Hello -
[EMAIL PROTECTED] wrote:
Hi all,
I am performing hundreds of kruskal wallis tests and trying to figure
out how to create a file of the p.values I obtain.
This is the code I use for the tests:
A2<-kruskal.test(X2~treatment)
A3<-kruskal.test(X3~treatment)
A4<-kruskal.test(X4~treatment)
A5<-kruskal.test(X5~treatment)
A6<-kruskal.test(X6~treatment)
A7<-kruskal.test(X7~treatment)
A8<-kruskal.test(X8~treatment)
A9<-kruskal.test(X9~treatment)
etc.
Whenever you find yourself typing variations on a theme, there is
probably a shortcut.
Try,
## begin sample R code
## create test data.frame
test <- data.frame(X2 = rnorm(100), X3 = rnorm(100), X4 = rnorm(100),
treatment = rep(c("A", "B"), times = 150))
## apply the kw test to all columns of the data.frame, except treatment
## note: NOT using the model formula version of kr, see ?kruskal.test
kr <- lapply(test[!names(test) %in% "treatment"],
kruskal.test, g = test$treatment)
## use sapply (basically like lapply) to extract p.value
## note that the trick is that "[" is actually a function
## see ?Extract
sapply(kr, "[", "p.value")
## end R code
One note of caution, applying hundreds of tests and only recording the
<.05 p-values is biased, you'll find chance relationships that aren't
really there. In my testing above on random data, I had a few <.05, and
one *highly* significant p-value, just be chance.
Hope this helps,
Erik
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
