Mann-Whitney by group
On Mon, Jul 16, 2012 at 3:39 PM, Oxenstierna <david.chertudi at gmail.com> wrote:
lapply(thing, function(x) x[['p.value']]) --works very well, thank you.
Not to be a chore, but I'm interested in comparing the results of
wilcox.test--and the methodology we've employed so far--with the results and
methodology of wilcox_test (library("coin")). So, I'd like to compare
groups 5 and 6 across A through H using wilcox_test, and then I'd like to
extract the p-values. Going through the same methodology as above, but
replacing wilcox.test with wilcox_test has failed, and so has the p.value
extraction method: lapply(thing, function(x) x[['p.value']]) .
I believe the latter failure has to do with the fact that the coin package
has a built-in class and built-in extraction method (pvalue() to extract and
class "IndependenceTest"), but I don't know how to work around it. For
example, for a single comparison: wilcox_test(A~Group, Dtb) works fine, and
pvalue(wilcox.test(A~Group, Dtb)) extracts the p-value.
So, any ideas about how to compare groups 5 and 6 across A through H using
wilcox_test?
I think there are a few things at play here. 1) coin uses so-called S4 objects, so `[[` style subsetting isn't going to work. The "right way" is, as you have found to use the pvalue() function. 2) It looks like you need to use the formula intervace for wilcox_test. Unfortunately, this makes things a little more complicated as you'll need to construct the formula programmatically. A one liner looks something like this. lapply(LETTERS[1:8], function(x) pvalue(wilcox_test(as.formula(paste(x, "~ Group ")), Dtb))) Where lapply loops over the letters A,B, etc. and makes the string `A ~ Group`, converts it to a formula, passes that to wilcox_test, then gets the pvalue and returns it. In two lines you could do: thing <- lapply(LETTERS[1:8], function(x) wilcox_test(as.formula(paste(x, "~ Group")), Dtb)) thing2 <- lapply(thing, pvalue) Where thing has all the test result objects, and thing2 collects the pvalues. Hope this helps, Michael