From k@ro||@@koncev|c|u@ @end|ng |rom gm@||@com  Sat Dec  7 19:55:36 2019
From: k@ro||@@koncev|c|u@ @end|ng |rom gm@||@com (Karolis =?utf-8?Q?Koncevi=C4=8Dius?=)
Date: Sat, 7 Dec 2019 20:55:36 +0200
Subject: [Rd] Inconsistencies in wilcox.test
Message-ID: <20191207185536.b6cmmkzywwyuateq@PMW>

Hello,

Writing to share some things I've found about wilcox.test() that seem a
a bit inconsistent.

1. Inf values are not removed if paired=TRUE

# returns different results (Inf is removed):
wilcox.test(c(1,2,3,4), c(0,9,8,7))
wilcox.test(c(1,2,3,4), c(0,9,8,Inf))

# returns the same result (Inf is left as value with highest rank):
wilcox.test(c(1,2,3,4), c(0,9,8,7), paired=TRUE)
wilcox.test(c(1,2,3,4), c(0,9,8,Inf), paired=TRUE)

2. tolerance issues with paired=TRUE.

wilcox.test(c(4, 3, 2), c(3, 2, 1), paired=TRUE)
# ...
# Warning:  cannot compute exact p-value with ties

wilcox.test(c(0.4,0.3,0.2), c(0.3,0.2,0.1), paired=TRUE)
# ...
# no warning

3. Always 'x observations are missing' when paired=TRUE

wilcox.test(c(1,2), c(NA_integer_,NA_integer_), paired=TRUE)
# ...
# Error:  not enough (finite) 'x' observations

4. No indication if normal approximation was used:

# different numbers, but same "method" name
wilcox.test(rnorm(10), exact=FALSE, correct=FALSE)
wilcox.test(rnorm(10), exact=TRUE, correct=FALSE)


 From all of these I am pretty sure the 1st one is likely unintended,
so attaching a small patch to adjust it. Can also try patching others if 
consensus is reached that the behavioiur has to be modified.

Kind regards,
Karolis Koncevi?ius.

---

Index: wilcox.test.R
===================================================================
--- wilcox.test.R  (revision 77540)
+++ wilcox.test.R  (working copy)
@@ -42,7 +42,7 @@
          if(paired) {
              if(length(x) != length(y))
                  stop("'x' and 'y' must have the same length")
-            OK <- complete.cases(x, y)
+            OK <- is.finite(x) & is.finite(y)
              x <- x[OK] - y[OK]
              y <- NULL
          }



[Rd] Inconsistencies in wilcox.test
Karolis =?utf-8?Q?Koncevi=C4=8Dius?=