Last updated on 2025-09-02 21:50:35 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.3 | 4.42 | 157.29 | 161.71 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.2.3 | 3.07 | 99.47 | 102.54 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.2.3 | 266.59 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.2.3 | 267.99 | ERROR | |||
| r-devel-windows-x86_64 | 0.2.3 | 5.00 | 155.00 | 160.00 | OK | |
| r-patched-linux-x86_64 | 0.2.3 | 3.91 | 152.25 | 156.16 | OK | |
| r-release-linux-x86_64 | 0.2.3 | 4.13 | 154.81 | 158.94 | OK | |
| r-release-macos-arm64 | 0.2.3 | 74.00 | OK | |||
| r-release-macos-x86_64 | 0.2.3 | 147.00 | OK | |||
| r-release-windows-x86_64 | 0.2.3 | 7.00 | 159.00 | 166.00 | OK | |
| r-oldrel-macos-arm64 | 0.2.3 | 65.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.2.3 | 144.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.2.3 | 8.00 | 218.00 | 226.00 | OK |
Version: 0.2.3
Check: tests
Result: ERROR
Running ‘andersondarling_behaviour.r’ [0s/1s]
Running ‘andersondarling_correctness.r’ [2s/2s]
Running ‘andersondarling_errors.r’ [0s/1s]
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Running ‘bartlett_behaviour.r’ [0s/1s]
Running ‘bartlett_correctness.r’ [4s/5s]
Running ‘bartlett_errors.r’ [0s/1s]
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Running ‘brownforsythe_behaviour.r’ [0s/1s]
Running ‘brownforsythe_correctness.r’ [12s/14s]
Running ‘brownforsythe_errors.r’ [0s/0s]
Running ‘brownforsythe_warnings.r’ [0s/1s]
Running ‘cor_pearson_behaviour.r’ [0s/1s]
Running ‘cor_pearson_correctness.r’ [1s/1s]
Running ‘cor_pearson_errors.r’ [0s/0s]
Running ‘cor_pearson_warnings.r’ [0s/0s]
Running ‘cosinor_behaviour.r’ [0s/1s]
Running ‘cosinor_correctness.r’ [25s/30s]
Running ‘cosinor_errors.r’ [0s/1s]
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Running ‘flignerkilleen_behaviour.r’ [0s/1s]
Running ‘flignerkilleen_correctness.r’ [4s/5s]
Running ‘flignerkilleen_errors.r’ [0s/1s]
Running ‘flignerkilleen_warnings.r’ [0s/0s]
Running ‘jarquebera_behaviour.r’ [0s/1s]
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Running ‘jarquebera_warnings.r’ [0s/1s]
Running ‘kolmogorovsmirnov_twosample_behavioiur.r’ [0s/1s]
Running ‘kolmogorovsmirnov_twosample_correctness.r’ [8s/8s]
Running ‘kolmogorovsmirnov_twosample_errors.r’ [0s/1s]
Running ‘kolmogorovsmirnov_twosample_warnings.r’ [0s/0s]
Running ‘kruskalwallis_behaviour.r’ [0s/1s]
Running ‘kruskalwallis_correctness.r’ [3s/5s]
Running ‘kruskalwallis_errors.r’ [0s/0s]
Running ‘kruskalwallis_warnings.r’ [0s/0s]
Running ‘levene_behaviour.r’ [0s/1s]
Running ‘levene_correctness.r’ [11s/15s]
Running ‘levene_errors.r’ [0s/0s]
Running ‘levene_warnings.r’ [0s/1s]
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Running ‘oneway_equalvar_warnings.r’ [0s/1s]
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Running ‘t_onesample_behaviour.r’ [0s/0s]
Running ‘t_onesample_correctness.r’ [1s/1s]
Running ‘t_onesample_errors.r’ [0s/0s]
Running ‘t_onesample_warnings.r’ [0s/1s]
Running ‘t_paired_behaviour.r’ [0s/1s]
Running ‘t_paired_correctness.r’ [1s/2s]
Running ‘t_paired_errors.r’ [0s/1s]
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Running ‘t_welch_behaviour.r’ [0s/1s]
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Running ‘wilcoxon_onesample_behaviour.r’ [0s/0s]
Running ‘wilcoxon_onesample_correctness.r’ [3s/4s]
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Running ‘wilcoxon_onesample_warnings.r’ [0s/0s]
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Running ‘wilcoxon_paired_correctness.r’ [4s/5s]
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Running ‘wilcoxon_paired_warnings.r’ [0s/0s]
Running ‘wilcoxon_twosample_behaviour.r’ [0s/1s]
Running ‘wilcoxon_twosample_correctness.r’ [5s/7s]
Running ‘wilcoxon_twosample_errors.r’ [0s/0s]
Running ‘wilcoxon_twosample_warnings.r’ [0s/0s]
Running the tests in ‘tests/wilcoxon_twosample_correctness.r’ failed.
Complete output:
> library(matrixTests)
>
> #--- functions -----------------------------------------------------------------
>
> base_wilcoxon_twosample <- function(mat1, mat2, null=0, alternative="two.sided", exact=NA, correct=TRUE) {
+ if(is.vector(mat1)) mat1 <- matrix(mat1, nrow=1)
+ if(is.vector(mat2)) mat2 <- matrix(mat2, nrow=1)
+ if(length(alternative)==1) alternative <- rep(alternative, nrow(mat1))
+ if(length(null)==1) null <- rep(null, nrow(mat1))
+ if(length(exact)==1) exact <- rep(exact, nrow(mat1))
+ if(length(correct)==1) correct <- rep(correct, nrow(mat1))
+
+ nx <- ny <- nxy <- stat <- p <- m0 <- numeric(nrow(mat1))
+ al <- character(nrow(mat1))
+ ext <- cor <- logical(nrow(mat1))
+ for(i in 1:nrow(mat1)) {
+ ex <- if(is.na(exact[i])) NULL else exact[i]
+
+ res <- wilcox.test(mat1[i,], mat2[i,], alternative=alternative[i], mu=null[i], exact=ex, correct=correct[i])
+
+ nx[i] <- sum(!is.na(mat1[i,]))
+ ny[i] <- sum(!is.na(mat2[i,]))
+ nxy[i] <- nx[i] + ny[i]
+ stat[i] <- res$statistic
+ p[i] <- res$p.value
+ al[i] <- res$alternative
+ m0[i] <- res$null.value
+
+ cor[i] <- grepl("continuity correction", res$method)
+ ext[i] <- if(is.na(exact[i])) (nx[i] < 50 & ny[i] < 50) else exact[i]
+ ext[i] <- if(length(unique(na.omit(c(mat1[i,]-m0[i], mat2[i,])))) != nxy[i]) FALSE else ext[i]
+ }
+
+ data.frame(obs.x=nx, obs.y=ny, obs.tot=nxy, statistic=stat, pvalue=p,
+ location.null=m0, alternative=al, exact=ext, corrected=cor,
+ stringsAsFactors=FALSE
+ )
+ }
>
>
> #--- montecarlo ----------------------------------------------------------------
>
> # 2 samples in one group and 4 in another
> x <- matrix(rnorm(2000), ncol=2)
> y <- matrix(rnorm(4000), ncol=4)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- base_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> res2 <- row_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> stopifnot(all.equal(res1, res2))
>
> # 51 samples in one group and 51 in another
> x <- matrix(rnorm(51000), ncol=51)
> y <- matrix(rnorm(51000), ncol=51)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- base_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> res2 <- row_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> stopifnot(all.equal(res1, res2))
>
> # 4 samples in one group and 51 in another
> x <- matrix(rnorm(4000), ncol=4)
> y <- matrix(rnorm(51000), ncol=51)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- base_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> res2 <- row_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> stopifnot(all.equal(res1, res2))
>
> # 6 samples per group with ties and zeroes
> x <- matrix(round(runif(6000, -15, 15)), ncol=6)
> y <- matrix(round(runif(6000, -15, 15)), ncol=6)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> mus[sample(length(mus), length(mus)/8)] <- 0
> mus[sample(length(mus), length(mus)/8)] <- 1
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- suppressWarnings(base_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor))
> res2 <- suppressWarnings(row_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor))
> stopifnot(all.equal(res1, res2))
Error: res1 and res2 are not equal:
Component "pvalue": Mean relative difference: 0.04114965
Component "corrected": 240 element mismatches
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.2.3
Check: tests
Result: ERROR
Running ‘andersondarling_behaviour.r’ [0s/1s]
Running ‘andersondarling_correctness.r’ [1s/1s]
Running ‘andersondarling_errors.r’ [0s/0s]
Running ‘andersondarling_warnings.r’ [0s/0s]
Running ‘bartlett_behaviour.r’ [0s/0s]
Running ‘bartlett_correctness.r’ [2s/3s]
Running ‘bartlett_errors.r’ [0s/0s]
Running ‘bartlett_warnings.r’ [0s/0s]
Running ‘brownforsythe_behaviour.r’ [0s/0s]
Running ‘brownforsythe_correctness.r’ [6s/8s]
Running ‘brownforsythe_errors.r’ [0s/0s]
Running ‘brownforsythe_warnings.r’ [0s/1s]
Running ‘cor_pearson_behaviour.r’ [0s/0s]
Running ‘cor_pearson_correctness.r’ [1s/1s]
Running ‘cor_pearson_errors.r’ [0s/0s]
Running ‘cor_pearson_warnings.r’ [0s/1s]
Running ‘cosinor_behaviour.r’ [0s/0s]
Running ‘cosinor_correctness.r’ [14s/17s]
Running ‘cosinor_errors.r’ [0s/1s]
Running ‘cosinor_warnings.r’ [0s/0s]
Running ‘f_var_behaviour.r’ [0s/1s]
Running ‘f_var_correctness.r’ [1s/1s]
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Running ‘flignerkilleen_behaviour.r’ [0s/0s]
Running ‘flignerkilleen_correctness.r’ [2s/3s]
Running ‘flignerkilleen_errors.r’ [0s/0s]
Running ‘flignerkilleen_warnings.r’ [0s/1s]
Running ‘jarquebera_behaviour.r’ [0s/0s]
Running ‘jarquebera_correctness.r’ [1s/1s]
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Running ‘kolmogorovsmirnov_twosample_behavioiur.r’ [0s/0s]
Running ‘kolmogorovsmirnov_twosample_correctness.r’ [5s/7s]
Running ‘kolmogorovsmirnov_twosample_errors.r’ [0s/0s]
Running ‘kolmogorovsmirnov_twosample_warnings.r’ [0s/1s]
Running ‘kruskalwallis_behaviour.r’ [0s/0s]
Running ‘kruskalwallis_correctness.r’ [2s/2s]
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Running ‘levene_behaviour.r’ [0s/1s]
Running ‘levene_correctness.r’ [6s/8s]
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Running ‘t_onesample_behaviour.r’ [0s/0s]
Running ‘t_onesample_correctness.r’ [1s/1s]
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Running ‘wilcoxon_onesample_behaviour.r’ [0s/0s]
Running ‘wilcoxon_onesample_correctness.r’ [1s/1s]
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Running ‘wilcoxon_twosample_behaviour.r’ [0s/0s]
Running ‘wilcoxon_twosample_correctness.r’ [3s/4s]
Running ‘wilcoxon_twosample_errors.r’ [0s/1s]
Running ‘wilcoxon_twosample_warnings.r’ [0s/0s]
Running the tests in ‘tests/wilcoxon_onesample_correctness.r’ failed.
Complete output:
> library(matrixTests)
>
> #--- functions -----------------------------------------------------------------
>
> base_wilcoxon_onesample <- function(mat, null=0, alternative="two.sided", exact=NA, correct=TRUE) {
+ if(is.vector(mat)) mat <- matrix(mat, nrow=1)
+ if(length(alternative)==1) alternative <- rep(alternative, nrow(mat))
+ if(length(null)==1) null <- rep(null, nrow(mat))
+ if(length(exact)==1) exact <- rep(exact, nrow(mat))
+ if(length(correct)==1) correct <- rep(correct, nrow(mat))
+
+ nx <- stat <- p <- m0 <- numeric(nrow(mat))
+ al <- character(nrow(mat))
+ ext <- cor <- logical(nrow(mat))
+ for(i in 1:nrow(mat)) {
+ vec <- mat[i,][!is.na(mat[i,])]
+ ex <- if(is.na(exact[i])) NULL else exact[i]
+
+ res <- wilcox.test(vec, alternative=alternative[i], mu=null[i], exact=ex, correct=correct[i])
+
+ nx[i] <- sum((vec-null[i]) != 0)
+ stat[i] <- res$statistic
+ p[i] <- res$p.value
+ al[i] <- res$alternative
+ m0[i] <- res$null.value
+
+ cor[i] <- grepl("continuity correction", res$method)
+ ext[i] <- if(is.na(exact[i])) (nx[i] < 50) else exact[i]
+ ext[i] <- if(length(unique(abs(vec-m0[i]))) != length(vec)) FALSE else ext[i]
+ ext[i] <- if(any((vec-m0[i]) == 0)) FALSE else ext[i]
+ }
+
+ data.frame(obs=nx, statistic=stat, pvalue=p, location.null=m0, alternative=al,
+ exact=ext, corrected=cor, stringsAsFactors=FALSE
+ )
+ }
>
>
> #--- montecarlo ----------------------------------------------------------------
>
> # 3 observations
> x <- matrix(rnorm(3000), ncol=3)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- base_wilcoxon_onesample(x, mus, alts, exact=ext, correct=cor)
> res2 <- row_wilcoxon_onesample(x, mus, alts, exact=ext, correct=cor)
> stopifnot(all.equal(res1, res2))
Error: res1 and res2 are not equal:
Component "pvalue": Mean relative difference: 0.1212563
Execution halted
Running the tests in ‘tests/wilcoxon_paired_correctness.r’ failed.
Complete output:
> library(matrixTests)
>
> #--- functions -----------------------------------------------------------------
>
> base_wilcoxon_paired <- function(mat1, mat2, null=0, alternative="two.sided", exact=NA, correct=TRUE) {
+ if(is.vector(mat1)) mat1 <- matrix(mat1, nrow=1)
+ if(is.vector(mat2)) mat2 <- matrix(mat2, nrow=1)
+ if(length(alternative)==1) alternative <- rep(alternative, nrow(mat1))
+ if(length(null)==1) null <- rep(null, nrow(mat1))
+ if(length(exact)==1) exact <- rep(exact, nrow(mat1))
+ if(length(correct)==1) correct <- rep(correct, nrow(mat1))
+
+ nx <- ny <- nxy <- stat <- p <- m0 <- numeric(nrow(mat1))
+ al <- character(nrow(mat1))
+ ext <- cor <- logical(nrow(mat1))
+ for(i in 1:nrow(mat1)) {
+ ex <- if(is.na(exact[i])) NULL else exact[i]
+ res <- wilcox.test(mat1[i,], mat2[i,], alternative=alternative[i], mu=null[i], paired=TRUE, exact=ex, correct=correct[i])
+
+ inds <- complete.cases(mat1[i,], mat2[i,])
+ vec1 <- mat1[i,inds]
+ vec2 <- mat2[i,inds]
+ nx[i] <- sum(!is.na(mat1[i,]))
+ ny[i] <- sum(!is.na(mat2[i,]))
+ nxy[i] <- sum((vec1 - vec2 - null[i]) != 0, na.rm=TRUE)
+ stat[i] <- res$statistic
+ p[i] <- res$p.value
+ al[i] <- res$alternative
+ m0[i] <- res$null.value
+
+ cor[i] <- grepl("continuity correction", res$method)
+ ext[i] <- if(is.na(exact[i])) (nxy[i] < 50) else exact[i]
+ ext[i] <- if(length(unique(abs(vec1-vec2-m0[i]))) != length(vec1)) FALSE else ext[i]
+ ext[i] <- if(any((vec1-vec2-m0[i]) == 0)) FALSE else ext[i]
+ }
+
+ data.frame(obs.x=nx, obs.y=ny, obs.paired=nxy, statistic=stat, pvalue=p,
+ location.null=m0, alternative=al, exact=ext, corrected=cor,
+ stringsAsFactors=FALSE
+ )
+ }
>
>
> #--- montecarlo ----------------------------------------------------------------
>
> # 4 paired samples
> x <- matrix(rnorm(4000), ncol=4)
> y <- matrix(rnorm(4000), ncol=4)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- base_wilcoxon_paired(x, y, mus, alts, exact=ext, correct=cor)
> res2 <- row_wilcoxon_paired(x, y, mus, alts, exact=ext, correct=cor)
> stopifnot(all.equal(res1, res2))
Error: res1 and res2 are not equal:
Component "pvalue": Mean relative difference: 0.05000619
Execution halted
Running the tests in ‘tests/wilcoxon_twosample_correctness.r’ failed.
Complete output:
> library(matrixTests)
>
> #--- functions -----------------------------------------------------------------
>
> base_wilcoxon_twosample <- function(mat1, mat2, null=0, alternative="two.sided", exact=NA, correct=TRUE) {
+ if(is.vector(mat1)) mat1 <- matrix(mat1, nrow=1)
+ if(is.vector(mat2)) mat2 <- matrix(mat2, nrow=1)
+ if(length(alternative)==1) alternative <- rep(alternative, nrow(mat1))
+ if(length(null)==1) null <- rep(null, nrow(mat1))
+ if(length(exact)==1) exact <- rep(exact, nrow(mat1))
+ if(length(correct)==1) correct <- rep(correct, nrow(mat1))
+
+ nx <- ny <- nxy <- stat <- p <- m0 <- numeric(nrow(mat1))
+ al <- character(nrow(mat1))
+ ext <- cor <- logical(nrow(mat1))
+ for(i in 1:nrow(mat1)) {
+ ex <- if(is.na(exact[i])) NULL else exact[i]
+
+ res <- wilcox.test(mat1[i,], mat2[i,], alternative=alternative[i], mu=null[i], exact=ex, correct=correct[i])
+
+ nx[i] <- sum(!is.na(mat1[i,]))
+ ny[i] <- sum(!is.na(mat2[i,]))
+ nxy[i] <- nx[i] + ny[i]
+ stat[i] <- res$statistic
+ p[i] <- res$p.value
+ al[i] <- res$alternative
+ m0[i] <- res$null.value
+
+ cor[i] <- grepl("continuity correction", res$method)
+ ext[i] <- if(is.na(exact[i])) (nx[i] < 50 & ny[i] < 50) else exact[i]
+ ext[i] <- if(length(unique(na.omit(c(mat1[i,]-m0[i], mat2[i,])))) != nxy[i]) FALSE else ext[i]
+ }
+
+ data.frame(obs.x=nx, obs.y=ny, obs.tot=nxy, statistic=stat, pvalue=p,
+ location.null=m0, alternative=al, exact=ext, corrected=cor,
+ stringsAsFactors=FALSE
+ )
+ }
>
>
> #--- montecarlo ----------------------------------------------------------------
>
> # 2 samples in one group and 4 in another
> x <- matrix(rnorm(2000), ncol=2)
> y <- matrix(rnorm(4000), ncol=4)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- base_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> res2 <- row_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> stopifnot(all.equal(res1, res2))
>
> # 51 samples in one group and 51 in another
> x <- matrix(rnorm(51000), ncol=51)
> y <- matrix(rnorm(51000), ncol=51)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- base_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> res2 <- row_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> stopifnot(all.equal(res1, res2))
>
> # 4 samples in one group and 51 in another
> x <- matrix(rnorm(4000), ncol=4)
> y <- matrix(rnorm(51000), ncol=51)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- base_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> res2 <- row_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> stopifnot(all.equal(res1, res2))
>
> # 6 samples per group with ties and zeroes
> x <- matrix(round(runif(6000, -15, 15)), ncol=6)
> y <- matrix(round(runif(6000, -15, 15)), ncol=6)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> mus[sample(length(mus), length(mus)/8)] <- 0
> mus[sample(length(mus), length(mus)/8)] <- 1
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- suppressWarnings(base_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor))
> res2 <- suppressWarnings(row_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor))
> stopifnot(all.equal(res1, res2))
Error: res1 and res2 are not equal:
Component "pvalue": Mean relative difference: 0.02750347
Component "corrected": 232 element mismatches
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.3
Check: tests
Result: ERROR
Running ‘andersondarling_behaviour.r’
Running ‘andersondarling_correctness.r’
Running ‘andersondarling_errors.r’
Running ‘andersondarling_warnings.r’
Running ‘bartlett_behaviour.r’
Running ‘bartlett_correctness.r’ [7s/12s]
Running ‘bartlett_errors.r’
Running ‘bartlett_warnings.r’
Running ‘brownforsythe_behaviour.r’
Running ‘brownforsythe_correctness.r’ [19s/47s]
Running ‘brownforsythe_errors.r’
Running ‘brownforsythe_warnings.r’
Running ‘cor_pearson_behaviour.r’
Running ‘cor_pearson_correctness.r’
Running ‘cor_pearson_errors.r’
Running ‘cor_pearson_warnings.r’
Running ‘cosinor_behaviour.r’
Running ‘cosinor_correctness.r’ [43s/116s]
Running ‘cosinor_errors.r’
Running ‘cosinor_warnings.r’
Running ‘f_var_behaviour.r’
Running ‘f_var_correctness.r’
Running ‘f_var_errors.r’
Running ‘f_var_warnings.r’
Running ‘flignerkilleen_behaviour.r’
Running ‘flignerkilleen_correctness.r’ [6s/13s]
Running ‘flignerkilleen_errors.r’
Running ‘flignerkilleen_warnings.r’
Running ‘jarquebera_behaviour.r’
Running ‘jarquebera_correctness.r’
Running ‘jarquebera_errors.r’
Running ‘jarquebera_warnings.r’
Running ‘kolmogorovsmirnov_twosample_behavioiur.r’
Running ‘kolmogorovsmirnov_twosample_correctness.r’ [14s/36s]
Running ‘kolmogorovsmirnov_twosample_errors.r’
Running ‘kolmogorovsmirnov_twosample_warnings.r’
Running ‘kruskalwallis_behaviour.r’
Running ‘kruskalwallis_correctness.r’ [6s/20s]
Running ‘kruskalwallis_errors.r’
Running ‘kruskalwallis_warnings.r’
Running ‘levene_behaviour.r’
Running ‘levene_correctness.r’ [18s/54s]
Running ‘levene_errors.r’
Running ‘levene_warnings.r’
Running ‘oneway_equalvar_behaviour.r’
Running ‘oneway_equalvar_correctness.r’ [11s/31s]
Running ‘oneway_equalvar_errors.r’
Running ‘oneway_equalvar_warnings.r’
Running ‘oneway_welch_behaviour.r’
Running ‘oneway_welch_correctness.r’ [8s/21s]
Running ‘oneway_welch_errors.r’
Running ‘oneway_welch_warnings.r’
Running ‘t_equalvar_behaviour.r’
Running ‘t_equalvar_correctness.r’
Running ‘t_equalvar_errors.r’
Running ‘t_equalvar_warnings.r’
Running ‘t_onesample_behaviour.r’
Running ‘t_onesample_correctness.r’
Running ‘t_onesample_errors.r’
Running ‘t_onesample_warnings.r’
Running ‘t_paired_behaviour.r’
Running ‘t_paired_correctness.r’
Running ‘t_paired_errors.r’
Running ‘t_paired_warnings.r’
Running ‘t_welch_behaviour.r’
Running ‘t_welch_correctness.r’
Running ‘t_welch_errors.r’
Running ‘t_welch_warnings.r’
Running ‘waerden_behaviour.r’
Running ‘waerden_correctness.r’ [6s/14s]
Running ‘waerden_errors.r’
Running ‘waerden_warnings.r’
Running ‘wilcoxon_onesample_behaviour.r’
Running ‘wilcoxon_onesample_correctness.r’
Running ‘wilcoxon_onesample_errors.r’
Running ‘wilcoxon_onesample_warnings.r’
Running ‘wilcoxon_paired_behaviour.r’
Running ‘wilcoxon_paired_correctness.r’
Running ‘wilcoxon_paired_errors.r’
Running ‘wilcoxon_paired_warnings.r’
Running ‘wilcoxon_twosample_behaviour.r’
Running ‘wilcoxon_twosample_correctness.r’ [9s/20s]
Running ‘wilcoxon_twosample_errors.r’
Running ‘wilcoxon_twosample_warnings.r’
Running the tests in ‘tests/wilcoxon_onesample_correctness.r’ failed.
Complete output:
> library(matrixTests)
>
> #--- functions -----------------------------------------------------------------
>
> base_wilcoxon_onesample <- function(mat, null=0, alternative="two.sided", exact=NA, correct=TRUE) {
+ if(is.vector(mat)) mat <- matrix(mat, nrow=1)
+ if(length(alternative)==1) alternative <- rep(alternative, nrow(mat))
+ if(length(null)==1) null <- rep(null, nrow(mat))
+ if(length(exact)==1) exact <- rep(exact, nrow(mat))
+ if(length(correct)==1) correct <- rep(correct, nrow(mat))
+
+ nx <- stat <- p <- m0 <- numeric(nrow(mat))
+ al <- character(nrow(mat))
+ ext <- cor <- logical(nrow(mat))
+ for(i in 1:nrow(mat)) {
+ vec <- mat[i,][!is.na(mat[i,])]
+ ex <- if(is.na(exact[i])) NULL else exact[i]
+
+ res <- wilcox.test(vec, alternative=alternative[i], mu=null[i], exact=ex, correct=correct[i])
+
+ nx[i] <- sum((vec-null[i]) != 0)
+ stat[i] <- res$statistic
+ p[i] <- res$p.value
+ al[i] <- res$alternative
+ m0[i] <- res$null.value
+
+ cor[i] <- grepl("continuity correction", res$method)
+ ext[i] <- if(is.na(exact[i])) (nx[i] < 50) else exact[i]
+ ext[i] <- if(length(unique(abs(vec-m0[i]))) != length(vec)) FALSE else ext[i]
+ ext[i] <- if(any((vec-m0[i]) == 0)) FALSE else ext[i]
+ }
+
+ data.frame(obs=nx, statistic=stat, pvalue=p, location.null=m0, alternative=al,
+ exact=ext, corrected=cor, stringsAsFactors=FALSE
+ )
+ }
>
>
> #--- montecarlo ----------------------------------------------------------------
>
> # 3 observations
> x <- matrix(rnorm(3000), ncol=3)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- base_wilcoxon_onesample(x, mus, alts, exact=ext, correct=cor)
> res2 <- row_wilcoxon_onesample(x, mus, alts, exact=ext, correct=cor)
> stopifnot(all.equal(res1, res2))
>
> # 60 observations
> x <- matrix(rnorm(60000), ncol=60)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- base_wilcoxon_onesample(x, mus, alts, exact=ext, correct=cor)
> res2 <- row_wilcoxon_onesample(x, mus, alts, exact=ext, correct=cor)
> stopifnot(all.equal(res1, res2))
>
> # 10 observations with ties and zeroes
> x <- matrix(round(runif(10000, -15, 15)), ncol=10)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> mus[sample(length(mus), length(mus)/8)] <- 0
> mus[sample(length(mus), length(mus)/8)] <- 1
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- suppressWarnings(base_wilcoxon_onesample(x, mus, alts, exact=ext, correct=cor))
> res2 <- suppressWarnings(row_wilcoxon_onesample(x, mus, alts, exact=ext, correct=cor))
> stopifnot(all.equal(res1, res2))
Error: res1 and res2 are not equal:
Component "pvalue": Mean relative difference: 0.01998388
Component "corrected": 285 element mismatches
Execution halted
Running the tests in ‘tests/wilcoxon_paired_correctness.r’ failed.
Complete output:
> library(matrixTests)
>
> #--- functions -----------------------------------------------------------------
>
> base_wilcoxon_paired <- function(mat1, mat2, null=0, alternative="two.sided", exact=NA, correct=TRUE) {
+ if(is.vector(mat1)) mat1 <- matrix(mat1, nrow=1)
+ if(is.vector(mat2)) mat2 <- matrix(mat2, nrow=1)
+ if(length(alternative)==1) alternative <- rep(alternative, nrow(mat1))
+ if(length(null)==1) null <- rep(null, nrow(mat1))
+ if(length(exact)==1) exact <- rep(exact, nrow(mat1))
+ if(length(correct)==1) correct <- rep(correct, nrow(mat1))
+
+ nx <- ny <- nxy <- stat <- p <- m0 <- numeric(nrow(mat1))
+ al <- character(nrow(mat1))
+ ext <- cor <- logical(nrow(mat1))
+ for(i in 1:nrow(mat1)) {
+ ex <- if(is.na(exact[i])) NULL else exact[i]
+ res <- wilcox.test(mat1[i,], mat2[i,], alternative=alternative[i], mu=null[i], paired=TRUE, exact=ex, correct=correct[i])
+
+ inds <- complete.cases(mat1[i,], mat2[i,])
+ vec1 <- mat1[i,inds]
+ vec2 <- mat2[i,inds]
+ nx[i] <- sum(!is.na(mat1[i,]))
+ ny[i] <- sum(!is.na(mat2[i,]))
+ nxy[i] <- sum((vec1 - vec2 - null[i]) != 0, na.rm=TRUE)
+ stat[i] <- res$statistic
+ p[i] <- res$p.value
+ al[i] <- res$alternative
+ m0[i] <- res$null.value
+
+ cor[i] <- grepl("continuity correction", res$method)
+ ext[i] <- if(is.na(exact[i])) (nxy[i] < 50) else exact[i]
+ ext[i] <- if(length(unique(abs(vec1-vec2-m0[i]))) != length(vec1)) FALSE else ext[i]
+ ext[i] <- if(any((vec1-vec2-m0[i]) == 0)) FALSE else ext[i]
+ }
+
+ data.frame(obs.x=nx, obs.y=ny, obs.paired=nxy, statistic=stat, pvalue=p,
+ location.null=m0, alternative=al, exact=ext, corrected=cor,
+ stringsAsFactors=FALSE
+ )
+ }
>
>
> #--- montecarlo ----------------------------------------------------------------
>
> # 4 paired samples
> x <- matrix(rnorm(4000), ncol=4)
> y <- matrix(rnorm(4000), ncol=4)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- base_wilcoxon_paired(x, y, mus, alts, exact=ext, correct=cor)
> res2 <- row_wilcoxon_paired(x, y, mus, alts, exact=ext, correct=cor)
> stopifnot(all.equal(res1, res2))
>
> # 60 paired samples
> x <- matrix(rnorm(60000), ncol=60)
> y <- matrix(rnorm(60000), ncol=60)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- base_wilcoxon_paired(x, y, mus, alts, exact=ext, correct=cor)
> res2 <- row_wilcoxon_paired(x, y, mus, alts, exact=ext, correct=cor)
> stopifnot(all.equal(res1, res2))
>
>
> # 6 paired samples per group with ties and zeroes
> x <- matrix(round(runif(6000, -10, 10)), ncol=6)
> y <- matrix(round(runif(6000, -10, 10)), ncol=6)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> mus[sample(length(mus), length(mus)/8)] <- 0
> mus[sample(length(mus), length(mus)/8)] <- 1
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- suppressWarnings(base_wilcoxon_paired(x, y, mus, alts, exact=ext, correct=cor))
> res2 <- suppressWarnings(row_wilcoxon_paired(x, y, mus, alts, exact=ext, correct=cor))
> stopifnot(all.equal(res1, res2))
Error: res1 and res2 are not equal:
Component "pvalue": Mean relative difference: 0.04199396
Component "corrected": 152 element mismatches
Execution halted
Running the tests in ‘tests/wilcoxon_twosample_correctness.r’ failed.
Complete output:
> library(matrixTests)
>
> #--- functions -----------------------------------------------------------------
>
> base_wilcoxon_twosample <- function(mat1, mat2, null=0, alternative="two.sided", exact=NA, correct=TRUE) {
+ if(is.vector(mat1)) mat1 <- matrix(mat1, nrow=1)
+ if(is.vector(mat2)) mat2 <- matrix(mat2, nrow=1)
+ if(length(alternative)==1) alternative <- rep(alternative, nrow(mat1))
+ if(length(null)==1) null <- rep(null, nrow(mat1))
+ if(length(exact)==1) exact <- rep(exact, nrow(mat1))
+ if(length(correct)==1) correct <- rep(correct, nrow(mat1))
+
+ nx <- ny <- nxy <- stat <- p <- m0 <- numeric(nrow(mat1))
+ al <- character(nrow(mat1))
+ ext <- cor <- logical(nrow(mat1))
+ for(i in 1:nrow(mat1)) {
+ ex <- if(is.na(exact[i])) NULL else exact[i]
+
+ res <- wilcox.test(mat1[i,], mat2[i,], alternative=alternative[i], mu=null[i], exact=ex, correct=correct[i])
+
+ nx[i] <- sum(!is.na(mat1[i,]))
+ ny[i] <- sum(!is.na(mat2[i,]))
+ nxy[i] <- nx[i] + ny[i]
+ stat[i] <- res$statistic
+ p[i] <- res$p.value
+ al[i] <- res$alternative
+ m0[i] <- res$null.value
+
+ cor[i] <- grepl("continuity correction", res$method)
+ ext[i] <- if(is.na(exact[i])) (nx[i] < 50 & ny[i] < 50) else exact[i]
+ ext[i] <- if(length(unique(na.omit(c(mat1[i,]-m0[i], mat2[i,])))) != nxy[i]) FALSE else ext[i]
+ }
+
+ data.frame(obs.x=nx, obs.y=ny, obs.tot=nxy, statistic=stat, pvalue=p,
+ location.null=m0, alternative=al, exact=ext, corrected=cor,
+ stringsAsFactors=FALSE
+ )
+ }
>
>
> #--- montecarlo ----------------------------------------------------------------
>
> # 2 samples in one group and 4 in another
> x <- matrix(rnorm(2000), ncol=2)
> y <- matrix(rnorm(4000), ncol=4)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- base_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> res2 <- row_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> stopifnot(all.equal(res1, res2))
>
> # 51 samples in one group and 51 in another
> x <- matrix(rnorm(51000), ncol=51)
> y <- matrix(rnorm(51000), ncol=51)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- base_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> res2 <- row_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> stopifnot(all.equal(res1, res2))
>
> # 4 samples in one group and 51 in another
> x <- matrix(rnorm(4000), ncol=4)
> y <- matrix(rnorm(51000), ncol=51)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- base_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> res2 <- row_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> stopifnot(all.equal(res1, res2))
>
> # 6 samples per group with ties and zeroes
> x <- matrix(round(runif(6000, -15, 15)), ncol=6)
> y <- matrix(round(runif(6000, -15, 15)), ncol=6)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> mus[sample(length(mus), length(mus)/8)] <- 0
> mus[sample(length(mus), length(mus)/8)] <- 1
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- suppressWarnings(base_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor))
> res2 <- suppressWarnings(row_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor))
> stopifnot(all.equal(res1, res2))
Error: res1 and res2 are not equal:
Component "pvalue": Mean relative difference: 0.02716666
Component "corrected": 217 element mismatches
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2.3
Check: tests
Result: ERROR
Running ‘andersondarling_behaviour.r’
Running ‘andersondarling_correctness.r’ [3s/11s]
Running ‘andersondarling_errors.r’
Running ‘andersondarling_warnings.r’
Running ‘bartlett_behaviour.r’
Running ‘bartlett_correctness.r’ [7s/26s]
Running ‘bartlett_errors.r’
Running ‘bartlett_warnings.r’
Running ‘brownforsythe_behaviour.r’
Running ‘brownforsythe_correctness.r’ [20s/53s]
Running ‘brownforsythe_errors.r’
Running ‘brownforsythe_warnings.r’
Running ‘cor_pearson_behaviour.r’
Running ‘cor_pearson_correctness.r’
Running ‘cor_pearson_errors.r’
Running ‘cor_pearson_warnings.r’
Running ‘cosinor_behaviour.r’
Running ‘cosinor_correctness.r’ [43s/86s]
Running ‘cosinor_errors.r’
Running ‘cosinor_warnings.r’
Running ‘f_var_behaviour.r’
Running ‘f_var_correctness.r’
Running ‘f_var_errors.r’
Running ‘f_var_warnings.r’
Running ‘flignerkilleen_behaviour.r’
Running ‘flignerkilleen_correctness.r’
Running ‘flignerkilleen_errors.r’
Running ‘flignerkilleen_warnings.r’
Running ‘jarquebera_behaviour.r’
Running ‘jarquebera_correctness.r’
Running ‘jarquebera_errors.r’
Running ‘jarquebera_warnings.r’
Running ‘kolmogorovsmirnov_twosample_behavioiur.r’
Running ‘kolmogorovsmirnov_twosample_correctness.r’ [15s/29s]
Running ‘kolmogorovsmirnov_twosample_errors.r’
Running ‘kolmogorovsmirnov_twosample_warnings.r’
Running ‘kruskalwallis_behaviour.r’
Running ‘kruskalwallis_correctness.r’
Running ‘kruskalwallis_errors.r’
Running ‘kruskalwallis_warnings.r’
Running ‘levene_behaviour.r’
Running ‘levene_correctness.r’ [20s/39s]
Running ‘levene_errors.r’
Running ‘levene_warnings.r’
Running ‘oneway_equalvar_behaviour.r’
Running ‘oneway_equalvar_correctness.r’ [11s/12s]
Running ‘oneway_equalvar_errors.r’
Running ‘oneway_equalvar_warnings.r’
Running ‘oneway_welch_behaviour.r’
Running ‘oneway_welch_correctness.r’
Running ‘oneway_welch_errors.r’
Running ‘oneway_welch_warnings.r’
Running ‘t_equalvar_behaviour.r’
Running ‘t_equalvar_correctness.r’
Running ‘t_equalvar_errors.r’
Running ‘t_equalvar_warnings.r’
Running ‘t_onesample_behaviour.r’
Running ‘t_onesample_correctness.r’
Running ‘t_onesample_errors.r’
Running ‘t_onesample_warnings.r’
Running ‘t_paired_behaviour.r’
Running ‘t_paired_correctness.r’
Running ‘t_paired_errors.r’
Running ‘t_paired_warnings.r’
Running ‘t_welch_behaviour.r’
Running ‘t_welch_correctness.r’
Running ‘t_welch_errors.r’
Running ‘t_welch_warnings.r’
Running ‘waerden_behaviour.r’
Running ‘waerden_correctness.r’
Running ‘waerden_errors.r’
Running ‘waerden_warnings.r’
Running ‘wilcoxon_onesample_behaviour.r’
Running ‘wilcoxon_onesample_correctness.r’
Running ‘wilcoxon_onesample_errors.r’
Running ‘wilcoxon_onesample_warnings.r’
Running ‘wilcoxon_paired_behaviour.r’
Running ‘wilcoxon_paired_correctness.r’
Running ‘wilcoxon_paired_errors.r’
Running ‘wilcoxon_paired_warnings.r’
Running ‘wilcoxon_twosample_behaviour.r’
Running ‘wilcoxon_twosample_correctness.r’
Running ‘wilcoxon_twosample_errors.r’
Running ‘wilcoxon_twosample_warnings.r’
Running the tests in ‘tests/wilcoxon_onesample_correctness.r’ failed.
Complete output:
> library(matrixTests)
>
> #--- functions -----------------------------------------------------------------
>
> base_wilcoxon_onesample <- function(mat, null=0, alternative="two.sided", exact=NA, correct=TRUE) {
+ if(is.vector(mat)) mat <- matrix(mat, nrow=1)
+ if(length(alternative)==1) alternative <- rep(alternative, nrow(mat))
+ if(length(null)==1) null <- rep(null, nrow(mat))
+ if(length(exact)==1) exact <- rep(exact, nrow(mat))
+ if(length(correct)==1) correct <- rep(correct, nrow(mat))
+
+ nx <- stat <- p <- m0 <- numeric(nrow(mat))
+ al <- character(nrow(mat))
+ ext <- cor <- logical(nrow(mat))
+ for(i in 1:nrow(mat)) {
+ vec <- mat[i,][!is.na(mat[i,])]
+ ex <- if(is.na(exact[i])) NULL else exact[i]
+
+ res <- wilcox.test(vec, alternative=alternative[i], mu=null[i], exact=ex, correct=correct[i])
+
+ nx[i] <- sum((vec-null[i]) != 0)
+ stat[i] <- res$statistic
+ p[i] <- res$p.value
+ al[i] <- res$alternative
+ m0[i] <- res$null.value
+
+ cor[i] <- grepl("continuity correction", res$method)
+ ext[i] <- if(is.na(exact[i])) (nx[i] < 50) else exact[i]
+ ext[i] <- if(length(unique(abs(vec-m0[i]))) != length(vec)) FALSE else ext[i]
+ ext[i] <- if(any((vec-m0[i]) == 0)) FALSE else ext[i]
+ }
+
+ data.frame(obs=nx, statistic=stat, pvalue=p, location.null=m0, alternative=al,
+ exact=ext, corrected=cor, stringsAsFactors=FALSE
+ )
+ }
>
>
> #--- montecarlo ----------------------------------------------------------------
>
> # 3 observations
> x <- matrix(rnorm(3000), ncol=3)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- base_wilcoxon_onesample(x, mus, alts, exact=ext, correct=cor)
> res2 <- row_wilcoxon_onesample(x, mus, alts, exact=ext, correct=cor)
> stopifnot(all.equal(res1, res2))
>
> # 60 observations
> x <- matrix(rnorm(60000), ncol=60)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- base_wilcoxon_onesample(x, mus, alts, exact=ext, correct=cor)
> res2 <- row_wilcoxon_onesample(x, mus, alts, exact=ext, correct=cor)
> stopifnot(all.equal(res1, res2))
>
> # 10 observations with ties and zeroes
> x <- matrix(round(runif(10000, -15, 15)), ncol=10)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> mus[sample(length(mus), length(mus)/8)] <- 0
> mus[sample(length(mus), length(mus)/8)] <- 1
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- suppressWarnings(base_wilcoxon_onesample(x, mus, alts, exact=ext, correct=cor))
> res2 <- suppressWarnings(row_wilcoxon_onesample(x, mus, alts, exact=ext, correct=cor))
> stopifnot(all.equal(res1, res2))
Error: res1 and res2 are not equal:
Component "pvalue": Mean relative difference: 0.01809046
Component "corrected": 281 element mismatches
Execution halted
Running the tests in ‘tests/wilcoxon_paired_correctness.r’ failed.
Complete output:
> library(matrixTests)
>
> #--- functions -----------------------------------------------------------------
>
> base_wilcoxon_paired <- function(mat1, mat2, null=0, alternative="two.sided", exact=NA, correct=TRUE) {
+ if(is.vector(mat1)) mat1 <- matrix(mat1, nrow=1)
+ if(is.vector(mat2)) mat2 <- matrix(mat2, nrow=1)
+ if(length(alternative)==1) alternative <- rep(alternative, nrow(mat1))
+ if(length(null)==1) null <- rep(null, nrow(mat1))
+ if(length(exact)==1) exact <- rep(exact, nrow(mat1))
+ if(length(correct)==1) correct <- rep(correct, nrow(mat1))
+
+ nx <- ny <- nxy <- stat <- p <- m0 <- numeric(nrow(mat1))
+ al <- character(nrow(mat1))
+ ext <- cor <- logical(nrow(mat1))
+ for(i in 1:nrow(mat1)) {
+ ex <- if(is.na(exact[i])) NULL else exact[i]
+ res <- wilcox.test(mat1[i,], mat2[i,], alternative=alternative[i], mu=null[i], paired=TRUE, exact=ex, correct=correct[i])
+
+ inds <- complete.cases(mat1[i,], mat2[i,])
+ vec1 <- mat1[i,inds]
+ vec2 <- mat2[i,inds]
+ nx[i] <- sum(!is.na(mat1[i,]))
+ ny[i] <- sum(!is.na(mat2[i,]))
+ nxy[i] <- sum((vec1 - vec2 - null[i]) != 0, na.rm=TRUE)
+ stat[i] <- res$statistic
+ p[i] <- res$p.value
+ al[i] <- res$alternative
+ m0[i] <- res$null.value
+
+ cor[i] <- grepl("continuity correction", res$method)
+ ext[i] <- if(is.na(exact[i])) (nxy[i] < 50) else exact[i]
+ ext[i] <- if(length(unique(abs(vec1-vec2-m0[i]))) != length(vec1)) FALSE else ext[i]
+ ext[i] <- if(any((vec1-vec2-m0[i]) == 0)) FALSE else ext[i]
+ }
+
+ data.frame(obs.x=nx, obs.y=ny, obs.paired=nxy, statistic=stat, pvalue=p,
+ location.null=m0, alternative=al, exact=ext, corrected=cor,
+ stringsAsFactors=FALSE
+ )
+ }
>
>
> #--- montecarlo ----------------------------------------------------------------
>
> # 4 paired samples
> x <- matrix(rnorm(4000), ncol=4)
> y <- matrix(rnorm(4000), ncol=4)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- base_wilcoxon_paired(x, y, mus, alts, exact=ext, correct=cor)
> res2 <- row_wilcoxon_paired(x, y, mus, alts, exact=ext, correct=cor)
> stopifnot(all.equal(res1, res2))
>
> # 60 paired samples
> x <- matrix(rnorm(60000), ncol=60)
> y <- matrix(rnorm(60000), ncol=60)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- base_wilcoxon_paired(x, y, mus, alts, exact=ext, correct=cor)
> res2 <- row_wilcoxon_paired(x, y, mus, alts, exact=ext, correct=cor)
> stopifnot(all.equal(res1, res2))
>
>
> # 6 paired samples per group with ties and zeroes
> x <- matrix(round(runif(6000, -10, 10)), ncol=6)
> y <- matrix(round(runif(6000, -10, 10)), ncol=6)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> mus[sample(length(mus), length(mus)/8)] <- 0
> mus[sample(length(mus), length(mus)/8)] <- 1
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- suppressWarnings(base_wilcoxon_paired(x, y, mus, alts, exact=ext, correct=cor))
> res2 <- suppressWarnings(row_wilcoxon_paired(x, y, mus, alts, exact=ext, correct=cor))
> stopifnot(all.equal(res1, res2))
Error: res1 and res2 are not equal:
Component "pvalue": Mean relative difference: 0.04557973
Component "corrected": 113 element mismatches
Execution halted
Running the tests in ‘tests/wilcoxon_twosample_correctness.r’ failed.
Complete output:
> library(matrixTests)
>
> #--- functions -----------------------------------------------------------------
>
> base_wilcoxon_twosample <- function(mat1, mat2, null=0, alternative="two.sided", exact=NA, correct=TRUE) {
+ if(is.vector(mat1)) mat1 <- matrix(mat1, nrow=1)
+ if(is.vector(mat2)) mat2 <- matrix(mat2, nrow=1)
+ if(length(alternative)==1) alternative <- rep(alternative, nrow(mat1))
+ if(length(null)==1) null <- rep(null, nrow(mat1))
+ if(length(exact)==1) exact <- rep(exact, nrow(mat1))
+ if(length(correct)==1) correct <- rep(correct, nrow(mat1))
+
+ nx <- ny <- nxy <- stat <- p <- m0 <- numeric(nrow(mat1))
+ al <- character(nrow(mat1))
+ ext <- cor <- logical(nrow(mat1))
+ for(i in 1:nrow(mat1)) {
+ ex <- if(is.na(exact[i])) NULL else exact[i]
+
+ res <- wilcox.test(mat1[i,], mat2[i,], alternative=alternative[i], mu=null[i], exact=ex, correct=correct[i])
+
+ nx[i] <- sum(!is.na(mat1[i,]))
+ ny[i] <- sum(!is.na(mat2[i,]))
+ nxy[i] <- nx[i] + ny[i]
+ stat[i] <- res$statistic
+ p[i] <- res$p.value
+ al[i] <- res$alternative
+ m0[i] <- res$null.value
+
+ cor[i] <- grepl("continuity correction", res$method)
+ ext[i] <- if(is.na(exact[i])) (nx[i] < 50 & ny[i] < 50) else exact[i]
+ ext[i] <- if(length(unique(na.omit(c(mat1[i,]-m0[i], mat2[i,])))) != nxy[i]) FALSE else ext[i]
+ }
+
+ data.frame(obs.x=nx, obs.y=ny, obs.tot=nxy, statistic=stat, pvalue=p,
+ location.null=m0, alternative=al, exact=ext, corrected=cor,
+ stringsAsFactors=FALSE
+ )
+ }
>
>
> #--- montecarlo ----------------------------------------------------------------
>
> # 2 samples in one group and 4 in another
> x <- matrix(rnorm(2000), ncol=2)
> y <- matrix(rnorm(4000), ncol=4)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- base_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> res2 <- row_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> stopifnot(all.equal(res1, res2))
>
> # 51 samples in one group and 51 in another
> x <- matrix(rnorm(51000), ncol=51)
> y <- matrix(rnorm(51000), ncol=51)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- base_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> res2 <- row_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> stopifnot(all.equal(res1, res2))
>
> # 4 samples in one group and 51 in another
> x <- matrix(rnorm(4000), ncol=4)
> y <- matrix(rnorm(51000), ncol=51)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- base_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> res2 <- row_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor)
> stopifnot(all.equal(res1, res2))
>
> # 6 samples per group with ties and zeroes
> x <- matrix(round(runif(6000, -15, 15)), ncol=6)
> y <- matrix(round(runif(6000, -15, 15)), ncol=6)
> alts <- sample(c("t", "g", "l"), nrow(x), replace=TRUE)
> mus <- runif(nrow(x), -1, 1)
> mus[sample(length(mus), length(mus)/8)] <- 0
> mus[sample(length(mus), length(mus)/8)] <- 1
> cor <- sample(c(TRUE, FALSE), nrow(x), replace=TRUE)
> ext <- sample(c(TRUE, FALSE, NA), nrow(x), replace=TRUE)
> res1 <- suppressWarnings(base_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor))
> res2 <- suppressWarnings(row_wilcoxon_twosample(x, y, mus, alts, exact=ext, correct=cor))
> stopifnot(all.equal(res1, res2))
Error: res1 and res2 are not equal:
Component "pvalue": Mean relative difference: 0.02675795
Component "corrected": 228 element mismatches
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc