Chi-square testing in each group.

chisq.test_by_group.r

library(dplyr)
library(broom)
library(lazyeval)

df <- data_frame(
  group = rep(letters[1:2], each = 50),
  cat1 = letters[round(runif(100) * 5) + 1],
  cat2 = letters[round(runif(100) * 3) + 1]
) 

do_test <- function(.data, test_func, ...){
  fun <- substitute(test_func)
  .call <- lazyeval::make_call(fun, lazyeval::lazy_dots(...))
  .call <- lazyeval::make_call(quote(list), .call)
  summarise_(.data, test = .call) %>% rowwise %>% glance(test)
}

df %>%
  group_by(group) %>%
  do_test(., chisq.test, cat1, cat2, simulate.p.value = TRUE, B = 10)
# Source: local data frame [2 x 5]
# Groups: group [2]
# 
# group statistic   p.value parameter
# <chr>     <dbl>     <dbl>     <lgl>
# 1     a  9.588062 0.7272727        NA
# 2     b 17.190908 0.6363636        NA
# ... with 1 more variables: method <fctr>