There must be an R-ly way to call wilcox.test over multiple observations in parallel using group_by. I've spent a good deal of time reading up on this but still can't figure out a call to wilcox.test that does the job. Example data and code below, using magrittr pipes and summarize().
library(dplyr)
library(magrittr)
# create a data frame where x is the dependent variable, id1 is a category variable (here with five levels), and id2 is a binary category variable used for the two-sample wilcoxon test
df <- data.frame(x=abs(rnorm(50)),id1=rep(1:5,10), id2=rep(1:2,25))
# make sure piping and grouping are called correctly, with "sum" function as a well-behaving example function
df %>% group_by(id1) %>% summarise(s=sum(x))
df %>% group_by(id1,id2) %>% summarise(s=sum(x))
# make sure wilcox.test is called correctly
wilcox.test(x~id2, data=df, paired=FALSE)$p.value
# yet, cannot call wilcox.test within pipe with summarise (regardless of group_by). Expected output is five p-values (one for each level of id1)
df %>% group_by(id1) %>% summarise(w=wilcox.test(x~id2, data=., paired=FALSE)$p.value)
df %>% summarise(wilcox.test(x~id2, data=., paired=FALSE))
# even specifying formula argument by name doesn't help
df %>% group_by(id1) %>% summarise(w=wilcox.test(formula=x~id2, data=., paired=FALSE)$p.value)
The buggy calls yield this error:
Error in wilcox.test.formula(c(1.09057358373486,
2.28465932554436, 0.885617572657959, : 'formula' missing or incorrect
Thanks for your help; I hope it will be helpful to others with similar questions as well.
You can do this with base R (although the result is a cumbersome list):
by(df, df$id1, function(x) { wilcox.test(x~id2, data=x, paired=FALSE)$p.value })
or with dplyr:
ddply(df, .(id1), function(x) { wilcox.test(x~id2, data=x, paired=FALSE)$p.value })
id1 V1
1 1 0.3095238
2 2 1.0000000
3 3 0.8412698
4 4 0.6904762
5 5 0.3095238