# Package MKinfer

## Introduction

Package MKinfer includes a collection of functions for the computation of various confidence intervals (Altman et al. 2000; Hedderich and Sachs 2018) including bootstrapped versions (Davison and Hinkley 1997) as well as Hsu (Hedderich and Sachs 2018), permutation (Janssen 1997), bootstrap (Davison and Hinkley 1997) and multiple imputation (Barnard and Rubin 1999) t-test and Wilcoxon tests. Graphical visualization by volcano and Bland-Altman plots (Bland and Altman 1986; Shieh 2018).

library(MKinfer)

## Confidence Intervals

### Binomial Proportion

There are several functions for computing confidence intervals. We can compute 12 different confidence intervals for binomial proportions (DasGupta, Cai, and Brown 2001); e.g.

## default: "wilson"
binomCI(x = 12, n = 50)
##
##  wilson confidence interval
##
## 95 percent confidence interval:
##          2.5 %    97.5 %
## prob 0.1429739 0.3741268
##
## sample estimate:
## prob
## 0.24
##
## standard error of prob
##             0.05896867
## Clopper-Pearson interval
binomCI(x = 12, n = 50, method = "clopper-pearson")
##
##  clopper-pearson confidence interval
##
## 95 percent confidence interval:
##          2.5 %    97.5 %
## prob 0.1306099 0.3816907
##
## sample estimate:
## prob
## 0.24
## identical to
binom.test(x = 12, n = 50)$conf.int ## [1] 0.1306099 0.3816907 ## attr(,"conf.level") ## [1] 0.95 For all intervals implemented see the help page of function binomCI. One can also compute bootstrap intervals via function boot.ci of package boot (Davison and Hinkley 1997) as well as one-sided intervals. ### Difference of Two Binomial Proportions There are several functions for computing confidence intervals. We can compute different confidence intervals for the difference of two binomial proportions (independent (Newcombe 1998a) and paired case (Newcombe 1998b)); e.g. ## default: wilson binomDiffCI(a = 5, b = 0, c = 51, d = 29) ## ## wilson confidence interval (independent proportions) ## ## 95 percent confidence interval: ## 2.5 % 97.5 % ## difference of independent proportions -0.03813715 0.19256 ## ## sample estimate: ## difference of proportions ## 0.08928571 ## ## additional information: ## proportion of group 1 proportion of group 2 ## 0.08928571 0.00000000 ## default: wilson with continuity correction binomDiffCI(a = 212, b = 144, c = 256, d = 707, paired = TRUE) ## ## wilson-cc confidence interval (paired data) ## ## 95 percent confidence interval: ## 2.5 % 97.5 % ## difference of proportions (paired data) -0.1141915 -0.05543347 ## ## sample estimate: ## difference of proportions ## -0.08491281 ## ## additional information: ## proportion of group 1 proportion of group 2 ## 0.2699014 0.3548143 For all intervals implemented see the help page of function binomDiffCI. One can also compute boostrap intervals via function boot.ci of package boot (Davison and Hinkley 1997) as well as one-sided intervals. ### Mean and SD We can compute confidence intervals for mean and SD (Altman et al. 2000, @Davison1997). x <- rnorm(50, mean = 2, sd = 3) ## mean and SD unknown normCI(x) ## ## Exact confidence interval(s) ## ## 95 percent confidence intervals: ## 2.5 % 97.5 % ## mean 2.124462 3.702408 ## sd 2.319012 3.459453 ## ## sample estimates: ## mean sd ## 2.913435 2.776150 ## ## additional information: ## SE of mean ## 0.3926068 meanCI(x) ## ## Exact confidence interval(s) ## ## 95 percent confidence interval: ## 2.5 % 97.5 % ## mean 2.124462 3.702408 ## ## sample estimates: ## mean sd ## 2.913435 2.776150 ## ## additional information: ## SE of mean ## 0.3926068 sdCI(x) ## ## Exact confidence interval(s) ## ## 95 percent confidence interval: ## 2.5 % 97.5 % ## sd 2.319012 3.459453 ## ## sample estimates: ## mean sd ## 2.913435 2.776150 ## ## additional information: ## SE of mean ## 0.3926068 ## SD known normCI(x, sd = 3) ## ## Exact confidence interval(s) ## ## 95 percent confidence interval: ## 2.5 % 97.5 % ## mean 2.081893 3.744977 ## ## sample estimate: ## mean ## 2.913435 ## ## additional information: ## SE of mean ## 0.4242641 ## mean known normCI(x, mean = 2, alternative = "less") ## ## Exact confidence interval(s) ## ## 95 percent confidence interval: ## 0 % 95 % ## sd 0 3.336161 ## ## sample estimate: ## sd ## 2.77615 ## bootstrap meanCI(x, boot = TRUE) ## ## Bootstrap confidence interval(s) ## ## BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS ## Based on 9999 bootstrap replicates ## ## CALL : ## boot.ci(boot.out = boot.out, conf = 1 - alpha, type = bootci.type) ## ## Intervals : ## Level Normal Basic Studentized ## 95% ( 2.158, 3.679 ) ( 2.153, 3.679 ) ( 2.099, 3.696 ) ## ## Level Percentile BCa ## 95% ( 2.148, 3.674 ) ( 2.153, 3.678 ) ## Calculations and Intervals on Original Scale ## ## sample estimates: ## mean sd ## 2.913435 2.776150 ### Difference in Means We can compute confidence interval for the difference of means (Altman et al. 2000; Hedderich and Sachs 2018; Davison and Hinkley 1997). x <- rnorm(20) y <- rnorm(20, sd = 2) ## paired normDiffCI(x, y, paired = TRUE) ## ## Confidence interval (paired) ## ## 95 percent confidence interval: ## 2.5 % 97.5 % ## mean of differences -1.970102 -0.5777699 ## ## sample estimates: ## mean of differences sd of differences ## -1.273936 1.487488 ## ## additional information: ## SE of mean of differences ## 0.3326124 ## compare normCI(x-y) ## ## Exact confidence interval(s) ## ## 95 percent confidence intervals: ## 2.5 % 97.5 % ## mean -1.970102 -0.5777699 ## sd 1.131220 2.1725828 ## ## sample estimates: ## mean sd ## -1.273936 1.487488 ## ## additional information: ## SE of mean ## 0.3326124 ## bootstrap normDiffCI(x, y, paired = TRUE, boot = TRUE) ## ## Bootstrap confidence interval (paired) ## ## BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS ## Based on 9999 bootstrap replicates ## ## CALL : ## boot.ci(boot.out = boot.out, conf = 1 - alpha, type = bootci.type) ## ## Intervals : ## Level Normal Basic Studentized ## 95% (-1.911, -0.633 ) (-1.875, -0.602 ) (-2.058, -0.635 ) ## ## Level Percentile BCa ## 95% (-1.946, -0.673 ) (-1.985, -0.700 ) ## Calculations and Intervals on Original Scale ## ## sample estimates: ## mean of differences sd of differences ## -1.273936 1.487488 ## unpaired y <- rnorm(10, mean = 1, sd = 2) ## classical normDiffCI(x, y, method = "classical") ## ## Classical confidence interval (unpaired) ## ## 95 percent confidence interval: ## 2.5 % 97.5 % ## difference in means -2.232198 -0.2761183 ## ## sample estimate: ## difference in means ## -1.254158 ## ## additional information: ## SE of difference in means Cohen's d (SMD) ## 0.4774635 -1.0173203 ## ## mean of x SD of x mean of y SD of y ## -0.2824006 0.9255027 0.9717575 1.7088044 ## Welch (default as in case of function t.test) normDiffCI(x, y, method = "welch") ## ## Welch confidence interval (unpaired) ## ## 95 percent confidence interval: ## 2.5 % 97.5 % ## difference in means -2.518334 0.01001801 ## ## sample estimate: ## difference in means ## -1.254158 ## ## additional information: ## SE of difference in means Cohen's d (SMD) ## 0.5786441 -0.6453623 ## ## mean of x SD of x mean of y SD of y ## -0.2824006 0.9255027 0.9717575 1.7088044 ## Hsu normDiffCI(x, y, method = "hsu") ## ## Hsu confidence interval (unpaired) ## ## 95 percent confidence interval: ## 2.5 % 97.5 % ## difference in means -2.563142 0.05482592 ## ## sample estimate: ## difference in means ## -1.254158 ## ## additional information: ## SE of difference in means Cohen's d (SMD) ## 0.5786441 -0.6453623 ## ## mean of x SD of x mean of y SD of y ## -0.2824006 0.9255027 0.9717575 1.7088044 ## bootstrap: assuming equal variances normDiffCI(x, y, method = "classical", boot = TRUE, bootci.type = "bca") ## ## Bootstrap confidence interval (equal variances, unpaired) ## ## BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS ## Based on 9999 bootstrap replicates ## ## CALL : ## boot.ci(boot.out = boot.out, conf = 1 - alpha, type = bootci.type) ## ## Intervals : ## Level BCa ## 95% (-2.414, -0.259 ) ## Calculations and Intervals on Original Scale ## ## sample estimate: ## difference in means ## -1.254158 ## ## additional information: ## SE of difference in means Cohen's d (SMD) ## 0.4774635 -1.0173203 ## ## mean of x SD of x mean of y SD of y ## -0.2824006 0.9255027 0.9717575 1.7088044 ## bootstrap: assuming unequal variances normDiffCI(x, y, method = "welch", boot = TRUE, bootci.type = "bca") ## ## Bootstrap confidence interval (unequal variances, unpaired) ## ## BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS ## Based on 9999 bootstrap replicates ## ## CALL : ## boot.ci(boot.out = boot.out, conf = 1 - alpha, type = bootci.type) ## ## Intervals : ## Level BCa ## 95% (-2.403, -0.239 ) ## Calculations and Intervals on Original Scale ## ## sample estimate: ## difference in means ## -1.254158 ## ## additional information: ## SE of difference in means Cohen's d (SMD) ## 0.5786441 -0.6453623 ## ## mean of x SD of x mean of y SD of y ## -0.2824006 0.9255027 0.9717575 1.7088044 In case of unequal variances and unequal sample sizes per group the classical confidence interval may have a bad coverage (too long or too short), as is indicated by the small Monte-Carlo simulation study below. M <- 100 CIhsu <- CIwelch <- CIclass <- matrix(NA, nrow = M, ncol = 2) for(i in 1:M){ x <- rnorm(10) y <- rnorm(30, sd = 0.1) CIclass[i,] <- normDiffCI(x, y, method = "classical")$conf.int
CIwelch[i,] <- normDiffCI(x, y, method = "welch")$conf.int CIhsu[i,] <- normDiffCI(x, y, method = "hsu")$conf.int
}
## coverage probabilies
## classical
sum(CIclass[,1] < 0 & 0 < CIclass[,2])/M
## [1] 0.72
## Welch
sum(CIwelch[,1] < 0 & 0 < CIwelch[,2])/M
## [1] 0.96
## Hsu
sum(CIhsu[,1] < 0 & 0 < CIhsu[,2])/M
## [1] 0.96

### Coefficient of Variation

We provide 12 different confidence intervals for the (classical) coefficient of variation (Gulhar, Kibria, and Ahmed 2012; Davison and Hinkley 1997); e.g.

x <- rnorm(100, mean = 10, sd = 2) # CV = 0.2
## default: "miller"
cvCI(x)
##
##  Miller (1991) confidence interval
##
## 95 percent confidence interval:
##        2.5 %    97.5 %
## CV 0.1735241 0.2323381
##
## sample estimate:
##        CV
## 0.2029311
##
## standard error of CV
##           0.01500383
## Gulhar et al. (2012)
cvCI(x, method = "gulhar")
##
##  Gulhar et al (2012) confidence interval
##
## 95 percent confidence interval:
##        2.5 %  97.5 %
## CV 0.1781749 0.23574
##
## sample estimate:
##        CV
## 0.2029311
## bootstrap
cvCI(x, method = "boot")
##
##  Bootstrap confidence interval
##
## BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS
## Based on 9999 bootstrap replicates
##
## CALL :
## boot.ci(boot.out = boot.out, conf = 1 - alpha, type = bootci.type)
##
## Intervals :
## Level      Normal              Basic
## 95%   ( 0.1776,  0.2311 )   ( 0.1770,  0.2309 )
##
## Level     Percentile            BCa
## 95%   ( 0.1750,  0.2289 )   ( 0.1802,  0.2344 )
## Calculations and Intervals on Original Scale
##
## sample estimate:
##        CV
## 0.2029311

For all intervals implemented see the help page of function cvCI.

We start with the computation of confidence intervals for quantiles (Hedderich and Sachs 2018; Davison and Hinkley 1997).

x <- rexp(100, rate = 0.5)
## exact
quantileCI(x = x, prob = 0.95)
##
##  exact confidence interval
##
## 95.1 percent confidence interval:
##                 2.45 %  97.55 %
## 95 % quantile 3.740187 6.829714
##
## sample estimate:
## 95 % quantile
##      5.612109
## asymptotic
quantileCI(x = x, prob = 0.95, method = "asymptotic")
##
##  asymptotic confidence interval
##
## 95 percent confidence interval:
##                  2.5 %   97.5 %
## 95 % quantile 3.740187 10.28008
##
## sample estimate:
## 95 % quantile
##      5.612109
## boot
quantileCI(x = x, prob = 0.95, method = "boot")
##
##  bootstrap confidence interval
##
## BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS
## Based on 9999 bootstrap replicates
##
## CALL :
## boot.ci(boot.out = boot.out, conf = 1 - alpha, type = bootci.type)
##
## Intervals :
## Level      Normal              Basic
## 95%   ( 4.036,  7.212 )   ( 4.475,  7.488 )
##
## Level     Percentile            BCa
## 95%   ( 3.737,  6.749 )   ( 3.759,  6.830 )
## Calculations and Intervals on Original Scale
##
## sample estimate:
## 95 % quantile
##      5.612109

Next, we consider the median.

## exact
medianCI(x = x)
##
##  exact confidence interval
##
## 95.2 percent confidence interval:
##           2.4 %   97.6 %
## median 1.066793 2.185352
##
## sample estimate:
##   median
## 1.727343
## asymptotic
medianCI(x = x, method = "asymptotic")
##
##  asymptotic confidence interval
##
## 95 percent confidence interval:
##           2.5 %   97.5 %
## median 1.183349 2.271613
##
## sample estimate:
##   median
## 1.727343
## boot
medianCI(x = x, method = "boot")
##
##  bootstrap confidence interval
##
## BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS
## Based on 9999 bootstrap replicates
##
## CALL :
## boot.ci(boot.out = boot.out, conf = 1 - alpha, type = bootci.type)
##
## Intervals :
## Level      Normal              Basic
## 95%   ( 1.185,  2.324 )   ( 1.183,  2.264 )
##
## Level     Percentile            BCa
## 95%   ( 1.191,  2.272 )   ( 1.187,  2.251 )
## Calculations and Intervals on Original Scale
##
## sample estimate:
##   median
## 1.727343

Finally, we take a look at MAD (median absolute deviation) where by default the standardized MAD is used (see function mad).

## exact
madCI(x = x)
##
##  exact confidence interval
##
## 95.2 percent confidence interval:
##        2.4 %   97.6 %
##
## sample estimate:
## 1.687878
## aysymptotic
madCI(x = x, method = "asymptotic")
##
##  asymptotic confidence interval
##
## 95 percent confidence interval:
##        2.5 %   97.5 %
##
## sample estimate:
## 1.687878
## boot
madCI(x = x, method = "boot")
##
##  bootstrap confidence interval
##
## BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS
## Based on 9999 bootstrap replicates
##
## CALL :
## boot.ci(boot.out = boot.out, conf = 1 - alpha, type = bootci.type)
##
## Intervals :
## Level      Normal              Basic
## 95%   ( 1.389,  2.133 )   ( 1.397,  2.112 )
##
## Level     Percentile            BCa
## 95%   ( 1.264,  1.979 )   ( 1.368,  2.083 )
## Calculations and Intervals on Original Scale
##
## sample estimate:
## 1.687878
## unstandardized
madCI(x = x, constant = 1)
##
##  exact confidence interval
##
## 95.2 percent confidence interval:
##         2.4 %   97.6 %
##
## sample estimate:
## 1.138458

## Hsu Two-Sample t-Test

The Hsu two-sample t-test is an alternative to the Welch two-sample t-test using a different formula for computing the degrees of freedom of the respective t-distribution (Hedderich and Sachs 2018). The following code is taken and adapted from the help page of the t.test function.

t.test(1:10, y = c(7:20))      # P = .00001855
##
##  Welch Two Sample t-test
##
## data:  1:10 and c(7:20)
## t = -5.4349, df = 21.982, p-value = 1.855e-05
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -11.052802  -4.947198
## sample estimates:
## mean of x mean of y
##       5.5      13.5
t.test(1:10, y = c(7:20, 200)) # P = .1245    -- NOT significant anymore
##
##  Welch Two Sample t-test
##
## data:  1:10 and c(7:20, 200)
## t = -1.6329, df = 14.165, p-value = 0.1245
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -47.242900   6.376233
## sample estimates:
## mean of x mean of y
##   5.50000  25.93333
hsu.t.test(1:10, y = c(7:20))
##
##  Hsu Two Sample t-test
##
## data:  1:10 and c(7:20)
## t = -5.4349, df = 9, p-value = 0.0004137
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -11.329805  -4.670195
## sample estimates:
## mean of x mean of y   SD of x   SD of y
##   5.50000  13.50000   3.02765   4.18330
hsu.t.test(1:10, y = c(7:20, 200))
##
##  Hsu Two Sample t-test
##
## data:  1:10 and c(7:20, 200)
## t = -1.6329, df = 9, p-value = 0.1369
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -48.740846   7.874179
## sample estimates:
## mean of x mean of y   SD of x   SD of y
##   5.50000  25.93333   3.02765  48.32253
## Traditional interface
with(sleep, t.test(extra[group == 1], extra[group == 2]))
##
##  Welch Two Sample t-test
##
## data:  extra[group == 1] and extra[group == 2]
## t = -1.8608, df = 17.776, p-value = 0.07939
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -3.3654832  0.2054832
## sample estimates:
## mean of x mean of y
##      0.75      2.33
with(sleep, hsu.t.test(extra[group == 1], extra[group == 2]))
##
##  Hsu Two Sample t-test
##
## data:  extra[group == 1] and extra[group == 2]
## t = -1.8608, df = 9, p-value = 0.09569
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -3.5007773  0.3407773
## sample estimates:
## mean of x mean of y   SD of x   SD of y
##  0.750000  2.330000  1.789010  2.002249
## Formula interface
t.test(extra ~ group, data = sleep)
##
##  Welch Two Sample t-test
##
## data:  extra by group
## t = -1.8608, df = 17.776, p-value = 0.07939
## alternative hypothesis: true difference in means between group 1 and group 2 is not equal to 0
## 95 percent confidence interval:
##  -3.3654832  0.2054832
## sample estimates:
## mean in group 1 mean in group 2
##            0.75            2.33
hsu.t.test(extra ~ group, data = sleep)
##
##  Hsu Two Sample t-test
##
## data:  extra by group
## t = -1.8608, df = 9, p-value = 0.09569
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -3.5007773  0.3407773
## sample estimates:
## mean of x mean of y   SD of x   SD of y
##  0.750000  2.330000  1.789010  2.002249

## Bootstrap t-Test

One and two sample bootstrap t-tests with equal or unequal variances in the two sample case (Efron and Tibshirani 1993).

boot.t.test(1:10, y = c(7:20)) # without bootstrap: P = .00001855
##
##  Bootstrap Welch Two Sample t-test
##
## data:  1:10 and c(7:20)
## bootstrap p-value < 2.2e-16
## bootstrap difference of means (SE) = -7.993101 (1.40367)
## 95 percent bootstrap percentile confidence interval:
##  -10.72929  -5.20000
##
## Results without bootstrap:
## t = -5.4349, df = 21.982, p-value = 1.855e-05
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -11.052802  -4.947198
## sample estimates:
## mean of x mean of y
##       5.5      13.5
boot.t.test(1:10, y = c(7:20, 200)) # without bootstrap: P = .1245
##
##  Bootstrap Welch Two Sample t-test
##
## data:  1:10 and c(7:20, 200)
## bootstrap p-value = 0.0256
## bootstrap difference of means (SE) = -20.44501 (9.946611)
## 95 percent bootstrap percentile confidence interval:
##  -46.600000  -5.966667
##
## Results without bootstrap:
## t = -1.6329, df = 14.165, p-value = 0.1245
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -47.242900   6.376233
## sample estimates:
## mean of x mean of y
##   5.50000  25.93333
## Traditional interface
with(sleep, boot.t.test(extra[group == 1], extra[group == 2]))
##
##  Bootstrap Welch Two Sample t-test
##
## data:  extra[group == 1] and extra[group == 2]
## bootstrap p-value = 0.08441
## bootstrap difference of means (SE) = -1.587207 (0.7968061)
## 95 percent bootstrap percentile confidence interval:
##  -3.16  0.02
##
## Results without bootstrap:
## t = -1.8608, df = 17.776, p-value = 0.07939
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -3.3654832  0.2054832
## sample estimates:
## mean of x mean of y
##      0.75      2.33
## Formula interface
boot.t.test(extra ~ group, data = sleep)
##
##  Bootstrap Welch Two Sample t-test
##
## data:  extra by group
## bootstrap p-value = 0.07841
## bootstrap difference of means (SE) = -1.570834 (0.7978016)
## 95 percent bootstrap percentile confidence interval:
##  -3.140000e+00  2.220446e-17
##
## Results without bootstrap:
## t = -1.8608, df = 17.776, p-value = 0.07939
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -3.3654832  0.2054832
## sample estimates:
## mean in group 1 mean in group 2
##            0.75            2.33

## Permutation t-Test

One and two sample permutation t-tests with equal (Efron and Tibshirani 1993) or unequal variances (Janssen 1997) in the two sample case.

perm.t.test(1:10, y = c(7:20)) # without permutation: P = .00001855
##
##  Permutation Welch Two Sample t-test
##
## data:  1:10 and c(7:20)
## (Monte-Carlo) permutation p-value < 2.2e-16
## permutation difference of means (SE) = -8.001337 (2.25463)
## 95 percent (Monte-Carlo) permutation percentile confidence interval:
##  -12.400000  -3.657143
##
## Results without permutation:
## t = -5.4349, df = 21.982, p-value = 1.855e-05
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -11.052802  -4.947198
## sample estimates:
## mean of x mean of y
##       5.5      13.5
## permutation confidence interval sensitive to outlier!
perm.t.test(1:10, y = c(7:20, 200)) # without permutation: P = .1245
##
##  Permutation Welch Two Sample t-test
##
## data:  1:10 and c(7:20, 200)
## (Monte-Carlo) permutation p-value = 1e-04
## permutation difference of means (SE) = -20.58772 (15.31681)
## 95 percent (Monte-Carlo) permutation percentile confidence interval:
##  -36.86667   1.80000
##
## Results without permutation:
## t = -1.6329, df = 14.165, p-value = 0.1245
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -47.242900   6.376233
## sample estimates:
## mean of x mean of y
##   5.50000  25.93333
## Traditional interface
with(sleep, perm.t.test(extra[group == 1], extra[group == 2]))
##
##  Permutation Welch Two Sample t-test
##
## data:  extra[group == 1] and extra[group == 2]
## (Monte-Carlo) permutation p-value = 0.08041
## permutation difference of means (SE) = -1.591447 (0.9016237)
## 95 percent (Monte-Carlo) permutation percentile confidence interval:
##  -3.40  0.16
##
## Results without permutation:
## t = -1.8608, df = 17.776, p-value = 0.07939
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -3.3654832  0.2054832
## sample estimates:
## mean of x mean of y
##      0.75      2.33
## Formula interface
res <- perm.t.test(extra ~ group, data = sleep)
res
##
##  Permutation Welch Two Sample t-test
##
## data:  extra by group
## (Monte-Carlo) permutation p-value = 0.07371
## permutation difference of means (SE) = -1.576044 (0.9024485)
## 95 percent (Monte-Carlo) permutation percentile confidence interval:
##  -3.30  0.14
##
## Results without permutation:
## t = -1.8608, df = 17.776, p-value = 0.07939
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -3.3654832  0.2054832
## sample estimates:
## mean in group 1 mean in group 2
##            0.75            2.33

In case of skewed distributions, one may use function p2ses to compute an alternative standardized effect size (SES) as proposed by Botta-Dukat (Botta-Dukát 2018).

p2ses(res$p.value) ## [1] 1.754212 ## Multiple Imputation t-Test Function mi.t.test can be used to compute a multiple imputation t-test by applying the approch of Rubin (Rubin 1987) in combination with the adjustment of Barnard and Rubin (Barnard and Rubin 1999). ## Generate some data set.seed(123) x <- rnorm(25, mean = 1) x[sample(1:25, 5)] <- NA y <- rnorm(20, mean = -1) y[sample(1:20, 4)] <- NA pair <- c(rnorm(25, mean = 1), rnorm(20, mean = -1)) g <- factor(c(rep("yes", 25), rep("no", 20))) D <- data.frame(ID = 1:45, response = c(x, y), pair = pair, group = g) ## Use Amelia to impute missing values library(Amelia) ## Lade nötiges Paket: Rcpp ## ## ## ## Amelia II: Multiple Imputation ## ## (Version 1.8.1, built: 2022-11-18) ## ## Copyright (C) 2005-2023 James Honaker, Gary King and Matthew Blackwell ## ## Refer to http://gking.harvard.edu/amelia/ for more information ## ## res <- amelia(D, m = 10, p2s = 0, idvars = "ID", noms = "group") ## Per protocol analysis (Welch two-sample t-test) t.test(response ~ group, data = D) ## ## Welch Two Sample t-test ## ## data: response by group ## t = -6.9214, df = 33.69, p-value = 5.903e-08 ## alternative hypothesis: true difference in means between group no and group yes is not equal to 0 ## 95 percent confidence interval: ## -2.628749 -1.435125 ## sample estimates: ## mean in group no mean in group yes ## -1.0862469 0.9456901 ## Intention to treat analysis (Multiple Imputation Welch two-sample t-test) mi.t.test(res, x = "response", y = "group") ## ## Multiple Imputation Welch Two Sample t-test ## ## data: Variable response: group no vs group yes ## number of imputations: 10 ## t = -6.6457, df = 25.142, p-value = 5.63e-07 ## alternative hypothesis: true difference in means is not equal to 0 ## 95 percent confidence interval: ## -2.668011 -1.405862 ## sample estimates: ## mean (no) SD (no) mean (yes) SD (yes) ## -1.0809584 0.9379070 0.9559786 1.0203219 ## Per protocol analysis (Two-sample t-test) t.test(response ~ group, data = D, var.equal = TRUE) ## ## Two Sample t-test ## ## data: response by group ## t = -6.8168, df = 34, p-value = 7.643e-08 ## alternative hypothesis: true difference in means between group no and group yes is not equal to 0 ## 95 percent confidence interval: ## -2.637703 -1.426171 ## sample estimates: ## mean in group no mean in group yes ## -1.0862469 0.9456901 ## Intention to treat analysis (Multiple Imputation two-sample t-test) mi.t.test(res, x = "response", y = "group", var.equal = TRUE) ## ## Multiple Imputation Two Sample t-test ## ## data: Variable response: group no vs group yes ## number of imputations: 10 ## t = -6.5736, df = 26.042, p-value = 5.656e-07 ## alternative hypothesis: true difference in means is not equal to 0 ## 95 percent confidence interval: ## -2.673828 -1.400046 ## sample estimates: ## mean (no) SD (no) mean (yes) SD (yes) ## -1.0809584 0.9379070 0.9559786 1.0203219 ## Specifying alternatives mi.t.test(res, x = "response", y = "group", alternative = "less") ## ## Multiple Imputation Welch Two Sample t-test ## ## data: Variable response: group no vs group yes ## number of imputations: 10 ## t = -6.6457, df = 25.142, p-value = 2.815e-07 ## alternative hypothesis: true difference in means is less than 0 ## 95 percent confidence interval: ## -Inf -1.5135 ## sample estimates: ## mean (no) SD (no) mean (yes) SD (yes) ## -1.0809584 0.9379070 0.9559786 1.0203219 mi.t.test(res, x = "response", y = "group", alternative = "greater") ## ## Multiple Imputation Welch Two Sample t-test ## ## data: Variable response: group no vs group yes ## number of imputations: 10 ## t = -6.6457, df = 25.142, p-value = 1 ## alternative hypothesis: true difference in means is greater than 0 ## 95 percent confidence interval: ## -2.560374 Inf ## sample estimates: ## mean (no) SD (no) mean (yes) SD (yes) ## -1.0809584 0.9379070 0.9559786 1.0203219 ## One sample test t.test(D$response[D$group == "yes"]) ## ## One Sample t-test ## ## data: D$response[D$group == "yes"] ## t = 4.5054, df = 19, p-value = 0.0002422 ## alternative hypothesis: true mean is not equal to 0 ## 95 percent confidence interval: ## 0.5063618 1.3850184 ## sample estimates: ## mean of x ## 0.9456901 mi.t.test(res, x = "response", subset = D$group == "yes")
##
##  Multiple Imputation One Sample t-test
##
## data:  Variable response
## number of imputations: 10
## t = 4.6847, df = 18.494, p-value = 0.0001725
## alternative hypothesis: true mean is not equal to 0
## 95 percent confidence interval:
##  0.5280752 1.3838820
## sample estimates:
##      mean        SD
## 0.9559786 1.0203219
mi.t.test(res, x = "response", mu = -1, subset = D$group == "yes", alternative = "less") ## ## Multiple Imputation One Sample t-test ## ## data: Variable response ## number of imputations: 10 ## t = 9.5851, df = 18.494, p-value = 1 ## alternative hypothesis: true mean is less than -1 ## 95 percent confidence interval: ## -Inf 1.309328 ## sample estimates: ## mean SD ## 0.9559786 1.0203219 mi.t.test(res, x = "response", mu = -1, subset = D$group == "yes",
alternative = "greater")
##
##  Multiple Imputation One Sample t-test
##
## data:  Variable response
## number of imputations: 10
## t = 9.5851, df = 18.494, p-value = 6.655e-09
## alternative hypothesis: true mean is greater than -1
## 95 percent confidence interval:
##  0.6026297       Inf
## sample estimates:
##      mean        SD
## 0.9559786 1.0203219
## paired test
t.test(D$response, D$pair, paired = TRUE)
##
##  Paired t-test
##
## data:  D$response and D$pair
## t = -1.3532, df = 35, p-value = 0.1847
## alternative hypothesis: true mean difference is not equal to 0
## 95 percent confidence interval:
##  -0.6976921  0.1395993
## sample estimates:
## mean difference
##      -0.2790464
mi.t.test(res, x = "response", y = "pair", paired = TRUE)
##
##  Multiple Imputation Paired t-test
##
## data:  Variables response and pair
## number of imputations: 10
## t = -1.0455, df = 39.974, p-value = 0.3021
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -0.5680741  0.1807237
## sample estimates:
## mean of difference   SD of difference
##         -0.1936752          1.2426515

Function mi.t.test also works with package mice.

library(mice)
##
## Attache Paket: 'mice'
## Das folgende Objekt ist maskiert 'package:stats':
##
##     filter
## Die folgenden Objekte sind maskiert von 'package:base':
##
##     cbind, rbind
res.mice <- mice(D, m = 10, print = FALSE)
mi.t.test(res.mice, x = "response", y = "group")
##
##  Multiple Imputation Welch Two Sample t-test
##
## data:  Variable response: group no vs group yes
## number of imputations: 10
## t = -7.2111, df = 29.735, p-value = 5.289e-08
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -2.6351 -1.4716
## sample estimates:
##  mean (no)    SD (no) mean (yes)   SD (yes)
## -1.0771373  0.8585436  0.9762127  1.0261920

## Multiple Imputation Wilcoxon Tests

Function mi.wilcox.test can be used to compute multiple imputation Wilcoxon tests by applying the median p rule (MPR) approach; see Section 13.3 in approach (Martin and Iris 2019).

## Per protocol analysis (Exact Wilcoxon rank sum test)
library(exactRankTests)
##  Package 'exactRankTests' is no longer under development.
##  Please consider using package 'coin' instead.
wilcox.exact(response ~ group, data = D, conf.int = TRUE)
##
##  Exact Wilcoxon rank sum test
##
## data:  response by group
## W = 12, p-value = 7.444e-08
## alternative hypothesis: true mu is not equal to 0
## 95 percent confidence interval:
##  -2.664671 -1.329111
## sample estimates:
## difference in location
##              -1.989152
## Intention to treat analysis (Multiple Imputation Exact Wilcoxon rank sum test)
mi.wilcox.test(res, x = "response", y = "group")
##
##  Multiple Imputation Exact Wilcoxon rank sum test
##
## data:  Variable response: group no vs group yes
## number of imputations: 10
## W = 20, p-value = 1.712e-09
## alternative hypothesis: true mu is not equal to 0
## 95 percent confidence interval:
##  -2.489225 -1.317255
## sample estimates:
## difference in location
##              -1.882414
## Specifying alternatives
mi.wilcox.test(res, x = "response", y = "group", alternative = "less")
##
##  Multiple Imputation Exact Wilcoxon rank sum test
##
## data:  Variable response: group no vs group yes
## number of imputations: 10
## W = 20, p-value = 8.562e-10
## alternative hypothesis: true mu is less than 0
## 95 percent confidence interval:
##       -Inf -1.424056
## sample estimates:
## difference in location
##              -1.882414
mi.wilcox.test(res, x = "response", y = "group", alternative = "greater")
##
##  Multiple Imputation Exact Wilcoxon rank sum test
##
## data:  Variable response: group no vs group yes
## number of imputations: 10
## W = 20, p-value = 1
## alternative hypothesis: true mu is greater than 0
## 95 percent confidence interval:
##  -2.371565       Inf
## sample estimates:
## difference in location
##              -1.882414
## One sample test
wilcox.exact(D$response[D$group == "yes"], conf.int = TRUE)
##
##  Exact Wilcoxon signed rank test
##
## data:  D$response[D$group == "yes"]
## V = 197, p-value = 0.0001678
## alternative hypothesis: true mu is not equal to 0
## 95 percent confidence interval:
##  0.4856837 1.3892099
## sample estimates:
## (pseudo)median
##      0.9151479
mi.wilcox.test(res, x = "response", subset = D$group == "yes") ## ## Multiple Imputation Exact Wilcoxon signed rank test ## ## data: Variable response ## number of imputations: 10 ## V = 306, p-value = 1.83e-05 ## alternative hypothesis: true mu is not equal to 0 ## 95 percent confidence interval: ## 0.5338009 1.3042666 ## sample estimates: ## (pseudo)median ## 0.9033367 mi.wilcox.test(res, x = "response", mu = -1, subset = D$group == "yes",
alternative = "less")
##
##  Multiple Imputation Exact Wilcoxon signed rank test
##
## data:  Variable response
## number of imputations: 10
## V = 325, p-value = 1
## alternative hypothesis: true mu is less than -1
## 95 percent confidence interval:
##      -Inf 1.406019
## sample estimates:
## (pseudo)median
##      0.9710047
mi.wilcox.test(res, x = "response", mu = -1, subset = D$group == "yes", alternative = "greater") ## ## Multiple Imputation Exact Wilcoxon signed rank test ## ## data: Variable response ## number of imputations: 10 ## V = 325, p-value = 2.98e-08 ## alternative hypothesis: true mu is greater than -1 ## 95 percent confidence interval: ## 0.6708086 Inf ## sample estimates: ## (pseudo)median ## 0.9710047 ## paired test wilcox.exact(D$response, D$pair, paired = TRUE, conf.int = TRUE) ## ## Exact Wilcoxon signed rank test ## ## data: D$response and D$pair ## V = 244, p-value = 0.1663 ## alternative hypothesis: true mu is not equal to 0 ## 95 percent confidence interval: ## -0.6467313 0.1005468 ## sample estimates: ## (pseudo)median ## -0.2795692 mi.wilcox.test(res, x = "response", y = "pair", paired = TRUE) ## ## Multiple Imputation Exact Wilcoxon signed rank test ## ## data: Variables response and pair ## number of imputations: 10 ## V = 436, p-value = 0.3641 ## alternative hypothesis: true mu is not equal to 0 ## 95 percent confidence interval: ## -0.5120206 0.2049652 ## sample estimates: ## (pseudo)median ## -0.1683673 Function mi.wilcox.test also works with package mice. mi.wilcox.test(res.mice, x = "response", y = "group") ## ## Multiple Imputation Exact Wilcoxon rank sum test ## ## data: Variable response: group no vs group yes ## number of imputations: 10 ## W = 16, p-value = 5.3e-10 ## alternative hypothesis: true mu is not equal to 0 ## 95 percent confidence interval: ## -2.533659 -1.452234 ## sample estimates: ## difference in location ## -2.002101 ## Repeated Measures One-Way ANOVA We provide a simple wrapper function that allows to compute a classical repeated measures one-way ANOVA as well as a respective mixed effects model. In addition, the non-parametric Friedman and Quade tests can be computed. set.seed(123) outcome <- c(rnorm(10), rnorm(10, mean = 1.5), rnorm(10, mean = 1)) timepoints <- factor(rep(1:3, each = 10)) patients <- factor(rep(1:10, times = 3)) rm.oneway.test(outcome, timepoints, patients) ## ## Repeated measures 1-way ANOVA ## ## data: outcome, timepoints and patients ## F = 6.5898, num df = 2, denom df = 18, p-value = 0.007122 rm.oneway.test(outcome, timepoints, patients, method = "lme") ## ## Mixed-effects 1-way ANOVA ## ## data: outcome, timepoints and patients ## F = 7.3674, num df = 2, denom df = 18, p-value = 0.004596 rm.oneway.test(outcome, timepoints, patients, method = "friedman") ## ## Friedman rank sum test ## ## data: outcome, timepoints and patients ## Friedman chi-squared = 12.8, df = 2, p-value = 0.001662 rm.oneway.test(outcome, timepoints, patients, method = "quade") ## ## Quade test ## ## data: outcome, timepoints and patients ## Quade F = 7.2906, num df = 2, denom df = 18, p-value = 0.004795 ## Volcano Plots Volcano plots can be used to visualize the results when many tests have been applied. They show a measure of effect size in combination with (adjusted) p values. ## Generate some data x <- matrix(rnorm(1000, mean = 10), nrow = 10) g1 <- rep("control", 10) y1 <- matrix(rnorm(500, mean = 11.75), nrow = 10) y2 <- matrix(rnorm(500, mean = 9.75, sd = 3), nrow = 10) g2 <- rep("treatment", 10) group <- factor(c(g1, g2)) Data <- rbind(x, cbind(y1, y2)) ## compute Hsu t-test pvals <- apply(Data, 2, function(x, group) hsu.t.test(x ~ group)$p.value,
group = group)
## compute log-fold change
logfc <- function(x, group){
res <- tapply(x, group, mean)
log2(res[1]/res[2])
}
lfcs <- apply(Data, 2, logfc, group = group)
effect.low = -0.25, effect.high = 0.25,
xlab = "log-fold change", ylab = "-log10(adj. p value)")

## Bland-Altman plots

Bland-Altman plots are used to visually compare two methods of measurement. We can generate classical Bland-Altman plots (Bland and Altman 1986; Shieh 2018).

data("fingsys")
baplot(fingsys$fingsys, fingsys$armsys,
title = "Approximative Confidence Intervals",
type = "parametric", ci.type = "approximate")
## $mean of differences ## estimate 2.5 % 97.5 % ## 4.295000 2.261102 6.328898 ## ##$lower LoA (2.5 %)
##  estimate     2.5 %    97.5 %
## -24.32967 -27.81137 -20.84797
##
## $upper LoA (97.5 %) ## estimate 2.5 % 97.5 % ## 32.91967 29.43797 36.40137 baplot(fingsys$fingsys, fingsys$armsys, title = "Exact Confidence Intervals", type = "parametric", ci.type = "exact") ## Warning in qt(conf.alpha/2, df, zp * sqrt(n)): eventuell wurde in 'pnt{final}' ## nicht die volle Genauigkeit erreicht ## Warning in qt(1 - conf.alpha/2, df, zp * sqrt(n)): eventuell wurde in ## 'pnt{final}' nicht die volle Genauigkeit erreicht ## Warning in qt(1 - conf.alpha/2, df, zp * sqrt(n)): eventuell wurde in ## 'pnt{final}' nicht die volle Genauigkeit erreicht ##$mean of differences
## estimate    2.5 %   97.5 %
## 4.295000 2.261102 6.328898
##
## $lower LoA (2.5 %) ## estimate 2.5 % 97.5 % ## -24.32967 -28.07305 -21.09776 ## ##$upper LoA (97.5 %)
## estimate    2.5 %   97.5 %
## 32.91967 29.68776 36.66305

baplot(fingsys$fingsys, fingsys$armsys,
title = "Bootstrap Confidence Intervals",
type = "parametric", ci.type = "boot", R = 999)
## $mean of differences ## estimate 2.5 % 97.5 % ## 4.295000 2.219930 6.250611 ## ##$lower LoA (2.5 %)
##  estimate     2.5 %    97.5 %
## -24.32967 -29.53826 -20.48664
##
## $upper LoA (97.5 %) ## estimate 2.5 % 97.5 % ## 32.91967 29.37463 37.50405 In the following nonparametric Bland-Altman plots, the median is used instead of the mean in combination with empirical quantiles for the lower and upper limit of agreement. data("fingsys") baplot(fingsys$fingsys, fingsys$armsys, title = "Approximative Confidence Intervals", type = "nonparametric", ci.type = "approximate") ##$median of differences
## estimate    2.5 %   97.5 %
##      4.5      2.0      8.0
##
## $lower LoA (2.5 %) ## estimate.2.5% 2.5 % 97.5 % ## -24.025 -48.000 -20.000 ## ##$upper LoA (97.5 %)
## estimate.97.5%          2.5 %         97.5 %
##             34             28             60

baplot(fingsys$fingsys, fingsys$armsys,
title = "Exact Confidence Intervals",
type = "nonparametric", ci.type = "exact")
## $median of differences ## estimate 2.5 % 97.5 % ## 4.5 2.0 8.0 ## ##$lower LoA (2.5 %)
## estimate.2.5%         2.5 %        97.5 %
##       -24.025       -41.000       -18.000
##
## $upper LoA (97.5 %) ## estimate.97.5% 2.5 % 97.5 % ## 34 27 45 baplot(fingsys$fingsys, fingsys$armsys, title = "Bootstrap Confidence Intervals", type = "nonparametric", ci.type = "boot", R = 999) ##$median of differences
## estimate    2.5 %   97.5 %
##      4.5      2.0      8.0
##
## $lower LoA (2.5 %) ## estimate.2.5% 2.5 % 97.5 % ## -24.025 -30.275 -18.000 ## ##$upper LoA (97.5 %)
## estimate.97.5%          2.5 %         97.5 %
##         34.000         27.025         38.175

## Imputation of Standard Deviations for Changes from Baseline

The function imputeSD can be used to impute standard deviations for changes from baseline adopting the approach of the Cochrane handbook (Higgins et al. 2019, Section 6.5.2.8).

SD1 <- c(0.149, 0.022, 0.036, 0.085, 0.125, NA, 0.139, 0.124, 0.038)
SD2 <- c(NA, 0.039, 0.038, 0.087, 0.125, NA, 0.135, 0.126, 0.038)
SDchange <- c(NA, NA, NA, 0.026, 0.058, NA, NA, NA, NA)
imputeSD(SD1, SD2, SDchange)
##     SD1   SD2 SDchange       Cor SDchange.min SDchange.mean SDchange.max
## 1 0.149 0.149       NA        NA   0.04491608    0.05829769   0.06913600
## 2 0.022 0.039       NA        NA   0.01915642    0.02050235   0.02176520
## 3 0.036 0.038       NA        NA   0.01132754    0.01460887   0.01727787
## 4 0.085 0.087    0.026 0.9545639   0.02600000    0.02600000   0.02600000
## 5 0.125 0.125    0.058 0.8923520   0.05800000    0.05800000   0.05800000
## 6    NA    NA       NA        NA           NA            NA           NA
## 7 0.139 0.135       NA        NA   0.04148755    0.05374591   0.06368696
## 8 0.124 0.126       NA        NA   0.03773311    0.04894677   0.05803262
## 9 0.038 0.038       NA        NA   0.01145511    0.01486787   0.01763200

Correlations can also be provided via argument corr. This option may particularly be useful, if no complete data is available.

SDchange2 <- rep(NA, 9)
imputeSD(SD1, SD2, SDchange2, corr = c(0.85, 0.9, 0.95))
##     SD1   SD2 SDchange Cor SDchange.min SDchange.mean SDchange.max
## 1 0.149 0.149       NA  NA   0.04711794    0.06663483   0.08161066
## 2 0.022 0.039       NA  NA   0.01935975    0.02146159   0.02337520
## 3 0.036 0.038       NA  NA   0.01186592    0.01666133   0.02035682
## 4 0.085 0.087       NA  NA   0.02726720    0.03850974   0.04714340
## 5 0.125 0.125       NA  NA   0.03952847    0.05590170   0.06846532
## 6    NA    NA       NA  NA           NA            NA           NA
## 7 0.139 0.135       NA  NA   0.04350287    0.06139218   0.07513654
## 8 0.124 0.126       NA  NA   0.03957777    0.05593568   0.06849234
## 9 0.038 0.038       NA  NA   0.01201666    0.01699412   0.02081346

## Pairwise Comparisons

Function pairwise.fun enables the application of arbitrary functions for pairwise comparisons.

pairwise.wilcox.test(airquality$Ozone, airquality$Month,
p.adjust.method = "none")
## Warning in wilcox.test.default(xi, xj, paired = paired, ...): kann bei
## Bindungen keinen exakten p-Wert Berechnen

## Warning in wilcox.test.default(xi, xj, paired = paired, ...): kann bei
## Bindungen keinen exakten p-Wert Berechnen

## Warning in wilcox.test.default(xi, xj, paired = paired, ...): kann bei
## Bindungen keinen exakten p-Wert Berechnen

## Warning in wilcox.test.default(xi, xj, paired = paired, ...): kann bei
## Bindungen keinen exakten p-Wert Berechnen

## Warning in wilcox.test.default(xi, xj, paired = paired, ...): kann bei
## Bindungen keinen exakten p-Wert Berechnen

## Warning in wilcox.test.default(xi, xj, paired = paired, ...): kann bei
## Bindungen keinen exakten p-Wert Berechnen

## Warning in wilcox.test.default(xi, xj, paired = paired, ...): kann bei
## Bindungen keinen exakten p-Wert Berechnen

## Warning in wilcox.test.default(xi, xj, paired = paired, ...): kann bei
## Bindungen keinen exakten p-Wert Berechnen

## Warning in wilcox.test.default(xi, xj, paired = paired, ...): kann bei
## Bindungen keinen exakten p-Wert Berechnen

## Warning in wilcox.test.default(xi, xj, paired = paired, ...): kann bei
## Bindungen keinen exakten p-Wert Berechnen
##
##  Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data:  airquality$Ozone and airquality$Month
##
##   5       6       7       8
## 6 0.19250 -       -       -
## 7 3e-05   0.01414 -       -
## 8 0.00012 0.02591 0.86195 -
## 9 0.11859 0.95887 0.00074 0.00325
##
## P value adjustment method: none
## To avoid the warnings
pairwise.fun(airquality$Ozone, airquality$Month,
fun = function(x, y) wilcox.exact(x, y)$p.value) ## 5 vs 6 5 vs 7 5 vs 8 5 vs 9 6 vs 7 6 vs 8 ## 1.897186e-01 1.087205e-05 6.108735e-05 1.171796e-01 1.183753e-02 2.333564e-02 ## 6 vs 9 7 vs 8 7 vs 9 8 vs 9 ## 9.528659e-01 8.595683e-01 5.281796e-04 2.714694e-03 The function is also the basis for our functions pairwise.wilcox.exact and pairwise.ext.t.test, which in contrast to the standard functions pairwise.wilcox.test and pairwise.t.test generate a much more detailed output. In addition, pairwise.wilcox.exact is based on wilcox.exact instead of wilcox.test. pairwise.wilcox.exact(airquality$Ozone, airquality$Month) ## ## Pairwise Exact Wilcoxon rank sum tests ## ## data: airquality$Ozone and airquality$Month ## alternative hypothesis: true location shift is not equal to 0 ## ## groups W diff. in location 2.5% 97.5% p-value adj. p-value ## 1 5 vs 6 152.0 6.5 -5 18 1.897186e-01 0.5691559000 ## 2 5 vs 7 566.5 37.5 21 51 1.087205e-05 0.0001087205 ## 3 5 vs 8 548.5 31.5 14 53 6.108735e-05 0.0005497862 ## 4 5 vs 9 470.0 5.5 -2 13 1.171796e-01 0.4687184000 ## 5 6 vs 7 182.5 28.5 8 51 1.183753e-02 0.0710251900 ## 6 6 vs 8 176.5 23.5 2 53 2.333564e-02 0.1166782000 ## 7 6 vs 9 128.5 -0.5 -12 10 9.528659e-01 1.0000000000 ## 8 7 vs 8 328.0 -2.5 -21 19 8.595683e-01 1.0000000000 ## 9 7 vs 9 176.5 -30.5 -44 -13 5.281796e-04 0.0042254370 ## 10 8 vs 9 202.0 -23.5 -46 -7 2.714694e-03 0.0190028600 Furthermore, function pairwise.ext.t.test also enables pairwise Student, Welch, Hsu, bootstrap and permutation t tests. pairwise.t.test(airquality$Ozone, airquality$Month, pool.sd = FALSE) ## ## Pairwise comparisons using t tests with non-pooled SD ## ## data: airquality$Ozone and airquality$Month ## ## 5 6 7 8 ## 6 1.00000 - - - ## 7 0.00026 0.01527 - - ## 8 0.00195 0.02135 1.00000 - ## 9 0.86321 1.00000 0.00589 0.01721 ## ## P value adjustment method: holm pairwise.ext.t.test(airquality$Ozone, airquality$Month) ## ## Pairwise Welch Two Sample t-tests ## ## data: airquality$Ozone and airquality$Month ## alternative hypothesis: true difference in means is not equal to 0 ## ## groups t df diff. in means SE 2.5% 97.5% ## 1 5 vs 6 0.78010090 16.93764 5.8290598 7.472187 -9.940299 21.59842 ## 2 5 vs 7 4.68198923 44.84296 35.5000000 7.582247 20.227090 50.77291 ## 3 5 vs 8 4.07487966 39.27916 36.3461538 8.919565 18.308730 54.38358 ## 4 5 vs 9 1.25274697 52.95697 7.8328912 6.252572 -4.708419 20.37420 ## 5 6 vs 7 3.41859846 24.79227 29.6709402 8.679270 11.788050 47.55383 ## 6 6 vs 8 3.09220573 29.98945 30.5170940 9.869037 10.361530 50.67265 ## 7 6 vs 9 0.26556793 17.61281 2.0038314 7.545457 -13.873600 17.88127 ## 8 7 vs 8 0.08501814 47.63564 0.8461538 9.952627 -19.168900 20.86121 ## 9 7 vs 9 -3.61450643 46.58247 -27.6671088 7.654464 -43.069550 -12.26467 ## 10 8 vs 9 -3.17483051 40.37577 -28.5132626 8.981035 -46.659350 -10.36718 ## p-value adj. p-value ## 1 4.460968e-01 1.0000000000 ## 2 2.646679e-05 0.0002646679 ## 3 2.168566e-04 0.0019517090 ## 4 2.158016e-01 0.8632062000 ## 5 2.181685e-03 0.0152717900 ## 6 4.269318e-03 0.0213465900 ## 7 7.936555e-01 1.0000000000 ## 8 9.326033e-01 1.0000000000 ## 9 7.361032e-04 0.0058888260 ## 10 2.868290e-03 0.0172097400 pairwise.ext.t.test(airquality$Ozone, airquality$Month, method = "hsu.t.test") ## ## Pairwise Hsu Two Sample t-tests ## ## data: airquality$Ozone and airquality$Month ## alternative hypothesis: true difference in means is not equal to 0 ## ## groups t df diff. in means SE 2.5% 97.5% ## 1 5 vs 6 0.78010090 8 5.8290598 7.472187 -11.401830 23.05995 ## 2 5 vs 7 4.68198923 25 35.5000000 7.582247 19.884070 51.11593 ## 3 5 vs 8 4.07487966 25 36.3461538 8.919565 17.975970 54.71634 ## 4 5 vs 9 1.25274697 25 7.8328912 6.252572 -5.044523 20.71031 ## 5 6 vs 7 3.41859846 8 29.6709402 8.679270 9.656507 49.68537 ## 6 6 vs 8 3.09220573 8 30.5170940 9.869037 7.759053 53.27514 ## 7 6 vs 9 0.26556793 8 2.0038314 7.545457 -15.396020 19.40369 ## 8 7 vs 8 0.08501814 25 0.8461538 9.952627 -19.651670 21.34397 ## 9 7 vs 9 -3.61450643 25 -27.6671088 7.654464 -43.431770 -11.90245 ## 10 8 vs 9 -3.17483051 25 -28.5132626 8.981035 -47.010050 -10.01648 ## p-value adj. p-value ## 1 0.4577885000 1.000000000 ## 2 0.0000849598 0.000849598 ## 3 0.0004086781 0.003678103 ## 4 0.2218896000 0.887558600 ## 5 0.0091067660 0.054640600 ## 6 0.0148398900 0.074199430 ## 7 0.7972873000 1.000000000 ## 8 0.9329242000 1.000000000 ## 9 0.0013234440 0.010587550 ## 10 0.0039521140 0.027664800 pairwise.ext.t.test(airquality$Ozone, airquality$Month, method = "boot.t.test") ## ## Pairwise Bootstrap Welch Two Sample t-tests ## ## data: airquality$Ozone and airquality$Month ## alternative hypothesis: true difference in means is not equal to 0 ## ## groups diff. in means SE 2.5% 97.5% p-value adj. p-value ## 1 5 vs 6 5.9575517 6.965299 -7.72265 20.56880 0.43324330 1.00000000 ## 2 5 vs 7 35.4748436 7.389274 20.42308 50.07692 0.00020002 0.00200020 ## 3 5 vs 8 36.3571088 8.668791 19.53846 53.65577 0.00040004 0.00360036 ## 4 5 vs 9 7.8721992 6.025929 -4.40630 19.80564 0.23522350 0.94089410 ## 5 6 vs 7 29.6692870 8.267833 13.05214 45.43248 0.00420042 0.02400240 ## 6 6 vs 8 30.4539454 9.443246 11.50214 49.38932 0.00400040 0.02400240 ## 7 6 vs 9 1.9831826 7.050480 -12.91341 15.68238 0.82248220 1.00000000 ## 8 7 vs 8 0.8754337 9.705470 -17.46346 19.88654 0.92589260 1.00000000 ## 9 7 vs 9 -27.7096602 7.465314 -42.40723 -12.95146 0.00060006 0.00480048 ## 10 8 vs 9 -28.4483592 8.739157 -46.08362 -11.52062 0.00220022 0.01540154 pairwise.ext.t.test(airquality$Ozone, airquality$Month, method = "perm.t.test") ## ## Pairwise Permutation Welch Two Sample t-tests ## ## data: airquality$Ozone and airquality\$Month
## alternative hypothesis: true difference in means is not equal to 0
##
##    groups diff. in means        SE       2.5%     97.5%    p-value adj. p-value
## 1  5 vs 6      5.9171567  7.859164  -7.345085  23.62393 0.49304930   1.00000000
## 2  5 vs 7     35.4156570  9.003950  17.996150  52.92308 0.00000000   0.00000000
## 3  5 vs 8     36.2758122 10.191180  16.538460  56.15385 0.00010001   0.00090009
## 4  5 vs 9      7.7036415  6.314074  -4.539788  19.75066 0.22332230   0.89328930
## 5  6 vs 7     29.5471551 12.051430   4.897436  52.31197 0.00520052   0.03120312
## 6  6 vs 8     30.5021455 14.372630   1.205128  57.29487 0.00970097   0.04850485
## 7  6 vs 9      2.0813652  8.435290 -15.938700  17.11111 0.79797980   1.00000000
## 8  7 vs 8      0.8314293  9.854760 -18.461540  20.15385 0.93169320   1.00000000
## 9  7 vs 9    -27.7240971  8.365606 -43.954910 -11.27586 0.00100010   0.00800080
## 10 8 vs 9    -28.3760056  9.501787 -46.814320 -10.12334 0.00190019   0.01330133

## sessionInfo

sessionInfo()
## R version 4.2.3 Patched (2023-04-07 r84210)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Linux Mint 21.1
##
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/libf77blas.so.3.10.3
## LAPACK: /home/kohlm/RTOP/Rbranch/lib/libRlapack.so
##
## locale:
##  [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C
##  [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=C
##  [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8
##  [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C
## [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base
##
## other attached packages:
## [1] exactRankTests_0.8-35 mice_3.15.0           Amelia_1.8.1
## [4] Rcpp_1.0.10           MKinfer_1.1
##
## loaded via a namespace (and not attached):
##  [1] gmp_0.7-1          highr_0.10         bslib_0.4.2        compiler_4.2.3
##  [5] pillar_1.9.0       jquerylib_0.1.4    miceadds_3.16-18   arrangements_1.1.9
##  [9] tools_4.2.3        boot_1.3-28.1      digest_0.6.31      lattice_0.21-8
## [13] jsonlite_1.8.4     evaluate_0.20      lifecycle_1.0.3    tibble_3.2.1
## [17] gtable_0.3.3       nlme_3.1-162       pkgconfig_2.0.3    rlang_1.1.0
## [21] DBI_1.1.3          cli_3.6.1          yaml_2.3.7         xfun_0.38
## [25] fastmap_1.1.1      withr_2.5.0        MKdescr_0.8        dplyr_1.1.1
## [29] knitr_1.42         mitools_2.4        generics_0.1.3     vctrs_0.6.1
## [33] sass_0.4.5         grid_4.2.3         tidyselect_1.2.0   glue_1.6.2
## [37] R6_2.5.1           fansi_1.0.4        foreign_0.8-84     rmarkdown_2.21
## [41] farver_2.1.1       tidyr_1.3.0        purrr_1.0.1        ggplot2_3.4.2
## [45] magrittr_2.0.3     backports_1.4.1    scales_1.2.1       htmltools_0.5.5
## [49] colorspace_2.1-0   labeling_0.4.2     utf8_1.2.3         munsell_0.5.0
## [53] broom_1.0.4        cachem_1.0.7

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