), "ad" (Anderson-Darling), "wass" (Wasserstein), "dts" (DTS test).
seed	Numeric, for set.seed() used in test_shift_equivalence() for bootstrap.
ylab	Character, label for y-axis. If NULL (default), uses variable name
color_palette	Character, color palette to use. One of "viridis", "plasma", "inferno", "magma", or "cividis"
combine_plots	Logical, whether to return combined plot using patchwork (TRUE) or list of individual plots (FALSE)
distribution	Character, theoretical distribution for Q-Q plot comparison. Default is "norm" for normal distribution
show_colors	Logical, whether to use colors (TRUE) or grayscale (FALSE)
show_legend	Logical, whether to display legend in plots (default TRUE)

Details

The location-shift assumption is assessed by applying a test of H0: equality of distributions to median-centered data. One of the tests from the twosamples package can be used. The empirical CDF plot includes 95% confidence bands for the difference between distributions, computed using the sfsmisc::KSd function based on the Kolmogorov-Smirnov distribution. These bands help assess whether observed differences between median-centered distributions exceed what would be expected under the location-shift assumption.

Value

If combine_plots = TRUE, returns a combined ggplot object created by patchwork. If FALSE, returns a list of four ggplot objects named 'boxplot', 'density', 'wormplot', and 'ecdf'.

Note

Uses twosamples for distribution comparison and KSd from sfsmisc for exact confidence bands.

References

O'Dowd, C. (2025). Statistical Code Examples. https://codowd.com/code (accessed November 28, 2025).

Maechler M (2024). sfsmisc: Utilities from 'Seminar fuer Statistik' ETH Zurich. R package version 1.1-20, https://CRAN.R-project.org/package=sfsmisc.

Examples

library(wmwAUC)

data(Ex2)
da <- Ex2
qp = quadruplot(y ~ group, data = da, ref_level = 'control')
qp

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Synthetic data

Description

Synthetic data

Usage

data(simulation1)

Format

A list containing simulation results (N=10000, n=1000):

eauc

Empirical AUC values

pval_wt

Traditional wilcox.test p-values

pval_wmw

WMW p-values under H0: AUC = 0.5

---

Synthetic data

Description

Synthetic data

Usage

data(simulation2)

Format

A list containing simulation results (N=10000, n=1000):

eauc

Empirical AUC values

pval_wt

Traditional wilcox.test p-values

pval_wmw

WMW p-values under H0: AUC = 0.5

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Synthetic data

Description

Synthetic data

Usage

data(simulation3)

Format

A list containing simulation results (N=500, n=300):

wmw_ci

95% confidence intervals obtained by pseudomedian_ci()

wt_ci

95% confidence intervals obtained by wilcox.test()

eauc

Values of eAUC

pseudomedian

Values of the pseudomedian

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P-value for Wilcoxon-Mann-Whitney Test of No Group Discrimination (Continuous Variables)

Description

Tests $\mathrm{H_0\colon AUC} = 0.5$ vs $\mathrm{H_1\colon AUC} \neq 0.5$ with proper finite-sample corrections

Usage

wmw_pvalue(x, y, alternative = "two.sided")

Arguments

x	Numeric vector of cases/group 1 values
y	Numeric vector of controls/reference group values
alternative	character: "two.sided", "greater", or "less"

Details

Implements the Bias-Corrected (BC) variance estimator with second-order U-statistic correction to provide honest p-values under $\mathrm{H_0\colon AUC} = 0.5$. Uses three-tier approach: permutation $(n < 20)$, bias-corrected $(20 \le n < 50)$, asymptotic with correction $n \ge 50$.

For medium samples, the naive variance estimators $\widehat{\mathrm{Var}}(G(X))$ and $\widehat{\mathrm{Var}}(F(Y))$ are corrected by subtracting O(1/n) bias terms of the form $(n_1 n_2)^{-1} \sum_i \hat{G}(X_i)(1 - \hat{G}(X_i))$ to prevent variance underestimation that would inflate Type I error rates.

Function assumes $x$ represents cases and $y$ represents the reference level, in accord with wilcox.test() and wmw_test(). Internal calculations convert to P(X < Y) framework to match theoretical derivations.

Value

p-value

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P-value for Wilcoxon-Mann-Whitney Test of No Group Discrimination (With Possible Ties)

Description

Tests $\mathrm{H_0\colon AUC} = 0.5$ vs $\mathrm{H_1\colon AUC} \neq 0.5$ with exact finite-sample unbiased variance estimation for arbitrary tie patterns

Usage

wmw_pvalue_ties(x, y, alternative = "two.sided")

Arguments

x	Numeric vector of cases/group 1 values
y	Numeric vector of controls/reference group values
alternative	character: "two.sided", "greater", or "less"

Details

Implements the Exact finite-sample Unbiased (EU) variance estimator derived from Hoeffding decomposition theory. Uses tie-corrected kernel $h(x,y) = \mathbf{1}\{x < y\} + \frac{1}{2}\mathbf{1}\{x = y\}$ with universal second-order correction factor to provide honest p-values under $\mathrm{H_0\colon AUC} = 0.5$ regardless of tie structure.

Uses three-tier approach: permutation $(n < 20)$, exact unbiased estimator $(20 \le n < 50)$, asymptotic with corrections $n \ge 50$.

The unbiased variance estimator is constructed as a specific linear combination:

$\widetilde{\mathrm{Var}}(\hat{A}) = \frac{n_2\hat{\zeta}_1^2 + n_1\hat{\zeta}_2^2 - \frac{M-1}{M}\hat{v}}{M+1}$

where $\hat{v}$ is the pooled sample variance of kernel values and $\hat{\zeta}_1^2, \hat{\zeta}_2^2$ are row/column mean variances.

Welch-Satterthwaite degrees of freedom account for bias correction structure:

$\nu = \frac{(\hat{\sigma}^2)^2}{\frac{(n_2\hat{\zeta}_1^2/(M+1))^2}{n_1-2} + \frac{(n_1\hat{\zeta}_2^2/(M+1))^2}{n_2-2} + \frac{((M-1)\hat{v}/(M(M+1)))^2}{M-3}}$

Function uses mid-rank tie handling throughout, ensuring theoretical consistency with the corrected null hypothesis framework.

Function assumes $x$ represents cases and $y$ represents the reference level, in accord with wilcox.test() and wmw_test(). Internal calculations convert to P(X < Y) framework to match theoretical derivations.

Value

p-value

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Wilcoxon-Mann-Whitney Test of No Group Discrimination

Description

Performs distribution-free Wilcoxon-Mann-Whitney test for AUC-detectable group discrimination, testing $\mathrm{H_0\colon AUC} = 0.5$ against $\mathrm{H_1\colon AUC} \neq 0.5$. Under location-shift assumption, equivalently tests zero location difference.

Usage

wmw_test(
  formula,
  data,
  ref_level = NULL,
  special_case = FALSE,
  alternative = c("two.sided", "greater", "less"),
  pvalue_method = "EU",
  ci_method = "hanley",
  conf_level = 0.95,
  n_grid = 100,
  ...
)

Arguments

formula	Formula of the form response ~ group
data	Data frame containing continuous response variable and grouping factor
ref_level	Character, reference level of grouping factor (if NULL, uses first level)
special_case	Logical, location-shift assumption (default FALSE)
alternative	Character, alternative hypothesis is c("two.sided", "greater", "less")
pvalue_method	Character, method ('EU', 'BC') used for computing p-values; 'BC' assumes continuous data (default 'EU')
ci_method	Character, confidence interval method for eAUC: c('hanley', 'boot', 'none')
conf_level	Numeric, confidence level for intervals (default 0.95)
n_grid	Numeric, number of grid points for search in pseudomedian_ci() (default 100)
...	Additional arguments passed to roc_with_ci()

Details

The function tests the null hypothesis $\mathrm{H_0\colon AUC} = 0.5$ against $\mathrm{H_0\colon AUC} \neq 0.5$, where AUC represents the Area Under the ROC Curve and - following the convention of wilcox.test() - equals the probability $P(X > Y)$ that a randomly selected observation from the first group exceeds a randomly selected observation from the second group.

For response ~ group, observations from the non-reference group constitute $X$, while observations from the reference group (specified by ref_level) constitute $Y$. Thus AUC = P(non-reference > reference). If ref_level is not specified, the first factor level is used as reference. The U statistic and the resulting empirical AUC (eAUC) are calculated consistently with this group assignment.

The test statistic is eAUC, which estimates the true AUC. The empirical ROC curve (eROC) is constructed by varying the classification threshold across all observed values and computing sensitivity and 1-specificity at each threshold.

When special_case = TRUE, the function additionally reports location-shift parameters under the assumption that $F_1(x) = F_2(x - \delta)$. Under this assumption, the discrimination test $\mathrm{H_0\colon AUC} = 0.5$ is mathematically equivalent to testing H0: $\delta = 0$ (zero location shift). In this special case, eAUC takes the dual role of both test statistic and effect size for the location difference.

Confidence intervals for the true AUC are computed using either the Hanley and McNeil (1982) method based on asymptotic normality, or bootstrap resampling. If bootstrap resampling is selected, it is also used for constructing the confidence band for the ROC curve.

The function uses ⁠Exact Unbiased⁠ ('EU') method for computing p-values that can handle any type of data (continuous, discrete, mixed). The Bias-Corrected ('BC') method that requires continuous data is provided through pvalue_method = 'BC' option.

Constructs confidence intervals for the pseudomedian via test inversion. Under location-shift assumptions ($G(x) = F(x - \delta)$), the pseudomedian represents the location difference between groups.

Statistical Methodology: Unlike standard implementations that assume the erroneously broad null hypothesis $\mathrm{H_0\colon F = G}$, this function derives p-values under the correct null hypothesis $\mathrm{H_0\colon AUC} = 0.5$ that WMW actually tests. P-values are computed using asymptotic distribution theory with two methods of finite-sample bias corrections:

1. Exact Unbiased ('EU') estimation of variance of eAUC which handles any type of data (continuous, discrete, mixed);

2. Bias Correction ('BC') sample-size dependent method to maintain proper Type I error control. Confidence intervals for the pseudomedian are obtained by inverting the test.

Value

Object of class 'wmw_test' containing:

special_case	Logical indicating whether special case (location-shift) analysis was performed
n	Named vector with components n1, n2 giving sample sizes for each group
U_statistic	U statistic
p_value	P-value for testing H0: AUC = 0.5
alternative	Alternative hypothesis specification
pvalue_method	Character string describing the test method
data_name	Character string giving the name of the data
pseudomedian	Hodges-Lehmann median difference estimate (when special_case = TRUE)
pseudomedian_conf_int	Confidence interval for the location shift (when special_case = TRUE)
pseudomedian_conf_level	Confidence level for the confidence interval for HL estimator (when special_case = TRUE)
ci_method	Method used to compute confidence interval for AUC
roc_object	ROC analysis object returned by roc_with_ci function
auc	Empirical AUC (eAUC), the standardized U statistic
auc_conf_int	Confidence interval for true AUC using Hanley-McNeil or bootstrap method
x_vals	Numeric vector of observations from non-reference group
y_vals	Numeric vector of observations from reference group
groups	Character vector of group labels from original data
group_levels	Character vector of factor levels for grouping variable
group_ref_level	Character string indicating which level corresponds to reference group

References

Wilcoxon, F. (1945). Individual comparisons by ranking methods. Biometrics Bulletin, 1(6), 80-83.

Mann, H. B., & Whitney, D. R. (1947). On a test of whether one of two random variables is stochastically larger than the other. The Annals of Mathematical Statistics, 18(1), 50-60.

Van Dantzig, D. (1951). On the consistency and the power of Wilcoxon's two sample test. Proceedings KNAW, Series A, 54(1), 1-8.

Birnbaum, Z. W. (1956). On a use of the Mann-Whitney statistic. In Proceedings of the Third Berkeley Symposium on Mathematical Statistics and Probability, Volume 1: Contributions to the Theory of Statistics (Vol. 3, pp. 13-18). University of California Press.

Bamber, D. (1975). The area above the ordinal dominance graph and the area below the receiver operating characteristic graph. Journal of mathematical psychology, 12(4), 387-415.

Lehmann, E. L., & Abrera, H. B. D. (1975). Nonparametrics. Statistical methods based on ranks. San Francisco, CA, Holden-Day.

Hanley, J. A., & McNeil, B. J. (1982). The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology, 143(1), 29-36.

Cliff, N. (1993). Dominance statistics: Ordinal analyses to answer ordinal questions. Psychological bulletin, 114(3), 494.

Arcones, M. A., Kvam, P. H., & Samaniego, F. J. (2002). Nonparametric estimation of a distribution subject to a stochastic precedence constraint. Journal of the American Statistical Association, 97(457), 170-182.

Pepe, M. S. (2003). The statistical evaluation of medical tests for classification and prediction. Oxford university press.

Conroy, R. M. (2012). What hypotheses do “nonparametric” two-group tests actually test?. The Stata Journal, 12(2), 182-190.

del Barrio, E., Cuesta-Albertos, J. A., & Matrán, C. (2025). Invariant measures of disagreement with stochastic dominance. The American Statistician, 1-13.

Grendar, M. (2025). Wilcoxon-Mann-Whitney test of no group discrimination. arXiv:2511.20308.

See Also

print.wmw_test for formated output of wmw_test(). plot.wmw_test for plot of output of wmw_test(). wmw_pvalue for details on computing p-values in the continuous case ('BC') wmw_pvalue_ties for details on computing p-values in the 'EU' mode pseudomedian_ci for details on computing confidence intervals for pseudomedian quadruplot for exploratory data analysis plots that assist in evaluating location-shift assumption validity. wilcox.test for Wilcoxon-Mann-Whitney test in base R.

Examples

library('wmwAUC')  
# Ex 1

library('gemR')
data(MS)
da <- MS
# preparing data frame
class(da$proteins) <- setdiff(class(da$proteins), "AsIs")
df <- as.data.frame(da$proteins)
df$MS <- da$MS
# WMW test 
wmd <- wmw_test(P19099 ~ MS, data = df, ref_level = 'no')
wmd
plot(wmd)
# EDA to assess location shift assumption validity
qp <- quadruplot(P19099 ~ MS, data = df, ref_level = 'no')
qp
# => location shift assumption is not valid


# Ex 2

data(Ex2)
da <- Ex2
# WMW test
wmd <- wmw_test(y ~ group, data = da, ref_level = 'control')
wmd
plot(wmd)
# Check location-shift assumption with EDA
qp <- quadruplot(y ~ group, data = da, ref_level = 'control', test = 'ks')
qp
# => location-shift assumption not tenable
# Note that medians are essentially the same:
median(da$y[da$group == 'case'])
# 0.495
median(da$y[da$group == 'control'])
# 0.493
# Erroneous use of location-shift special case would falsely 
# conclude significant median difference despite identical medians
wml <- wmw_test(y ~ group, data = da, special_case = TRUE,
                ref_level = 'control')
wml


# Ex 3

library('gss')
data(wesdr)
da = wesdr
da$ret = as.factor(da$ret)
# WMW 
wmd <- wmw_test(bmi ~ ret, data = da, ref_level = '0')
wmd
plot(wmd)
# EDA to assess location shift assumption validity
qp <- quadruplot(bmi ~ ret, data = da, ref_level = '0')
qp
# => location shift assumption is tenable
# Special case of WMW test
wml <- wmw_test(bmi ~ ret, data = da, ref_level = '0', 
                ci_method = 'boot', special_case = TRUE)
wml
plot(wml)

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